Synthesis and biological evaluation of novel 2-arylalkylthio-4-amino-6-benzyl pyrimidines as potent HIV-1 non-nucleoside reverse transcriptase inhibitors

An Amazing 30-Year Journey around the DABO Family: A Medicinal Chemistry Lesson on a Versatile Class of Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors

Since the emergence of AIDS, the non-nucleoside HIV-1 RT inhibitors (NNRTIs) have attracted the attention of scientists and clinicians due to their high potency and specificity combined with low toxicity. 3,4-Dihydro-2-alkoxy-6-benzyl-4-oxopyrimidines (DABOs) are a family of NNRTIs described since 1992, and the best members among S-, NH-, and N,N-DABOs showed high anti-HIV-1 potency in both cellular and enzymatic assays. During 30 years of research, the central 4-(3H)-pyrimidinone nucleus has been decorated with 2,6-dihaloaryl or cyclohexyl groups at the methylene at C6, alkyl- or (arylalkyl/aroylalkyl)thio/amino chains at C2, and hydrogen or a small alkyl group at C5. The further introduction of small (i.e., methoxy) groups at the C6 α-benzylic position furnished potency at the sub-nanomolar level against wild-type HIV-1 and at the nanomolar level against HIV-1 mutant strains. Importantly, some compounds of the DABO family exhibited preventative microbicidal activity, valuable in clinical settings where oral adherence rates are low.

Docking field-based QSAR and pharmacophore studies on the substituted pyrimidine derivatives targeting HIV-1 reverse transcriptase

HIV-1 reverse transcriptase (RT) is one of the most important enzymes required for viral replication, thus acting as an attractive target for antiretroviral therapy. Pyrimidine analogues reportedly have selective inhibition on HIV-1 RT with favorable antiviral activities in our previous study. To further explore the relationship between inhibitory activity and pharmacophoric characteristics, field-based QSAR models were generated and validated using Schrodinger Suite (correlation coefficient of .8078, cross-validated value of 0.5397 for training set and Q² of 0.4669, Pearson's r of .7357 for test set). Docking, pocket surfaces, and pharmacophore study were also investigated to define the binding pattern and pharmacophoric features, including (i) π-π interaction with residue Tyr181, Tyr188, and Trp229 and p-π interaction with His235 and (ii) hydrogen bond with residue Lys101 and halogen bond with residue Tyr188. The pharmacophore features of six-point hypothesis AADRRR.184, AAADRR.38, and AADRRR.26 further complimented to the docking and QSAR results. We also found that the protein-ligand complex exhibited high relative binding free energy. These observations could be potentially utilized to guide the rational design and optimization of novel HIV-1 RT inhibitors.

In vitro and in vivo pharmacological characterization of SSD114, a novel GABAB positive allosteric modulator

Positive allosteric modulators (PAMs) of the GABA_B receptor have emerged as a novel approach to the pharmacological manipulation of the GABA_B receptor, enhancing the effects of receptor agonists with few side effects. Here, we identified N-cyclohexyl-4-methoxy-6-(4-(trifluoromethyl)phenyl)pyrimidin-2-amine (SSD114) as a new compound with activity as a GABA_B PAM in in vitro and in vivo assays. SSD114 potentiated GABA-stimulated [³⁵S]GTPγS binding to native GABA_B receptors, whereas it had no effect when used alone. Its effect on GTPγS stimulation was suppressed when GABA-induced activation was blocked with CGP54626, a competitive antagonist of the GABA_B receptor. SSD114 failed to potentiate WIN55,212,2-, morphine- and quinpirole-induced [³⁵S]GTPγS binding to cortical and striatal membranes, respectively, indicating that it is a selective GABA_B PAM. Increasing SSD114 fixed concentrations induced a leftward shift of the GABA concentration-response curve, enhancing the potency of GABA rather than its efficacy. SSD114 concentration-response curves in the presence of fixed concentrations of GABA (1, 10, and 20μM) revealed a potentiating effect on GABA-stimulated binding of [³⁵S]GTPγS to rat cortical membranes, with EC₅₀ values in the low micromolar range. Bioluminescence resonance energy transfer (BRET) experiments in Chinese Hamster Ovary (CHO)-cells expressing GABA_B receptors showed that SSD114 potentiates the GABA inhibition of adenylyl-cyclase mediated by GABA_B receptors. Our compound is also effective in vivo potentiating baclofen-induced sedation/hypnosis in mice, with no effect when tested alone. These findings indicate that SSD114, a molecule with a different chemical structure compared to known GABA_B PAMs, is a novel GABA_B PAM with potential usefulness in the GABA_B-receptor research field.

Double Variational Binding--(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands

Variational quantitative binding–conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed for analyzing both genuine molecular cases and their simplified molecular input line entry system (SMILES) transformations, which were created via the controlled breaking of chemical bonds, so as to generate the longest SMILES molecular chain (LoSMoC) and Branching SMILES (BraS) conformations. The study identified the most active anti-HIV molecules, and analyzed their special and relevant bonding fragments (chemical alerts), and the recorded energetic and geometric docking results (i.e., binding and affinity energies, and the surface area and volume of bonding, respectively). Clear computational evidence was also produced concerning the ligand-receptor pocket binding efficacies of the LoSMoc and BraS conformation types, thus confirming their earlier presence (as suggested by variational quantitative structure-activity relationship, variational-QSAR) as active intermediates for the molecule-to-cell transduction process.

5-Iodo-2-arylalkylthio-6-aryl pyrimidin-4(3H)-ones as non-nucleoside anti-HBV agents

Pyrimidone derivatives have been synthesized and evaluated as anti-HBV agents, in which two compounds exhibited more potent activity than lamivudine.

Design and synthesis of pyrimidine molecules endowed with thiazolidin-4-one as new anticancer agents

Design and synthesis of new pyrimidine derivatives clubbed with thiazolidin-4-one from 4-(2-chlorophenyl)-6-(2,4-dichlorophenyl)pyrimidin-2-amine and their in vitro anticancer activities were screened at National Cancer Institute (NCI), USA against full NCI 60 cell lines. Compound 2 (NSC: 765735) exhibited remarkable growth inhibition at single dose (10 μM) and encourage chosen for broadcast at 10-fold dilutions of five different concentrations (0.01, 0.1, 1, 10 and 100 μM). The compound 2 was found better quality for Lung cancer cell line (HOP-92) by viewing growth inhibition (GI50 0.52) and no cytotoxicity seen (LC50 > 100). Molecular docking study was performed using Maestro 9.0 (Schrodinger Inc. USA) to provide binding mode into binding sites of CDK2. Compound 2 could be used as a lead compound for developing new potential anticancer agents.

Synthesis and biological evaluation of novel 2-arylalkylthio-5-iodine-6-substituted-benzyl-pyrimidine-4(3H)-ones as potent HIV-1 non-nucleoside reverse transcriptase inhibitors

A novel series of 2-arylalkylthio-5-iodine-6-substitutedbenzyl-pyrimidine-4(3H)-ones (S-DABOs) 8a-x had been synthesized via an efficient method. Their biological activity against HIV virus and RT assay were evaluated. Some compounds, especially 8h, 8l and 8n, displayed promising activity against HIV-1 RT with IC50 values in a range of 0.41 μM to 0.71 μM, which were much better than that of nevirapine. Molecular modeling studies revealed that the binding mode would be affected via forming an additional hydrogen bond by incorporating an oxygen atom on the C-2 side chain. The biological activity was in accordance with the docking results.

Nucleosides 7(9): synthesis, structure, and biological activity of new 6-arylidenamino-2-thio- and 2-benzylthiopyrimidine N-nucleosides

The condensation of 6-amino-2-thioxo-2,3-dihydro-1H-pyrimidine-4-one [compound (1)] with aromatic aldehydes (2) afforded azomethine derivatives (3). The formed azomethines underwent glycosidation with α-acetobromoglucose (4) to form the corresponding pyrimidine N-glycosides (6) and not S-glycosides (5). The interaction of (3) with 1-O-acetyl-2, 3, 5-tri-O-benzoyl-β-D-ribofuranose (8) afforded the corresponding pyrimidine N-riboside (10) and not S-riboside (9). Deacetylation and debenzoylation of each of (6) and (10) by using methanolic sodium methoxide afforded the corresponding free N-nucleosides (7) and (11), respectively. Next, the reaction of 2-benzylthio-6-benzylidenaminouracil (13) with (4) and (8) did not yield the corresponding protected N-nucleosides (14) and (17), whereas it afforded (15) and (18), respectively. The latter compounds (15) and (18) were stirred in methanolic sodium methoxide to yield the corresponding free N-nucleosides (16) and (19), respectively. The structures of products have been elucidated and reported and also some of the products were screened for their antimicrobial activity. Graphical Abstract:

Synthesis and biological evaluation of novel C5 halogen-functionalized S-DABO as potent HIV-1 non-nucleoside reverse transcriptase inhibitors

A series of novel S-DABO analogues (4a1-5a12) have been synthesized by an efficient method and evaluated as inhibitors of human immunodeficiency virus type-1 (HIV-1). The biological testing results clearly indicated that the substitution of halogen at the C5 position of pyrimidine ring could increase the anti-HIV-1 RT activity. The most active compounds showed activity in the low micromole range with IC(50) values (IC(50) 0.18-3.03 microM) comparable to nevirapine (IC(50) 4.12 microM). The docking showed that a new halogen bond was formed between halogen and carbonyl of TYR188 in the HIV-I RT.