Structure based design, synthesis and evaluation of new thienopyrimidine derivatives as anti-bacterial agents

Design, synthesis and anticancer evaluation of 4-Substituted 5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidines as dual topoisomerase I and II inhibitors

In this study, we herein report the design, synthesis, and anticancer assessment of a series of new 4-substituted 5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidines. The synthesis involved key intermediates such as the 2-aminoester derivative, which underwent a series of reactions to produce compounds 7a-7t. The optimized SNAr reactions, utilizing microwave irradiation in DMF, led to high yields and efficient preparation of the desired compounds. The biological evaluation revealed significant cytotoxicity of compounds 7b and 7t against MCF-7 breast cancer cell lines with IC50 values of 8.80 ± 0.08 and 7.45 ± 0.26 µM, respectively, demonstrating superior activity to standard controls like camptothecin and etoposide. Both the compounds exhibited dual topoisomerase I and II inhibition (7t > 7b), enhanced reactive oxygen species (ROS) generation in cancer cells, and halted cell cycle at the G2/M phase. Molecular docking and dynamics simulations further supported the higher binding affinity of compound 7t to topoisomerase enzymes compared to 7b and standard compounds. In silico ADME profiling of 7b and 7t confirmed their drug-likeness, while DFT calculations provided insight into their electronic properties.

2-(4-Bromobenzyl) tethered 4-amino aryl/alkyl-5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidines: design, synthesis, anticancer assessment via dual topoisomerase-I/II inhibition, and in silico studies

A series of 2-(4-bromobenzyl) tethered 4-amino aryl/alkyl-5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidines (7a-7u) were designed, synthesized, characterized and screened against a panel of cancer cell lines. Compound 7a, in particular, emerged as a potent antiproliferative agent against FaDu cells (HTB-43) with an IC50 value of 1.73 μM. 7a induced morphological alterations in FaDu cells were observed via brightfield microscopy and DAPI staining, confirming cytotoxicity. Autophagy and apoptotic effects of 7a were confirmed by acridine orange staining, Rhodamine 123 staining, and western blot analysis, which revealed dose-dependent increases in LC3A/B and cleaved caspase-3 levels, respectively. Further, 7a impaired cell migration and colony formation, as demonstrated by scratch and clonogenic assays. Additionally, 7a reduced oxidative stress and induced G2/M phase cell cycle arrest in MCF-7 cells. 7a emerged as a dual topoisomerase I and II inhibitor, and results were supported by molecular docking and simulation studies. In anti-inflammatory studies, 7a exhibited selective inhibition of COX-2 over COX-1, supporting its dual anticancer and anti-inflammatory properties.

Anticancer and Antibacterial Activeness of Fused Pyrimidines: Newfangled Updates

Pyrimidine-based heterocyclic compounds are garnering substantial interest due to their essential role as a class of natural and synthetic molecules. These compounds show a diverse array of biologically relevant activities, making them highly prospective candidates for clinical translation as therapeutic agents in combating various diseases. Pyrimidine derivatives and their fused analogues, such as thienopyrimidines, pyrazolopyrimidines, pyridopyrimidines, and pyrimidopyrimidines, hold immense possibility in both anticancer and antibacterial research. These compounds exhibit notable efficacy by targeting protein kinases, which are crucial enzymes regulating fundamental cellular processes like metabolism, migration, division, and growth. Through enzyme inhibition, these derivatives disrupt key cellular signaling pathways, thereby affecting critical cellular functions and viability. The advantage lies in the ubiquity of the pyrimidine structure across various natural compounds, enabling interactions with enzymes, genetic material, and cellular components pivotal for chemical and biological processes. This interaction plays a central role in modulating vital biological activities, making pyrimidine-containing compounds indispensable in drug discovery. In the realm of anticancer therapy, these compounds strategically target key proteins like EGFR, important for aberrant cell growth. Fused pyrimidine motifs, exemplified by various drugs, are designed to inhibit EGFR, thereby impeding tumor progression. Moreover, these compounds influence potent antibacterial activity, interfering with microbial growth through mechanisms ranging from DNA replication inhibition to other vital cellular functions. This dual activity, targeting both cancer cells and microbial pathogens, underscores the versatility and potential of pyrimidine derivatives in medical applications. This review provides insights into the structural characteristics, synthesis methods, and significant medicinal applications of fused pyrimidine derivatives, highlighting their double role in combating cancer and bacterial infections.

Designing Potent Anti-Cancer Agents: Synthesis and Molecular Docking Studies of Thieno[2,3-d][1,2,4]triazolo[1,5-a]pyrimidine Derivatives

A new series of thieno[2,3-d][1,2,4]triazolo[1,5-a]pyrimidines was designed and synthesized using readily available starting materials, specifically, β-enaminoester. Their cytotoxicity was screened against three cancer cell lines, namely, MCF-7, HCT-116, and PC-3. 2-(4-bromophenyl)triazole 10b and 2-(anthracen-9-yl)triazole 10e afforded excellent potency against MCF-7 cell lines (IC50 = 19.4 ± 0.22 and 14.5 ± 0.30 μM, respectively) compared with doxorubicin (IC50 = 40.0 ± 3.9 μM). The latter derivatives 10b and 10e were further subjected to in silico ADME and docking simulation studies against EGFR and PI3K and could serve as ideal leads for additional modification in the field of anticancer research.

The tRNA methyltransferase TrmB is critical for Acinetobacter baumannii stress responses and pulmonary infection

IMPORTANCE

As deficiencies in tRNA modifications have been linked to human diseases such as cancer and diabetes, much research has focused on the modifications' impacts on translational regulation in eukaryotes. However, the significance of tRNA modifications in bacterial physiology remains largely unexplored. In this paper, we demonstrate that the m7G tRNA methyltransferase TrmB is crucial for a top-priority pathogen, Acinetobacter baumannii, to respond to stressors encountered during infection, including oxidative stress, low pH, and iron deprivation. We show that loss of TrmB dramatically attenuates a murine pulmonary infection. Given the current efforts to use another tRNA methyltransferase, TrmD, as an antimicrobial therapeutic target, we propose that TrmB, and other tRNA methyltransferases, may also be viable options for drug development to combat multidrug-resistant A. baumannii.

Recent updates on thienopyrimidine derivatives as anticancer agents

Thienopyrimidine derivatives hold a unique place between fused pyrimidine compounds. They are important and widely represented in medicinal chemistry as they are structural analogs of purines. Thienopyrimidine derivatives have various biological activities. The current review discusses different synthetic methods for the preparation of heterocyclic thienopyrimidine derivatives. It also highlights the most recent research on the anticancer effects of thienopyrimidines through the inhibition of various enzymes and pathways, which was published within the last 9 years.

Graphical Abstract

Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation

The tRNA modification m¹G37, introduced by the tRNA methyltransferase TrmD, is thought to be essential for growth in bacteria because it suppresses translational frameshift errors at proline codons. However, because bacteria can tolerate high levels of mistranslation, it is unclear why loss of m¹G37 is not tolerated. Here, we addressed this question through experimental evolution of trmD mutant strains of Escherichia coli. Surprisingly, trmD mutant strains were viable even if the m¹G37 modification was completely abolished, and showed rapid recovery of growth rate, mainly via duplication or mutation of the proline-tRNA ligase gene proS. Growth assays and in vitro aminoacylation assays showed that G37-unmodified tRNA^Pro is aminoacylated less efficiently than m¹G37-modified tRNA^Pro, and that growth of trmD mutant strains can be largely restored by single mutations in proS that restore aminoacylation of G37-unmodified tRNA^Pro. These results show that inefficient aminoacylation of tRNA^Pro is the main reason for growth defects observed in trmD mutant strains and that proS may act as a gatekeeper of translational accuracy, preventing the use of error-prone unmodified tRNA^Pro in translation. Our work shows the utility of experimental evolution for uncovering the hidden functions of essential genes and has implications for the development of antibiotics targeting TrmD.

New C2- and N3-Modified Thieno[2,3-d]Pyrimidine Conjugates with Cytotoxicity in the Nanomolar Range

AIMS

The aim of the current study was to develop and explore a series of new cytotoxic agents based on the conjugation between the thieno[2,3-d]pyrimidine moiety and a second pharmacophore at the C2 or N3 position.

BACKGROUND

As the thieno[2,3-d]pyrimidine core is a bioisostere of the 4-anilinoquinazoline, various new thienopyrimidine derivatives were synthesized by modifying the structure of the clinically used anticancer quinazoline EGFR inhibitors of the first generation - gefitinib, and second generation - dacomitinib and canertinib. It was reported that some thieno[2,3-d]pyrimidine derivatives showed improved EGFR inhibitory activity. On the other hand, the benzimidazole heterocycle is present as a pharmacophore unit in the structure of many clinically used chemotherapeutic agents. Some 2-aminobenzimidazole derivatives, possessing anticancer activity, demonstrated EGFR inhibition and the benzimidazole derivative EGF816 is currently in the second phase of clinical trials.

OBJECTIVE

The objectives of the study were design of a novel series thieno[2,3-d]pyrimidines, synthesis of the compounds and investigation of their effects towards human cancer HT-29, MDA-MB-231, HeLa, HepG2 and to normal human Lep3 cell lines. (American Type Culture Collection, ATCC, Rockville, MD, USA) Methods: The synthetic protocol implemented cyclocondensation of 2-amino-thiophenes and nitriles in inert medium, aza-Michael addition to benzimidazole derivatives and nucleophylic substitution at the N3 place. MTS test was used in order to establish the cytotoxicity of the tested compounds. SAR analysis and in silico assessment of the inhibitory potential towards human oncogenic V^599EB-Raf were performed using Molinspiration tool and Molecular Operating environment software.

RESULTS

The MTS test data showed that almost all studied thieno[2,3-d]pyirimidines (9-13, 21-22 and 25) manifest high inhibiting effect on the cell proliferation at nanomolar concentrations, whereat compounds 9 (IC₅₀ = 130 nM) and 10 (IC₅₀ = 261 nM) containing amino acid moiety, and 21 (IC₅₀ = 108 nM) possesing two thienopyrimidine moieties attached to a 1,3-disubstituted benzimidazole linker, revealed many times lower toxicity against Lep3 cells compared to the cancer cells. Thienopyrimidines 11-13 possessed high selectivity against HeLa cells. Compound 13 showed high inhibitory activity against MDA-MB-231 and HepG2, with IC50 1.44 nM and 1.11 nM respectively. To outline the possible biological target of the studied coumpounds, their potential to interact with human oncogenic V^599EB-Raf was explored by a docking study. As a result, it was suggested that the benzimidazolyl and glycyl fragments could enhance the binding ability of the new compounds by increasing the number of hydrogen bond acceptors and by stabilizing the inactive form of the enzyme.

CONCLUSION

The thienopyrimidines tested in vitro towards human cancer HT-29, MDA-MB-231, HeLa, HepG2 and normal human Lep3 cell lines demonstrated cytotoxicity in nanomolar range. It was established that compounds 9, 10 and 21 showed many times lower toxicity against normal Lep3 cells that can provide a high selectivity towards all four cancer cell lines at small concentrations. Based on the analysis of the structure-activity relationship, the observed trends in the cytotoxicity could be related to the lipophilicity and the topological polar surface area of the tested compounds. The docking study on the potential of the new thieno[2,3-d]pyrimidine-4-ones to interact with mutant V^599EB-Raf showed that the compounds might be able to stabilize the enzyme in its inactive form.