SAR investigation and optimization of benzimidazole-based derivatives as antimicrobial agents against Gram-negative bacteria

Targeting DNA repair mechanisms: Spirobenzoxazinone and salicylamide derivatives as novel candidates for PARP-1 inhibition in cancer therapy

Poly(ADP-ribose) polymerase-1 (PARP-1) plays a crucial role in DNA repair, mediating approximately 90 % of ADP-ribosylation processes associated with DNA damage response. Consequently, inhibiting PARP-1 with small molecules represents a promising strategy for cancer therapy. Utilizing a structure-based design and molecular hybridization approach, we developed three novel series of spirobenzoxazinone-piperdine/salicylamide-based derivatives. These compounds were evaluated for their in vitro PARP-1 inhibitory activity, and their structure-activity relationships were analyzed. At 10 µM concentration, derivatives (18a-d) demonstrated nearly complete inhibition, and the spirocyclic derivative (7c) also achieved a considerable inhibitory effect, with IC50 values in the low micromolar range. The most promising compounds (7c, 18a-d) were tested for their antiproliferative activity against six cancer cell lines. Notably, compounds (7c) and (18d) exhibited significant antiproliferative effects against H1299 and FaDu cells, which correlated with their calculated logP values. These compounds were also tested against normal human skin fibroblasts (HSF), revealing a favorable safety profile compared to cancer cells. Basal anti-PARP-1 activity of the most promising compounds was validated in the HCT116 colorectal cancer cell line. Western blot analysis confirmed robust cleavage of PARP-1, indicating enzymatic inhibition and loss of PARP-1 activity. Combining these inhibitors with doxorubicin showed synergistic lethality in colony-formation assay. Finally, a molecular docking study was conducted to examine the binding modes of these compounds within the PARP-1 active site. The results demonstrated binding modes comparable to those of olaparib and other approved PARP-1 inhibitors, maintaining the key interactions necessary for activity. Based on these findings, compounds (7c) and (18d) emerge as promising candidates for further development in targeting anti-cancer drug resistance through PARP-1 inhibition.

Structural Optimization and MD Simulation Study of Benzimidazole Derivatives as Potent Mutant FLT3 Kinase Inhibitors Targeting AML

Acute myeloid leukemia (AML) is an aggressive hematological malignancy with poor survival rates in adults, posing a significant economic burden. FMS-like tyrosine kinase 3 (FLT3) mutations are linked to poor prognosis in AML and resistance to clinically approved FLT3 inhibitors. Previously, we reported a novel benzimidazole-based FLT3 inhibitor, 4ACP, with nanomolar activities against FLT3-ITD and FLT3-TKD mutants, showing selective cytotoxicity against FLT3-ITD+ AML cell lines. In this study, we synthesized 31 derivatives by modifying the 4-acetamidophenyl group and varying substituents at N1-phenyl and C2 positions. We identified compound 21l (3-acetamidophenyl) as the most potent derivative (FLT3-TKD(D835Y) IC50 = 1.47 nM). Linking 21l to a solvent-accessible group yielded compound 22b, which exhibited a sub-nanomolar activity against FLT-TKD(D835Y) mutant with an IC50 value of 0.48 nM. Compound 22b showed preferential antiproliferative activities against MOLM-14, MV4-11, MOLM-14-D835Y, and MOLM-14-F691L AML cell lines with IC50 values of 16.1, 10.5, 26.5, and 160.3 nM, respectively. 22b induced dose-dependent inhibition of FLT3, ERK, STAT5, and S6 phosphorylation, G0/G1 cell-cycle arrest, and apoptotic cell death at low nanomolar concentrations in MOLM-14 and MOLM-14-D835Y cells. It was more selective for FLT3-dependent cell lines, showing about 80-fold selectivity toward FLT3-TKD(D835Y) over KIT, indicating relative safety and lower myelosuppression potential. The molecular dynamics study of 4ACP and 22b was conducted to explain the significant changes in activity resulting from subtle structural alterations. Altogether, these findings establish 22b as a potent mutant FLT3 inhibitor, warranting further investigation and optimization to target resistant AML.

Investigating the Antibacterial Efficiency and Mechanism of Indole- and Naphthalimide-Mediated Benzimidazoles: Membrane Damage, Metabolic Inactivation, and Oxidative Stress against Bacillus subtilis

Resistance by bacteria to available antibiotics is a threat to human health, which demands the development of new antibacterial agents. Considering the prevailing conditions, we have developed a series of naphthalimide/indole benzimidazoles with diverse amines and aryl rings to avoid the molecular framework of conventional drug molecules to overcome the cross-resistance issue. Most of the synthesized compounds, especially electron-withdrawing and halide substituents, show broad-spectrum activity against both Gram-positive and Gram-negative bacterial strains. Preliminary studies indicate that compounds IB-14 and NB-8 display excellent antibacterial activity against Bacillus subtilis, exceeding the performance of the marketed drug amoxicillin. In addition to the rapid bactericidal effect, both compounds significantly inhibit the formation of biofilm, lowering the development of drug resistance. Moreover, both compounds exhibit fast-bactericidal properties, thus shortening the time of treatment and also resisting the emergence of drug resistance up to 20 passages. Further, biofunctional evaluation reveals that both compounds effectively disrupt the membrane, causing the leakage of cytoplasmic contents and loss in metabolic activity. Both compounds efficiently induce the reactive oxygen species (ROS), leading to the oxidation of GSH to GSSG, decreasing the GSH activity of the cell, and causing oxidative damage to cells. DNA studies show that compounds significantly bind to DNA and form DNA-IB-14/NB-8 complexes that inhibit the replication of DNA and protein. The significant binding affinity of compounds with HSA suggests easy transport of the developed antibacterial candidates to the target site through the carrier protein. These findings suggest that both compounds have broad-spectrum and multitargeting potential as antibacterial agents and provide a new possibility to overcome the global issue of the development of multidrug resistance by bacteria toward conventional antibiotics.

The anti-Acinetobacter baumannii therapeutic potential of azole hybrids: A mini-review

Acinetobacter baumannii is one of the major causes of severe hospital- and community-acquired infections, posing a significant threat to human lives. A. baumannii has already generated resistance to almost all of the currently available antibiotics, but no new class of antibacterials have been launched for the treatment of infections caused by A. baumannii in the last half century, creating an urgent need to develop novel antibacterials. Azoles as a broad class of five-membered nitrogen-containing aromatic heterocycles are privileged pharmacophores widely found in pharmaceuticals. Azoles could target on diverse enzymes, proteins, and receptors in A. baumannii via various noncovalent interactions. Particularly, azole hybrids have potential advantages in increasing therapeutic efficacy and circumventing drug resistance, representing useful scaffolds for the discovery of novel anti-A. baumannii agents. This review outlines the current scenario of the antibacterial therapeutic potential of azole hybrids against A. baumannii, developed from 2020 onwards, aiming to provide potential candidates for further preclinical/clinical evaluations and facilitate the rational design of more effective candidates.

Investigation of the cytotoxic activity, DFT calculation, and docking studies newly synthesized 1,3-disubstituted benzimidazolium chlorides on human liver cancer, lung cancer, and normal embryonic kidney cell lines

Three 1,3-disubstituted benzimidazolium salts (3a-c) were efficiently synthesized in moderate to high yields (52-83 %) and analyzed through NMR spectra. The anti-cancer efficiency of these compounds was tested on human liver cancer (HepG2), lung cancer (A549), and normal embryonic kidney (HEK-293T) cell lines. The results demonstrated that compound 3b emerges as a promising candidate for further investigation due to its high cytotoxicity, comparable to cisplatin. The optimized geometry, electronic properties, chemical parameters and frontier molecular orbitals of 3a-c were determined by DFT calculation using density functional theory (DFT) with the B3LYP/6-31++G(d,p) level in the ground state. In addition to the experimental studies, compounds 3a-c were docked against target protein PDB ID: 6V9C representing the HepG2 cell line.

Optimization of Ethoxzolamide Analogs with Improved Pharmacokinetic Properties for In Vivo Efficacy against Neisseria gonorrhoeae

Drug-resistant gonorrhea is caused by the bacterial pathogen Neisseria gonorrhoeae, for which there is no recommended oral treatment. We have demonstrated that the FDA-approved human carbonic anhydrase inhibitor ethoxzolamide potently inhibits N. gonorrhoeae; however, is not effective at reducing N. gonorrhoeae bioburden in a mouse model. Thus, we sought to optimize the pharmacokinetic properties of the ethoxzolamide scaffold. These efforts resulted in analogs with improved activity against N. gonorrhoeae, increased metabolic stability in mouse liver microsomes, and improved Caco-2 permeability compared to ethoxzolamide. Improvement in these properties resulted in increased plasma exposure in vivo after oral dosing. Top compounds were investigated for in vivo efficacy in a vaginal mouse model of gonococcal genital tract infection, and they significantly decreased the gonococcal burden compared to vehicle and ethoxzolamide controls. Altogether, results from this study provide evidence that ethoxzolamide-based compounds have the potential to be effective oral therapeutics against gonococcal infection.

Rational molecular design converting fascaplysin derivatives to potent broad-spectrum inhibitors against bacterial pathogens via targeting FtsZ

The filamentous temperature-sensitive mutant Z protein (FtsZ), a key player in bacterial cell division machinery, emerges as an attractive target to tackle the plight posed by the ever growing antibiotic resistance over the world. Therefore in this regard, agents with scaffold diversities and broad-spectrum antibacterial activity against Gram-positive and Gram-negative pathogens are highly needed. In this study, a new class of marine-derived fascaplysin derivatives has been designed and synthesized by Suzuki-Miyaura cross-coupling. Some compounds exhibited potent bactericidal activities against a panel of Gram-positive (MIC = 0.024-6.25 μg/mL) and Gram-negative (MIC = 1.56-12.5 μg/mL) bacteria including methicillin-resistant S. aureus (MRSA). They exerted their effects by dual action mechanism via disrupting the integrity of the bacterial cell membrane and targeting FtsZ protein. These compounds stimulated polymerization of FtsZ monomers and bundling of the polymers, and stabilized the resulting polymer network, thus leading to the dysfunction of FtsZ in cell division. In addition, these agents showed negligible hemolytic activity and low cytotoxicity to mammalian cells. The studies on docking and molecular dynamics simulations suggest that these inhibitors bind to the hydrophilic inter-domain cleft of FtsZ protein and the insights obtained in this study would facilitate the development of potential drugs with broad-spectrum bioactivities.

Chemical genetic approaches for the discovery of bacterial cell wall inhibitors

Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.

Design, Synthesis, and Biological Evaluation of Benzimidazole Derivatives as Potential Lassa Virus Inhibitors

The Lassa virus (LASV) causes Lassa fever, a highly infectious and lethal agent of acute viral hemorrhagic fever. At present, there are still no effective treatments available, creating an urgent need to develop novel therapeutics. Some benzimidazole compounds targeting the arenavirus envelope glycoprotein complex (GPC) are promising inhibitors of LASV. In this study, we synthesized two series of LASV inhibitors based on the benzimidazole structure. Lentiviral pseudotypes bearing the LASV GPC were established to identify virus entry inhibitors. Surface plasmon resonance (SPR) was further used to verify the binding activities of the potential compounds. Compounds 7d-Z, 7h-Z, 13c, 13d, and 13f showed relatively excellent antiviral activities with IC₅₀ values ranging from 7.58 to 15.46 nM and their SI values above 1251. These five representative compounds exhibited stronger binding affinity with low equilibrium dissociation constants (K_D < 8.25 × 10^-7 M) in SPR study. The compound 7h-Z displayed the most potent antiviral activity (IC₅₀ = 7.58 nM) with a relatively high SI value (2496), which could be further studied as a lead compound. The structure-activity relationship indicated that the compounds with lipophilic and spatially larger substituents might possess higher antiviral activity and a much larger safety margin. This study will provide some good guidance for the development of highly active compounds with a novel skeleton against LASV.