Synthesis and Structure-Activity Relationship of Some New Thiophene-Based Heterocycles as Potential Antimicrobial Agents

Pyrimido[1,2-a]benzimidazoles as inhibitors of oncoproteins ubiquitin specific protease 5 and MYCN in the childhood cancer neuroblastoma

The MYCN oncogene and histone deacetylases (HDACs) are key driver genes in the childhood cancer, neuroblastoma. We recently described a novel pyridobenzimidazole analogue, SE486-11, which enhanced the therapeutic effectiveness of HDAC inhibitors by increasing MYCN ubiquitination through effects on the deubiquitinase, ubiquitin-specific protease 5 (USP5). Here we describe the synthesis of a novel series of pyrimido[1,2-a]benzimidazole derivatives, and an evaluation of their cytopathic effects against non-malignant and human neuroblastoma cell lines. Among the tested analogues, 4-(4-methoxyphenyl)benzo[4,5]imidazo[1,2-a]pyrimidine (3a) was the most active compound against neuroblastoma cells (IC50 ≤ 2 µM), with low cytotoxicity (IC50 ≥ 15 µM) to normal cells. We show compound 3a bound to USP5 protein (Kd = 0.47 µM) in vitro and synergistically enhanced the efficacy of HDAC inhibitors against neuroblastoma cells. Moreover, knockdown of USP5 and MYCN in treated neuroblastoma cells showed that both USP5 and MYCN expression was necessary for the cytopathic activity of compound 3a, thus providing a clinically relevant rationale for further development of this of pyrimido[1,2-a]benzimidazole.

Pyridine Compounds with Antimicrobial and Antiviral Activities

In the context of the new life-threatening COVID-19 pandemic caused by the SARS-CoV-2 virus, finding new antiviral and antimicrobial compounds is a priority in current research. Pyridine is a privileged nucleus among heterocycles; its compounds have been noted for their therapeutic properties, such as antimicrobial, antiviral, antitumor, analgesic, anticonvulsant, anti-inflammatory, antioxidant, anti-Alzheimer’s, anti-ulcer or antidiabetic. It is known that a pyridine compound, which also contains a heterocycle, has improved therapeutic properties. The singular presence of the pyridine nucleus, or its one together with one or more heterocycles, as well as a simple hydrocarbon linker, or grafted with organic groups, gives the key molecule a certain geometry, which determines an interaction with a specific protein, and defines the antimicrobial and antiviral selectivity for the target molecule. Moreover, an important role of pyridine in medicinal chemistry is to improve water solubility due to its poor basicity. In this article, we aim to review the methods of synthesis of pyridine compounds, their antimicrobial and antiviral activities, the correlation of pharmaceutical properties with various groups present in molecules as well as the binding mode from Molecular Docking Studies.

Thiophene-containing compounds with antimicrobial activity

Thiophene, as a member of the group of five-membered heterocycles containing one heteroatom, is one of the simplest heterocyclic systems. Many synthetic strategies allow the accurate positioning of various functionalities onto the thiophene ring. This review provides a comprehensive, systematic and detailed account of the developments in the field of antimicrobial compounds featuring at least one thiophene ring in their structure, over the last decade.

Diverse Thiophenes as Scaffolds in Anti-cancer Drug Development: A Concise Review

Thiophenes are one of the abundantly found heterocyclic ring systems in many biologically active compounds. Moreover, various substituted thiophenes exert numerous pharmacological actions on account of their isosteric resemblance with compounds of natural origin, thus rendering them with diverse actions like antibacterial, antifungal, antiviral, anti-inflammatory, analgesic, antiallergic, hypotensives, etc. In this review, we specifically explore the chemotherapeutic potential of a variety of structures consisting of thiophene scaffolds as prospective anticancer agents.

Pyrimido[1,2-a]benzimidazoles: synthesis and perspective of their pharmacological use

The review presents data on the synthesis as well as studies of biological activity of new derivatives of pyrimido[1,2-a]benzimidazoles published over the last decade. The bibliography of the review includes 136 sources.

Nucleophilic Displacement Reaction on Tosyl Cellulose by L-Methionine to the Synthesis of Novel Water-Soluble Cellulose Derivative and Its Antibacterial Activity

A novel ampholytic cellulose derivative, cellulose-L-methionine, has been synthesized by means of an esterification reaction of microcrystalline cellulose with tosyl chloride (p-TsCl) in DMAc/LiCl (8%) at 8°C that was followed by nucleophilic displacement (SN) of the tosyl group by the L-methionine amino acid. The resulting structure of cellulose-L-methionine has been characterized by elemental analysis (CHNSO), Fourier-transform infrared spectroscopy (FTIR), proton nuclear magnetic resonance (1H-NMR), and scanning electron microscopy (SEM). The antibacterial activity of the synthesized product was screened against Gram-positive and Gram-negative microbial strains such as Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa, by the agar well diffusion method, and compared with commercial antibiotics such as ampicillin and chloramphenicol. It was found that antibacterial experiment revealed excellent antibacterial activity of the cellulose-methionine with respect to a minimal inhibitory concentration (MIC) reference.

Synthesis, ADMET Properties, and In Vitro Antimicrobial and Antibiofilm Activity of 5-Nitro-2-thiophenecarbaldehyde N-((E)-(5-Nitrothienyl)methylidene)hydrazone (KTU-286) against Staphylococcus aureus with Defined Resistance Mechanisms

The emergence of drug-resistant Staphylococcus aureus is responsible for high morbidity and mortality worldwide. New therapeutic options are needed to fight the increasing antimicrobial resistance among S. aureus in the clinical setting. We, therefore, characterized the in silico absorption, distribution, metabolism, elimination, and toxicity (ADMET) and in vitro antimicrobial activity of 5-nitro-2-thiophenecarbaldehyde N-((E)-(5-nitrothienyl)methylidene)hydrazone (KTU-286) against drug-resistant S. aureus strains with genetically defined resistance mechanisms. The antimicrobial activity of KTU-286 was determined by CLSI recommendations. The ADMET properties were estimated by using in silico modeling. The activity on biofilm integrity was examined by crystal violet assay. KTU-286 demonstrated low estimated toxicity and low skin permeability. The highest antimicrobial activity was observed among pan-susceptible (Pan-S) S. aureus (minimal inhibitory concentration (MIC) 0.5–2.0 µg/mL, IC₅₀ = 0.460 µg/mL), followed by vancomycin resistant S. aureus (VRSA) (MIC 4.0 µg/mL, IC₅₀ = 1.697 µg/mL) and methicillin-resistant S. aureus (MRSA) (MIC 1.0–16.0 µg/mL, IC₅₀ = 2.282 µg/mL). KTU-286 resulted in significant (p < 0.05) loss of S. aureus biofilm integrity in vitro. Further studies are needed for a better understanding of safety, synergistic relationship, and therapeutic potency of KTU-286.

Crystal structure, Hirshfeld surface analysis and inter-action energy, DFT and anti-bacterial activity studies of (Z)-4-hexyl-2-(4-methyl-benzyl-idene)-2H-benzo[b][1,4]thia-zin-3(4H)-one

The title compound, C22H25NOS, consists of methyl-benzyl-idene and benzo-thia-zine units linked to a hexyl moiety, where the thia-zine ring adopts a screw-boat conformation. In the crystal, inversion dimers are formed by weak C-HMthn⋯OBnzthz hydrogen bonds and are linked into chains extending along the a-axis direction by weak C-HBnz⋯OBnzthz (Bnz = benzene, Bnzthz = benzo-thia-zine and Mthn = methine) hydrogen bonds. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (59.2%) and H⋯C/C⋯H (27.9%) inter-actions. Hydrogen bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Computational chemistry indicates that in the crystal, the C-HBnz⋯OBnzthz and C-HMthn⋯OBnzthz hydrogen-bond energies are 75.3 and 56.5 kJ mol-1, respectively. Density functional theory (DFT) optimized structures at the B3LYP/ 6-311 G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap. Moreover, the anti-bacterial activity of the title compound was evaluated against gram-positive and gram-negative bacteria.

Crystal structure, Hirshfeld surface analysis and inter-action energy, DFT and anti-bacterial activity studies of ethyl 2-[(2Z)-2-(2-chloro-benzyl-idene)-3-oxo-3,4-di-hydro-2H-1,4-benzo-thia-zin-4-yl]acetate

The title compound, C19H16ClNO3S, consists of chloro-phenyl methyl-idene and di-hydro-benzo-thia-zine units linked to an acetate moiety, where the thia-zine ring adopts a screw-boat conformation. In the crystal, two sets of weak C-HPh⋯ODbt (Ph = phenyl and Dbt = di-hydro-benzo-thia-zine) hydrogen bonds form layers of mol-ecules parallel to the bc plane. The layers stack along the a-axis direction with inter-calation of the ester chains. The crystal studied was a two component twin with a refined BASF of 0.34961 (5). The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (37.5%), H⋯C/C⋯H (24.6%) and H⋯O/O⋯H (16.7%) inter-actions. Hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Computational chemistry indicates that in the crystal, C-HPh⋯ODbt hydrogen bond energies are 38.3 and 30.3 kJ mol-1. Density functional theory (DFT) optimized structures at the B3LYP/ 6-311 G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap. Moreover, the anti-bacterial activity of the title compound has been evaluated against gram-positive and gram-negative bacteria.

Design, Synthesis and Antimicrobial Evaluation of 1,3,4‐Oxadiazole/1,2,4‐Triazole‐Substituted Thiophenes

The increasing level of antimicrobial resistance in pathogenic bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a major public health concern. Thus, in this context, a novel series of 1,3,4‐oxadiazole‐substituted thiophenes (4 a–m) and 1,2,4‐triazole (6 a–m) substituted thiophene derivatives were synthesized. Characterization of all the synthesized derivatives was done by various spectroscopic techniques such as 1H NMR, 13C NMR spectroscopy and mass spectrometry, and evaluated for antimicrobial activity against various pathological strains using broth dilution and disc diffusion method. In particular, compound 6 e and 4 e exhibited significant inhibitory potential with MIC ranging from 2–7 μg mL−1 against S. aureus, B. subtilis, P. aeruginosa and E. coli. Additionally, compound 6 e was found to be highly potent against methicillin resistant S. aureus (MRSA; MIC=2 μg mL−1). Molecular docking studies were also performed to confer the possible mode of action and association studies indicate the binding of potent active compound with DHFR enzyme (Ka=2.10×103 M−1). Further, the mechanism of action has also been explored by atomic force microscopy (AFM), which reveals the bacterial cell wall deformity and cell wall rupturing that may lead to bacteria cell death. Additionally, in silico ADME prediction study suggested the drug like properties of active compounds.

Two isostructural 3-(5-ar-yloxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1-(thio-phen-2-yl)prop-2-en-1-ones: disorder and supra-molecular assembly

Two new chalcones containing both pyrazole and thio-phene substituents have been prepared and structurally characterized. 3-(3-Methyl-5-phen-oxy-1-phenyl-1H-pyrazol-4-yl)-1-(thio-phen-2-yl)prop-2-en-1-one, C23H18N2O2S (I), and 3-[3-methyl-5-(2-methyl-phen-oxy)-1-phenyl-1H-pyrazol-4-yl]-1-(thio-phen-2-yl)prop-2-en-1-one, C24H20N2O2S (II), are isomorphous as well as isostructural, and in each the thio-phene substituent is disordered over two sets of atomic sites having occupancies 0.844 (3) and 0.156 (3) in (I), and 0.883 (2) and 0.117 (2) in (II). In each structure, the mol-ecules are linked into sheets by a combination of C-H⋯N and C-H⋯O hydrogen bonds. Comparisons are made with some related compounds.

Synthesis of novel Schiff bases using 2-Amino-5-(3-fluoro-4-methoxyphenyl)thiophene-3-carbonitrile and 1,3-Disubstituted pyrazole-4-carboxaldehydes derivatives and their antimicrobial activity

2-Amino-5-(3-fluoro-4-methoxyphenyl)thiophene-3-carbonitrile have been synthesized from 1-(3-fluoro-4-methoxyphenyl)ethanone, malononitrile, a mild base and sulfur powder using Gewald synthesis technique and the intermediate was treated with 1,3-disubstituted pyrazole-4-carboxaldehyde to obtain the novel Schiff bases. 1,3-disubstituted pyrazole-4-carboxaldehyde derivatives have been synthesized by Vilsmeier-Haack reaction in the course of a multi-step reaction. The structure of novel compounds were established on the basis of their elemental analyses IR, ¹H NMR, ¹³C NMR, and mass spectral data and then screened for their in vitro antimicrobial activity. Among them 5a, 5c, 5f and 5h showed excellent activity when compared to other derivatives. Remaining derivatives showed moderate activity.

Crystal structure and Hirshfeld surface analysis of 5-methyl-1,2,4-triazolo[1,5-a]pyrimidine

The nine-membered ring system of the title compound, C6H6N4, is essentially planar. In the crystal, mol-ecules are linked via C-HTrz⋯NTrz and C-HPyrm⋯NTrz (Trz = triazole and Pyrm = pyrimidine) hydrogen bonds together with weaker C-HPyrm⋯NPyrm hydrogen bonds to form layers parallel to (02). The layers are further connected by π-π-stacking inter-actions between the nine-membered ring system [centroid-centroid = 3.7910 (8) Å], forming oblique stacks along the a-axis direction. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯N/N⋯H (40.1%), H⋯H (35.3%), H⋯C/C⋯H (9.5%), N⋯C/C⋯N (9.0%), N⋯N (3.1%) and C⋯C (3.0%) inter-actions and that hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. No significant C-H⋯π inter-actions are observed.

Ethyl 2-(5-methyl-1,2,4-triazolo[1,5-a]pyrimidin-7-yl)pent-4-enoate

In the title molecule, C13H16N4O2, the fused triazolopyrimidine ring system is planar. In the crystal, inversion-related C—H...O hydrogen bonds form dimers that are linked into chains extending along the a-axis direction by inversion-related C—H...π(ring) interactions.

Design and synthesis of novel 3-(thiophen-2-yl)-1,5-dihydro-2H-pyrrol-2-one derivatives bearing a hydrazone moiety as potential fungicides

BACKGROUND

Tetramic acid, thiophene and hydrazone derivatives were found to exhibit favorable antifungal activity. Aiming to discover novel template molecules with potent antifungal activity, a series of novel 3-(thiophen-2-yl)-1,5-dihydro-2H-pyrrol-2-one derivatives containing a hydrazone group were designed, synthesized, and evaluated for their antifungal activity.

RESULTS

The structures of 3-(thiophen-2-yl)-1,5-dihydro-2H-pyrrol-2-one derivatives bearing a hydrazone group were confirmed by FT-IR, 1H NMR, 13C NMR, 1H-1H NOESY, EI-MS and elemental analysis. Antifungal assays indicated that some title compounds exhibited antifungal activity against Fusarium graminearum (Fg), Rhizoctorzia solani (Rs), Botrytis cinerea (Bc) and Colletotrichum capsici (Cc) in vitro. Strikingly, the EC50 value of 5e against Rs was 1.26 µg/mL, which is better than that of drazoxolon (1.77 µg/mL). Meanwhile, title compounds 5b, 5d, 5e-5g, 5n-5q and 5t exhibited remarkable anti-Cc activity, with corresponding EC50 values of 7.65, 9.97, 6.04, 6.66, 7.84, 7.59, 9.47, 5.52, 6.41 and 7.53 µg/mL, respectively, which are better than that of drazoxolon (19.46 µg/mL).

CONCLUSIONS

A series of 3-(thiophen-2-yl)-1,5-dihydro-2H-pyrrol-2-one derivatives bearing a hydrazone group were designed, synthesized and evaluated for their antifungal activity against Fg, Rs, Bc and Cc. Bioassays indicated that some target compounds exhibited obvious antifungal activity against the above tested fungi. These results provide a significant basis for the further structural optimization of tetramic acid derivatives as potential fungicides.

Stereoselective synthesis, X-ray analysis, computational studies and biological evaluation of new thiazole derivatives as potential anticancer agents

Background

The synthesis of new thiazole derivatives is very important because of their diverse biological activities. Also , many drugs containing thiazole ring in their skeletons are available in the market such as Abafungin, Acotiamide, Alagebrium, Amiphenazole, Brecanavir, Carumonam, Cefepime, and Cefmatilen.

Results

Ethyl cyanoacetate reacted with phenylisothiocyanate, chloroacetone, in two different basic mediums to afford the thiazole derivative 6, which reacted with dimethylformamide- dimethyl acetal in the presence of DMF to afford the unexpected thiazole derivative 11. The structures of the thiazoles 6 and 11 were optimized using B3LYP/6-31G(d,p) method. The experimentally and theoretically geometric parameters agreed very well. Also, the natural charges at the different atomic sites were predicted. HOMO and LUMO demands were discussed. The anticancer activity of the prepared compounds was evaluated and showed moderate activity.

Conclusions

Synthesis of novel thiazole derivatives was done. The structure was established using X-ray and spectral analysis. Optimized molecular structures at the B3LYP/6-31G(d,p) level were investigated. Thiazole derivative 11 has more electropositive S-atom than thiazole 6. The HOMO–LUMO energy gap is lower in the former compared to the latter. The synthesized compounds showed moderate anticancer activity.

Electronic supplementary material

The online version of this article (10.1186/s13065-018-0420-7) contains supplementary material, which is available to authorized users.

One-pot sequential synthesis of tetrasubstituted thiophenes via sulfur ylide-like intermediates

Herein, we describe a novel approach for the practical synthesis of tetrasubstituted thiophenes 8. The developed method was particularly used for the facile preparation of thienyl heterocycles 8. The mechanism for this reaction is based on the formation of a sulfur ylide-like intermediate. It was clearly suggested by (i) the intramolecular cyclization of ketene N,S-acetals 7 to the corresponding thiophenes 8, (ii) 1H NMR studies of Meldrum's acid-substituted aminothioacetals 9, and (iii) substitution studies of the methoxy group on Meldrum's acid containing N,S-acetals 9b. Notably, in terms of structural effects on the reactivity and stability of sulfur ylide-like intermediates, 2-pyridyl substituted compound 7a exhibited superior properties over those of others.

Synthesis and Pharmacological Activities of Pyrazole Derivatives: A Review

Pyrazole and its derivatives are considered a pharmacologically important active scaffold that possesses almost all types of pharmacological activities. The presence of this nucleus in pharmacological agents of diverse therapeutic categories such as celecoxib, a potent anti-inflammatory, the antipsychotic CDPPB, the anti-obesity drug rimonabant, difenamizole, an analgesic, betazole, a H2-receptor agonist and the antidepressant agent fezolamide have proved the pharmacological potential of the pyrazole moiety. Owing to this diversity in the biological field, this nucleus has attracted the attention of many researchers to study its skeleton chemically and biologically. This review highlights the different synthesis methods and the pharmacological properties of pyrazole derivatives. Studies on the synthesis and biological activity of pyrazole derivatives developed by many scientists around the globe are reported.

Synthesis and Pharmacological Activities of Pyrazole Derivatives: A Review

Pyrazole and its derivatives are considered a pharmacologically important active scaffold that possesses almost all types of pharmacological activities. The presence of this nucleus in pharmacological agents of diverse therapeutic categories such as celecoxib, a potent anti-inflammatory, the antipsychotic CDPPB, the anti-obesity drug rimonabant, difenamizole, an analgesic, betazole, a H2-receptor agonist and the antidepressant agent fezolamide have proved the pharmacological potential of the pyrazole moiety. Owing to this diversity in the biological field, this nucleus has attracted the attention of many researchers to study its skeleton chemically and biologically. This review highlights the different synthesis methods and the pharmacological properties of pyrazole derivatives. Studies on the synthesis and biological activity of pyrazole derivatives developed by many scientists around the globe are reported.

Antimicrobial activity of thiophene derivatives derived from ethyl (E)-5-(3-(dimethylamino)acryloyl)-4-methyl-2-(phenylamino)thiophene-3-carboxylate

Background

The thiophene nucleus has been recognized as an important entity in the synthesis of heterocyclic compounds with promising pharmacological characteristics.

Results

A number of new heterocyclic compounds incorporating thiophene species have been prepared from the titled enaminone via the reaction with different nucleophiles and electrophiles. The structure elucidation of the designed compounds was derived from their spectral information. The results of antimicrobial activity of the prepared compounds revealed that derivatives 7b and 8 exhibited activity comparable to the standard drugs ampicillin and gentamicin for all tested bacteria species. Additionally, compound 3 displayed potent activity against Aspergillus fumigates, whereas compounds 5, 6, and 7a showed good activity against Syncephalastrum racemosum.

Conclusions

We have synthesized a number of new thiophene-containing compounds. The results of antimicrobial activity of the prepared compounds revealed that changing the substituents at position-2 of thiophene ring significantly affect their biological activity. The pyridine side chain derivatives in compounds 7a, 7b and 8 showed excellent antimicrobial activity.