Structure−Activity Relationships of Phenyl-Furanyl-Rhodanines as Inhibitors of RNA Polymerase with Antibacterial Activity on Biofilms

Inhibition of bacterial RNA polymerase function and protein-protein interactions: a promising approach for next-generation antibacterial therapeutics

The increasing prevalence of multidrug-resistant pathogens necessitates the urgent development of new antimicrobial agents with innovative modes of action for the next generation of antimicrobial therapy. Bacterial transcription has been identified and widely studied as a viable target for antimicrobial development. The main focus of these studies has been the discovery of inhibitors that bind directly to the core enzyme of RNA polymerase (RNAP). Over the past two decades, substantial advancements have been made in understanding the properties of protein-protein interactions (PPIs) and gaining structural insights into bacterial RNAP and its associated factors. This has led to the crucial role of computational methods in aiding the identification of new PPI inhibitors to affect the RNAP function. In this context, bacterial transcriptional PPIs present promising, albeit challenging, targets for the creation of new antimicrobials. This review will succinctly outline the structural foundation of bacterial transcription networks and provide a summary of the known small molecules that target transcription PPIs.

Thiazolidin-4-Ones as a Promising Scaffold in the Development of Antibiofilm Agents-A Review

Thiazolidin-4-ones have a broad range of medical and clinical implementation, which is important for pharmaceutical and medicinal chemistry. This heterocyclic core has been reported to possess a diversity of bioactivities, including antimicrobial and antibiofilm-forming potential. The resistance of biofilms to antibiotics or disinfectants is a serious medical problem. Therefore, there is a natural need to discover new effective structures with properties that inhibit biofilm formation. This review aims to analyze the antibiofilm features of thiazolidin-4-ones described in the literature over the last two decades. The information gathered in this review could benefit the rational design of new effective antibiofilm small molecules with thiazolidin-4-one cores.

Synthesis and Antibacterial evaluation of Rhodanine and Its related heterocyclic compounds against S. aureus and A. baumannii

Antimicrobial resistance is a serious challenge to modern medicine. Besides imposing high financial burden, multidrug resistant infections are directly responsible for high morbidity and mortality. Even though a number of antibiotics are currently available to treat infections caused by ESKAPE organisms, more and more bacterial strains are becoming resistant to these drugs. In these circumstances, there is an urgent unmet need for development of newer antimicrobials to treat the infections caused due to MDR organisms. Rhodanine and structurally related 5-membered heterocycles possess wide range of pharmacological activities. A number of these derivatives have shown good to potent inhibition against the various microorganisms. They are reported to alter the functions of DNA gyrase B, metallo-β-lactamases, pencilline binding protein (PBP), Mur ligases, RNA polymerase, Enoyl ACP reductases, 1-deoxy-d-xylulose-5-phosphate reductoisomerase. etc which are vital molecular targets involved in bacterial growth, survival and replication. In this study, we have generated a library of Rhodanine and related 5 membered heterocyclic derivatives and screened them against a panel of pathogens. Among all the compounds, 2a-i, 3a-b, 3g, 4, 6b-c, 6e, 6g, 12a-b and 14b-c have demonstrated good to moderate inhibition against S. aureus (MIC 0.125-8 µ g/mL). Further, compound 17b demonstrated moderate activity against A. baumannii (MIC 8 µ g/mL). In addition, compounds 2a, 2e, 4, 6c, 6g and 14b have shown good to mild inhibition against MDR S. aureus including VRSA (MIC 0.5-16 µ g/mL) with good selectivity index 20-1600. In addition, compound 2e has inhibited growth gradually after 6 h in time kill kinetic studies and not antagonized with the tested FDA approved drugs.

Syntheses, in vitro, and in silico studies of rhodanine-based schiff bases as potential α-amylase inhibitors and radicals (DPPH and ABTS) scavengers

A two-step reaction method was used to synthesize a series of rhodanine-based Schiff bases (2-33) that were characterized using spectroscopic techniques. All compounds were assessed for α-amylase inhibitory and radical scavenging (DPPH and ABTS) activities. In comparison to the standard acarbose (IC₅₀ = 9.08 ± 0.07 µM), all compounds demonstrated good to moderate α-amylase inhibitory activity (IC₅₀ = 10.91 ± 0.08-61.89 ± 0.102 µM). Compounds also demonstrated significantly higher DPPH (IC₅₀ = 10.33 ± 0.02-96.65 ± 0.03 µM) and ABTS (IC₅₀ = 12.01 ± 0.12-97.47 ± 0.13 µM) radical scavenging activities than ascorbic acid (DPPH, IC₅₀ = 15.08 ± 0.03 µM; ABTS, IC₅₀ = 16.09 ± 0.17 µM). The limited structure-activity relationship (SAR) suggests that the position and nature of the substituted groups on the phenyl ring have a vital role in varying inhibitory potential. Among the series, compounds with an electron-withdrawing group at the para position showed the highest potency. Kinetic studies revealed that the compounds followed a competitive mode of inhibition. Molecular docking results are found to agree with experimental findings, showing that compounds reside in the active pocket due to the main rhodanine moiety.

A New Synthesis Strategy for Rhodanine and Its Derivatives

Rhodanine and its derivatives have been known as privileged structures in pharmacological research because of their wide spectrum of biological activities, but the synthesis method of rhodanine skeleton is limited. In this paper, not only rhodanine skeleton, but also N-aryl rhodanines can be directly prepared via the reaction of thioureas and thioglycolic acid in one step catalyzed by protic acid, which provides a new approach of the synthesis of rhodanine and its derivatives. The developed strategy is straightforward, efficient, atom economical, and convenient in good yields.

Evaluation of Bacterial RNA Polymerase Inhibitors in a Staphylococcus aureus-Based Wound Infection Model in SKH1 Mice

Chronic wounds infected with pathogens such as Staphylococcus aureus represent a worldwide health concern, especially in patients with a compromised immune system. As antimicrobial resistance has become an immense global problem, novel antibiotics are urgently needed. One strategy to overcome this threatening situation is the search for drugs targeting novel binding sites on essential and validated enzymes such as the bacterial RNA polymerase (RNAP). In this work, we describe the establishment of an in vivo wound infection model based on the pathogen S. aureus and hairless Crl:SKH1-Hrhr (SKH1) mice. The model proved to be a valuable preclinical tool to study selected RNAP inhibitors after topical application. While rifampicin showed a reduction in the loss of body weight induced by the bacteria, an acceleration of wound healing kinetics, and a reduced number of colony forming units in the wound, the ureidothiophene-2-carboxylic acid 1 was inactive under in vivo conditions, probably due to strong plasma protein binding. The cocrystal structure of compound 1 with RNAP, that we hereby also present, will be of great value for applying appropriate structural modifications to further optimize the compound, especially in terms of plasma protein binding.

5-(1H-Indol-3-ylmethylene)-4-oxo-2-thioxothiazolidin-3-yl)alkancarboxylic Acids as Antimicrobial Agents: Synthesis, Biological Evaluation, and Molecular Docking Studies

Background: Infectious diseases symbolize a global consequential strain on public health security and impact on the socio-economic stability all over the world. The increasing resistance to the current antimicrobial treatment has resulted in crucial need for the discovery and development of novel entity for the infectious treatment with different modes of action that could target both sensitive and resistant strains. Methods: Compounds were synthesized using classical methods of organic synthesis. Results: All 20 synthesized compounds showed antibacterial activity against eight Gram-positive and Gram-negative bacterial species. It should be mentioned that all compounds exhibited better antibacterial potency than ampicillin against all bacteria tested. Furthermore, 18 compounds appeared to be more potent than streptomycin against Staphylococcus aureus, Enterobacter cloacae, Pseudomonas aeruginosa, Listeria monocytogenes, and Escherichia coli. Three the most active compounds 4h, 5b, and 5g appeared to be more potent against MRSA than ampicillin, while streptomycin did not show any bactericidal activity. All three compounds displayed better activity also against resistant strains P. aeruginosa and E. coli than ampicillin. Furthermore, all compounds were able to inhibit biofilm formation 2- to 4-times more than both reference drugs. Compounds were evaluated also for their antifungal activity against eight species. The evaluation revealed that all compounds exhibited antifungal activity better than the reference drugs bifonazole and ketoconazole. Molecular docking studies on antibacterial and antifungal targets were performed in order to elucidate the mechanism of antibacterial activity of synthesized compounds. Conclusion: All tested compounds showed good antibacterial and antifungal activity better than that of reference drugs and three the most active compounds could consider as lead compounds for the development of new more potent agents.

Synthesis, Characterization, Antibacterial and Antioxidant Potency of NSubstituted- 2-Sulfanylidene-1,3-Thiazolidin-4-one Derivatives and QSAR Study

BACKGROUND

Rhodanine is known for its potential and important role in the medicinal chemistry since its derivatives exhibit a wide range of pharmacological activities such as antibacterial, antifungal, antidiabetic, antitubercular, anti-HIV, antiparasitic, antioxidant, anticancer, antiproliferative and anthelmintic agents.

OBJECTIVES

Since N-substituted rhodanine synthons are rarely commercially available, it is desirable to develop a straightforward synthetic approach for the synthesis of these key building blocks. The objective was to synthesize a series of rhodanine derivatives and to investigate their antimicrobial and antioxidant activity. Also, in order to obtain an insight into their structure-activity relationship, QSAR studies on the antioxidant activity were performed.

METHODS

1H and 13C FTNMR spectra were recorded on Bruker Avance 600 MHz NMR Spectrometer, mass analysis was carried out on ESI+ mode by LC-MS/MS API 2000. 2,2-Diphenyl-1- picrylhydrazyl radical scavenging activity (% DPPH) was determined in dimethylsulfoxide (DMSO) as a solvent. The antibacterial activity was assessed against Bacillus subtilis, Staphylococcus aureus (Gram positive) and Escherichia coli, Pseudomonas aeruginosa (Gram negative) bacteria in terms of the minimum inhibitory concentrations (MICs) by a modified broth microdilution method.

RESULTS

A series of N-substituted-2-sulfanylidene-1,3-thiazolidin-4-ones were synthesized and characterized by 1H NMR, 13C NMR, FTIR, GC MS, LCMS/MS and C,H,N,S elemental analysis. Most of the synthesized compounds showed moderate to excellent antibacterial activity (MIC values from 125 μg/ml to 15.62 μg/mL) and DPPH scavenging activity (from 3.60% to 94.40%). Compound 2-thioxo-3- (4-(trifluoromethyl)-phenyl)thiazolidin-4-one showed the most potent activity against Escherichia coli (3.125 μg/mL), equivalent to antibiotic Amikacin sulphate and against Staphylococcus aureus (0.097 μg/ml), 100 times superior then antibiotic Amikacin sulphate. It has also shown a potent antioxidant activity (95% DPPH scavenging). Two best QSAR models, obtained by GETAWAY descriptor R7p+, Balabans molecular connectivity topological index and Narumi harmonic topological index (HNar), suggest that the enhanced antioxidant activity is related to the presence of pairs of atoms higher polarizability at the topological distance 7, substituted benzene ring and longer saturated aliphatic chain in N-substituents.

CONCLUSION

A series of novel N-substituted-2-thioxothiazolidin-4-one derivatives were designed, synthesized, characterized and evaluated for their antibacterial and antioxidant activity in vitro. Majority of the compounds showed excellent antibacterial activity compared to ampicillin and few of them have an excellent activity as compared to Chloramphenicol standard antibacterial drug. The QSAR study has clarified the importance of presenting a pairs of atoms higher polarizability, such as Cl and S at the specific distance, as well as the substituted benzene ring and a long saturated aliphatic chain in N-substituents for the enhanced antioxidant activity of 2-sulfanylidene-1,3- thiazolidin-4-one derivatives.

5-Hydroxymethylfurfural (HMF) in Organic Synthesis: A Review of its Recent Applications Towards Fine Chemicals

Background:

5-Hydroxymethylfurfural (5-HMF) is a biomass-derived platform chemical, which can be produced from carbohydrates. In the past decades, 5- HMF has received tremendous attention because of its wide applications in the production of various value-added chemicals, materials and biofuels. The manufacture and the catalytic conversion of 5-HMF to simple industrially-important bulk chemicals have been well reviewed. However, employing 5-HMF as a building block in organic synthesis has never been summarized exclusively, despite the rapid development in this area.

Objective:

The aim of this review is to bring a fresh perspective on the use of 5-HMF in organic synthesis, to the exclusion of already well documented conversion of 5-HMF towards relatively simple molecules such as 2,5-furandicarboxylic acid, 2,5-dimethylfuran and so on notably used as monomers or biofuels.

Conclusion:

As it has been shown throughout this review, 5-HMF has been the object of numerous studies on its use in fine chemical synthesis. Thanks to the presence of different functional groups on this platform chemical, it proved to be an excellent starting material for the preparation of various fine chemicals. The use of this C-6 synthon in novel synthetic routes is appealing, as it allows the incorporation of renewable carbonsources into the final targets.

Synthesis and antibacterial activity of new (2,4-dioxothiazolidin-5-yl/ylidene)acetic acid derivatives with thiazolidine-2,4-dione, rhodanine and 2-thiohydantoin moieties

A series of new (2,4-dioxothiazolidin-5-yl/ylidene)acetic acid derivatives with thiazolidine-2,4-dione, rhodanine and 2-thiohydantoin moiety (28–65) were synthesized by the reaction of (2,4-dioxothiazolidin-5-yl/ylidene)acetic acid chlorides with 5-(hydroxybenzylidene) thiazolidine-2,4-dione, rhodanine and 2-thiohydantoin derivatives. Obtained compounds (28–65) were tested on reference strains of Gram-positive bacteria and ones of the Gram-negative bacteria. The antibacterial activity of target compounds was determined by broth microdilution method. These derivatives showed antibacterial activity generally against Gram-positive bacterial strains. Most active compounds possess MIC = 3.91 mg/L. Our results suggest that presence of electron-withdrawing substituent at phenyl ring is favorable while geometry of molecule does not play important role in antibacterial response. It was confirmed the lack of direct influence of substitution pattern at phenyl ring on antibacterial activity of closely related compounds of series 1–3. The antibacterial activity of some compounds was similar or higher than the activity of commonly used reference drugs such as oxacillin and cefuroxime.

Small molecule inhibitors of bacterial transcription complex formation

Knoevenagel condensation was employed to generate a set of molecules potentially capable of inhibiting the RNA polymerase-σ⁷⁰/σ^A interaction in bacteria. Synthesis was achieved via reactions between a variety of indole-7-carbaldehydes and rhodanine, N-allylrhodanine, barbituric acid or thiobarbituric acid. A library of structurally diverse compounds was examined by enzyme-linked immunosorbent assay (ELISA) to assess the inhibition of the targeted protein-protein interaction. Inhibition of bacterial growth was also evaluated using Bacillus subtilis and Escherichia coli cultures. The structure-activity relationship studies demonstrated the significance of particular structural features of the synthesized molecules for RNA polymerase-σ⁷⁰/σ^A interaction inhibition and antibacterial activity. Docking was investigated as an in silico method for the further development of the compounds.

Expanding the biomass derived chemical space

The derivatization and covalent modification of biomass derived platform chemicals expand the biomass derived chemical spaces allowing for the preparation of new bioactive molecules and materials.

Biorefinery aims at the conversion of biomass and renewable feedstocks into fuels and platform chemicals, in analogy to conventional oil refinery. In the past years, the scientific community has defined a number of primary building blocks that can be obtained by direct biomass decomposition. However, the large potential of this “renewable chemical space” to contribute to the generation of value added bio-active compounds and materials still remains unexplored. In general, biomass derived building blocks feature a diverse range of chemical functionalities. In order to be integrated into value-added compounds, they require additional functionalization and/or covalent modification thereby generating secondary building blocks. The latter can be thus regarded as functional components of bio-active molecules or materials and represent an expansion of the renewable chemical space. This perspective highlights the most recent developments and opportunities for the synthesis of secondary biomass derived building blocks and their application to the preparation of value added products.

Superelectrophilic activation of 5-hydroxymethylfurfural and 2,5-diformylfuran: organic synthesis based on biomass-derived products

The reaction of 5-hydroxymethylfurfural (5-HMF) with arenes in superacidic trifluoromethanesulfonic acid (triflic acid, TfOH) as the solvent at room temperature for 1–24 h gives rise to 5-arylmethylfurfurals (yields of 17–91%) and 2-arylmethyl-5-(diarylmethyl)furans (yields of 10–37%). The formation of these two types of reaction products depends on the nucleophilicity of the arene. The same reactions under the action of acidic zeolites H-USY in high pressure tubes at 130 °C for 1 h result in the formation of only 5-arylmethylfurfurals (yields of 45–79%). 2,5-Diformylfuran (2,5-DFF) in the reaction with arenes under the action of AlBr₃ at room temperature for 1 h leads to 5-(diarylmethyl)furfurals (yields of 51–90%). The reactive protonated species of 5-HMF and 2,5-DFF were characterized by NMR spectroscopy in TfOH and studied by DFT calculations. These reactions show possibilities of organic synthesis based on biomass-derived 5-HMF and 2,5-DFF.

GSH Induced Controlled Release of Levofloxacin from a Purpose-Built Prodrug: Luminescence Response for Probing the Drug Release in Escherichia coli and Staphylococcus aureus

Fluoroquinolones are third-generation broad spectrum bactericidal antibiotics and work against both Gram-positive and Gram-negative bacteria. Levofloxacin (L), a fluoroquinolone, is widely used in anti-infective chemotherapy and treatment of urinary tract infection and pneumonia. The main pathogen for urinary tract infections is Escherichia coli, and Streptococcus pneumoniae is responsible for pneumonia, predominantly a lower respiratory tract infection. Poor permeability of L leads to the use of higher dose of this drug and excess drug in the outer cellular fluid leads to central nervous system (CNS) abnormality. One way to counter this is to improve the lipophilicity of the drug molecule, and accordingly, we have synthesized two new Levofloxacin derivatives, which participated in the spatiotemporal release of drug via disulfide bond cleavage induced by glutathione (GSH). Recent studies with Streptococcus mutants suggest that it is localized in epithelial lining fluid (ELF) of the normal lower respiratory tract and the effective [GSH] in ELF is ∼430 μM. E. coli typically cause urinary tract infections and the concentration of GSH in porcine bladder epithelium is reported as 0.6 mM for a healthy human. Thus, for the present study we have chosen two important bacteria (Gram + ve and Gram - ve), which are operational in regions having high extracellular GSH concentration. Interestingly, this supports our design of new lipophilic Levofloxacin based prodrugs, which released effective drug on reaction with GSH. Higher lipophilicity favored improved uptake of the prodrugs. Site specific release of the drug (L) could be achieved following a glutathione mediated biochemical transformation process through cleavage of a disulfide bond of these purpose-built prodrugs. Further, appropriate design helped us to demonstrate that it is possible also to control the kinetics of the drug release from respective prodrugs. Associated luminescence enhancement helps in probing the release of the drug from the prodrug in bacteria and helps in elucidating the mechanistic pathway of the transformation. Such an example is scarce in the contemporary literature.

Surface plasmon resonance – more than a screening technology: insights in the binding mode of σ70:core RNAP inhibitors

Aim: Antibiotic resistance has become a major health problem. The σ70:core interface of bacterial RNA polymerase is a promising drug target. Recently, the coiled-coil and lid-rudder-system of the β’ subunit has been identified as an inhibition hot spot. Materials & methods & Results: By using surface plasmon resonance-based assays, inhibitors of the protein–protein interaction were identified and competition with σ70 was shown. Effective inhibition was verified in an in vitro transcription and a σ70:core assembly assay. For one hit series, we found a correlation between activity and affinity. Mutant interaction studies suggest the inhibitors’ binding site. Conclusion: Surface plasmon resonance is a valuable technology in drug design, that has been used in this study to identify and evaluate σ70:core RNA polymerase inhibitors.

Synthesis and biological evaluation of new rhodanine analogues bearing 2-chloroquinoline and benzo[h]quinoline scaffolds as anticancer agents

Several rhodanine derivatives (9-39) were synthesized for evaluation of their potential as anticancer agents. Villsmeier cyclization to synthesize aza-aromatic aldehydes, rhodanine derivatives preparation and Knoevenagel type of condensation between the rhodanines and aza-aromatic aldehydes are key steps used for the synthesis of 31 compounds. In vitro antiproliferative activity of the synthesized rhodanine derivatives (9-39) was studied on a panel of six human tumor cell lines viz. HGC, MNK-74, MCF-7, MDAMB-231, DU-145 and PC-3 cell lines. Some of the compounds were capable of inhibiting the proliferation of cancer cell lines at a micromolar concentration. Six compounds are found to be potent against HGC cell lines; compound 15 is found to be active against HGC - Gastric, MCF7 - Breast Cancer and DU145 - Prostate Cancer cell lines; compound 39 is potent against MNK-74; four compounds are found to be potent against MCF-7 cell lines; three compounds are active against MDAMB-231; nine compounds are found to be potent against DU-145; three compounds are active against PC-3 cell lines. These compounds constitute a promising starting point for the development of novel and more potent anticancer agents in future.

Spiromastixones A-O, antibacterial chlorodepsidones from a deep-sea-derived Spiromastix sp. fungus

Fifteen new depsidone-based analogues named spiromastixones A-O (1-15) were isolated from the fermentation broth of a deep-sea Spiromastix sp. fungus. Their structures were elucidated on the basis of extensive NMR and mass spectroscopic analysis in association with chemical conversion. Spiromastixones A-O are classified into two subtypes based on the orientation of ring C relative to ring A, while the n-propyl substituents on rings A and C are rarely seen in natural products. Most analogues are substituted by various numbers of chlorine atoms. All compounds exhibited significant inhibition against Gram-positive bacteria including Staphylococcus aureus, Bacillus thuringiensis, and Bacillus subtilis with MIC values ranging from 0.125 to 8.0 μg/mL. In addition, compounds 6-10 displayed potent inhibitory effects against methicillin-resistant bacterial strains of S. aureus (MRSA) and S. epidermidis (MRSE), while 10 also inhibited the growth of the vancomycin-resistant bacteria Enterococcus faecalis and E. faecium (VRE). The structure-activity relationships are discussed.

Synthesis and biological activity of novel bis-indole inhibitors of bacterial transcription initiation complex formation

The synthesis of novel bis-indole amides and glyoxylamides as bacterial transcription complex formation inhibitors and their structure–activity relationships are discussed.

3-[(5-Chloro-2-hy-droxy-benzyl-idene)amino]-2-sulfanyl-idene-1,3-thia-zolidin-4-one

In the title compound, C10H7ClN2O2S2, the mean plane of the thioxo-thia-zolidine ring [maximum deviation = 0.032 (2) Å] is inclined to the benzene ring by 12.25 (4)°. There is a strong intra-molecular O-H⋯N hydrogen bond present. In the crystal, mol-ecules are linked via pairs of C-H⋯Cl hydrogen bonds, forming inversion dimers.

Efficient one-pot synthesis of 5-chloromethylfurfural (CMF) from carbohydrates in mild biphasic systems

5-Halomethylfurfurals can be considered as platform chemicals of high reactivity making them useful for the preparation of a variety of important compounds. In this study, a one-pot route for the conversion of carbohydrates into 5-chloromethylfurfural (CMF) in a simple and efficient (HCl-H3PO4/CHCl3) biphasic system has been investigated. Monosaccharides such as D-fructose, D-glucose and sorbose, disaccharides such as sucrose and cellobiose and polysaccharides such as cellulose were successfully converted into CMF in satisfactory yields under mild conditions. Our data shows that when using D-fructose the optimum yield of CMF was about 47%. This understanding allowed us to extent our work to biomaterials, such as wood powder and wood pulps with yields of CMF obtained being comparable to those seen with some of the enumerated mono and disaccharides. Overall, the proposed (HCl-H3PO4/CHCl3) optimized biphasic system provides a simple, mild, and cost-effective means to prepare CMF from renewable resources.

Progress and developments in tau aggregation inhibitors for Alzheimer disease

Pharmacological approaches directed toward Alzheimer disease are diversifying in parallel with a growing number of promising targets. Investigations on the microtubule-associated protein tau yielded innovative targets backed by recent findings about the central role of tau in numerous neurodegenerative diseases. In this review, we summarize the recent evolution in the development of nonpeptidic small molecules tau aggregation inhibitors (TAGIs) and their advancement toward clinical trials. The compounds are classified according to their chemical structures, providing correlative insights into their pharmacology. Overall, shared structure-activity traits are emerging, as well as specific binding modes related to their ability to engage in hydrogen bonding. Medicinal chemistry efforts on TAGIs together with encouraging in vivo data argue for successful translation to the clinic.

Peptide-based investigation of the Escherichia coli RNA polymerase σ(70):core interface as target site

The number of bacterial strains that are resistant against antibiotics increased dramatically during the past decades. This fact stresses the urgent need for the development of new antibacterial agents with novel modes of action targeting essential enzymes such as RNA polymerase (RNAP). Bacterial RNAP is a large multi-subunit complex consisting of a core enzyme (subunits: α(2)ββ'ω) and a dissociable sigma factor (σ(70); holo enzyme: α(2)ββ'ωσ(70)) that is responsible for promoter recognition and transcription initiation. The interface between core RNAP and σ(70) represents a promising binding site. Nevertheless, detailed studies investigating its druggability are rare. Compounds binding to this region could inhibit this protein-protein interaction and thus holo enzyme formation, resulting in inhibition of transcription initiation. Sixteen peptides covering different regions of the Escherichia coli σ(70):core interface were designed; some of them-all derived from σ(70) 2.2 region-led to a strong RNAP inhibition. Indeed, an ELISA-based experiment confirmed the most active peptide P07 to inhibit the σ(70):core interaction. Furthermore, an abortive transcription assay revealed that P07 impedes transcription initiation. In order to study the mechanism of action of P07 in more detail, molecular dynamics simulations and a rational amino acid replacement study were performed, leading to the conclusion that P07 binds to the coiled-coil region in β' and that its flexible N-terminus inhibits the enzyme by interaction with the β' lid-rudder-system (LRS). This work revisits the β' coiled-coil as a hot spot for the protein-protein interaction inhibition and expands it by introduction of the LRS as target site.

Influence of DNA template choice on transcription and inhibition of Escherichia coli RNA polymerase

In recent decades, quantitative transcription assays using bacterial RNA polymerase (RNAP) have been performed under widely diverse experimental conditions. We demonstrate that the template choice can influence the inhibitory potency of RNAP inhibitors. Furthermore, we illustrate that the sigma factor (σ(70)) surprisingly increases the transcription efficiency of templates with nonphysiological nonprokaryotic promoters. Our results might be a useful guideline in the early stages of using RNAP for drug discovery.

Privileged scaffolds or promiscuous binders: a comparative study on rhodanines and related heterocycles in medicinal chemistry

Rhodanines and related five-membered heterocycles with multiple heteroatoms have recently gained a reputation of being unselective compounds that appear as "frequent hitters" in screening campaigns and therefore have little value in drug discovery. However, this judgment appears to be based mostly on anecdotal evidence. Having identified various rhodanines and related compounds in screening campaigns, we decided to perform a systematic study on their promiscuity. An amount of 163 rhodanines, hydantoins, thiohydantoins, and thiazolidinediones were synthesized and tested against several targets. The compounds were also characterized with respect to aggregation and electrophilic reactivity, and the binding modes of rhodanines and related compounds in published X-ray cocrystal structures were analyzed. The results indicate that the exocyclic, double bonded sulfur atom in rhodanines and thiohydantoins, in addition to other structural features, offers a particularly high density of interaction sites for polar interactions and hydrogen bonds. This causes a promiscuous behavior at concentrations in the "screening range" but should not be regarded as a general knockout criterion that excludes such screening hits from further development. It is suggested that special criteria for target affinity and selectivity are applied to these classes of compounds and that their exceptional and potentially valuable biomolecular binding properties are consequently exploited in a useful way.

Furanyl-rhodanines are unattractive drug candidates for development as inhibitors of bacterial RNA polymerase

Previous studies suggest that furanyl-rhodanines might specifically inhibit bacterial RNA polymerase (RNAP). We further explored three compounds from this class. Although they inhibited RNAP, each compound also inhibited malate dehydrogenase and chymotrypsin. Using biosensors responsive to inhibition of macromolecular synthesis and membrane damaging assays, we concluded that in bacteria, one compound inhibited DNA synthesis and another caused membrane damage. The third rhodanine lacked antibacterial activity. We consider furanyl-rhodanines to be unattractive RNAP inhibitor drug candidates.

Design, synthesis and structure-activity studies of rhodanine derivatives as HIV-1 integrase inhibitors

Raltegravir was the first HIV-1 integrase inhibitor that gained FDA approval for use in the treatment of HIV-1 infection. Because of the emergence of IN inhibitor-resistant viral strains, there is a need to identify innovative second-generation IN inhibitors. Previously, we identified 2-thioxo-4-thiazolidinone (rhodanine)-containing compounds as IN inhibitors. Herein, we report the design, synthesis and docking studies of a series of novel rhodanine derivatives as IN inhibitors. All these compounds were further tested against human apurinic/apyrimidinic endonuclease 1 (APE1) to determine their selectivity. Two compounds showed significant cytotoxicity in a panel of human cancer cell lines. Taken together, our results show that rhodanines are a promising class of compounds for developing drugs with antiviral and anticancer properties.