Potent DNA Gyrase Inhibitor Research Articles

In-vitro and in-silico studies based discovery of 2-aryl-N-(4-morpholinophenyl)thiazol-4-amines as promising DNA gyrase inhibitors

Background: DNA gyrase is an important enzyme for the survival of bacteria. Many DNA gyrase inhibitors are in clinical practice. However, these inhibitors also encompass certain toxic and drug/food interactions. This warrants the development of a new template as DNA gyrase inhibitors. Therefore, this study aimed to deliver morpholine-based thiazoles (5a-5l) as safer DNA gyrase inhibitors.Methods: The 5a-5l were prepared by reacting compound 3 with various aryl thioamides. The structures of 5a-5l were ascertained by their spectral records. The 5a-5l were subjected to their antibacterial activity potential (serial plate dilution method), DNA gyrase inhibiting activity, and toxicity analysis (MTT assay) against HepG2 & Vero cell lines. The in-silico studies (pharmacokinetic parameters and molecular docking) of 5a-5l were likewise performed.Results: It was surprisingly observed that the MIC values of 5a-5l were equal to the MIC values of ciprofloxacin (12.5 µg/ml) against the tested bacteria, whereas the DNA gyrase inhibitory activity (IC50 in µg/ml) of 5h (3.52), 5g (3.76), 5f (3.88), 5e (4.08), 5l (4.11), 5b (4.28), 5k (4.28), 5i (4.30), and 5d (4.32) was equal/better than ciprofloxacin (4.32). The MTT assay also implied the non-cytotoxic nature of 5a-5l against HepG2 & Vero cell lines up to 200 µg/ml concentration. The docking outcomes indicated a similar binding pattern of 5a-5l and ciprofloxacin at the active site of DNA gyrase, wherein 5a-5l displayed a better binding affinity for the active site. The in-silico toxicity data employing the ProTox-II web server indicated no hepatotoxicity, carcinogenicity, immunotoxicity, mutagenicity, or cytotoxic effect of 5a-5l. Also, the SwissADME software supported the drug-likeliness properties and high gastrointestinal absorption of 5a-5l.Conclusion: Compounds 5h, 5g, 5f, 5e, 5l, 5b, 5k, 5i, and 5d are potent DNA gyrase inhibitors with promising safety profiles.Keywords: Discovery; Morpholine; Thiazole; DNA gyrase; MTT assay; Docking

Development of narrow-spectrum topoisomerase-targeting antibacterials against mycobacteria

New 2-pyrrolamidobenzothiazole-based inhibitors of mycobacterial DNA gyrase were discovered. Among these, compounds 49 and 51, show excellent antibacterial activity against Mycobacterium tuberculosis and Mycobacterium abscessus with a notable preference for mycobacteria. Both compounds can penetrate infected macrophages and reduce intracellular M. tuberculosis load. Compound 51 is a potent inhibitor of DNA gyrase (M. tuberculosis DNA gyrase IC50 = 4.1 nM, Escherichia coli DNA gyrase IC50 of <10 nM), selective for bacterial topoisomerases. It displays low MIC90 values (M. tuberculosis: 0.63 μM; M. abscessus: 2.5 μM), showing specificity for mycobacteria, and no apparent toxicity. Compound 49 not only displays potent antimycobacterial activity (MIC90 values of 2.5 μM for M. tuberculosis and 0.63 μM for M. abscessus) and selectivity for mycobacteria but also exhibits favorable solubility (kinetic solubility = 55 μM) and plasma protein binding (with a fraction unbound of 2.9 % for human and 4.7 % for mouse). These findings underscore the potential of fine-tuning molecular properties to develop DNA gyrase B inhibitors that specifically target the mycobacterial chemical space, mitigating the risk of resistance development in non-target pathogens and minimizing harm to the microbiome.

Synthesis, biological assessment and molecular docking study of new sulfur-linked 1,2,4-triazole and 1,2,3-triazole hybrid derivatives as potential DNA gyrase inhibitors

Abstract A series of new pyridine-1,2,4-triazole-tagged 1,2,3-triazole hybrid molecules were obtained. The new compounds were synthesized via click chemistry of 1,2,4-triazole-3-thiopropargyl compounds and various azides. All compounds were fully characterized through their spectroscopic analyses. Furthermore, cytotoxic activity was assessed by screening against three cancer cell lines including human colon carcinoma (HCT116), human cervix carcinoma (HeLa) and human breast adenocarcinoma (MCF7). In addition, antimicrobial assessment against one gram-positive (Staphylococcus aureus ATCC 29,213), two Gram-negative bacteria (Sarcina lutea and Escherichia coli ATCC 25,922) and one fungal (Candida albicans NRRL Y–477) microorganism‏.‏ Molecular docking studies of the synthesized compounds against DNA gyrase were used to identify their binding ability to the target enzyme. The best docked molecules unveiled binding affinities to the target ranging from −9.5 to −8.8 kcal mol−1. The adsorption, distribution, metabolic, excretion, and toxicity (ADME/Tox) and drug-likeness analyses of the best docked compounds were evaluated using in silico techniques. Based on in vitro and in silico findings, these pyridine-1,2,4-triazole-tagged 1,2,3-triazole hybrid molecules may be helpful in designing potential antimicrobial drug candidates.

Synthesis of ciprofloxacin-linked 1,2,3-triazole conjugates as potent antibacterial agents using click chemistry: exploring their function as DNA gyrase inhibitors via in silico- and in vitro-based studies.

The antibacterial efficacy of some newly developed C-3 carboxylic group-containing ciprofloxacin-linked 1,2,3-triazole conjugates was studied. Twenty-one compounds from three different series of triazoles were synthesized using click chemistry and evaluated for their antibacterial activity against nine different pathogenic strains, including three Gram-positive strains, i.e. Enterococcus faecalis (ATCC29212), Staphylococcus aureus (ATCC25923), Staphylococcus epidermidis (clinical isolate), and six Gram-negative bacterial strains, i.e. Escherichia coli (ATCC25922), Pseudomonas aeruginosa (ATCC27853), Salmonella typhi (clinical isolate), Proteus mirabilis (clinical isolate), Acinetobacter baumannii (clinical isolate) and Klebsiella pneumonia (clinical isolate). Among the compounds, 10, 10a, 10b, 10c, 10d, 11a, 11f, 12c, 12e and 12f showed excellent activity with MIC values upto 12.5 μg mL-1, whereas the control ciprofloxacin showed MIC values of 0.781-25 μg mL-1 towards various strains. In addition, the low toxicity profile of the synthesized molecules revealed that they are potent antibiotics. Molecular docking and MD analysis were performed using the protein structure of E. coli DNA gyrase B, which was further corroborated with an in vitro assay to evaluate the inhibition of DNA gyrase. The analysis revealed that compound 10b was the most potent inhibitor of DNA gyrase compared to ciprofloxacin, which was employed as the positive control. Furthermore, the structure of two title compounds (11a and 12d) was characterized using single-crystal analysis.

Catalytic action and bactericidal behavior of samarium/carbon spheres-doped manganese oxide nanostructures and their molecular docking analysis

The co-precipitation technique was adapted to synthesize different concentrations (2 % and 4 %) of samarium (Sm) doped constant equates of carbon spheres (Cs) and manganese oxide (MnO2). The principal objective of this investigation is to demonstrate confirmation that Sm/Cs-doped MnO2 nanostructures (NSs) owned antibacterial and catalytic attributes. Reduction in surface area manifested to agglomeration, NSs faces become inaccessible to initiate a reaction, can be overcome upon doping of Sm. Sm has the potential to increase the activity of metal oxide ascribed to its electron trapping effect. The structural morphologies, optical properties, functional groups, elemental composition, and d-spacing were determined by applying various characterizations. With the incorporation of CS and Sm, UV–vis spectra shifted towards lower wavelength and band gap energy (Eg) was reduced. MnO2 possessed orthorhombic structure, according to the XRD pattern and TEM exhibited long Burr-like morphology of undoped MnO2. SAED image illustrated that MnO2 is polycrystalline. 4 % Sm/CS doped MnO2 revealed the highest degradation (91 %) in a neutral environment. Furthermore, 4 % Sm/Cs doped-MnO2 revealed an inhibitory zone of 2.85 mm against Escherichia coli (E. coli). Additionally, an analysis of molecular docking revealed a binding interface with NRs and the functional domains of certain cellular proteins. Results indicated that Cs-doped MnO2 and Cs/Sm-doped MnO2 NRs are the most potent DNA gyrase and FabB enzyme inhibitors.

New sulfonamide-tethered coumarin derivatives as potential DNA gyrase inhibitors: Design, synthesis, antimicrobial evaluation, and in silico study

A new series of coumarin-6-sulfonamide derivatives 3–16 have been synthesized via simple and convenient coupling reaction of coumarin-6-sulfonyl chloride with different sulfa drugs and various amino-heterocycles. The antimicrobial activity of the new compounds was evaluated against S. aureus ATCC 6538, E. coli ATCC 25933, C. albicans ATCC 10231, and A. niger NRRL A-326. Compound 12 showed potent antimicrobial activities against all pathogenic strains, with MIC values of 4.88 μg/mL against S. aureus and 9.76 μg/mL against C. albicans, exceptionally 4-fold more potent than neomycin control drug (MIC= 19.53 and 39.06 μg/mL respectively), and an MIC value of 39.06 μg/mL against E. coli, equipotent with neomycin. Meanwhile, compound 10 was equipotent with neomycin against both S. aureus and C. albicans. Additionally, compound 14 was equipotent with neomycin against S. aureus, and 2-fold more potent that neomycin against C. albicans. Further investigations showed that compounds 10 and 12 strongly inhibited DNA gyrase (IC50= 2.463 and 1.793μg/mL respectively), with compound 12 being closely equipotent with the reference novobiocin drug (IC50= 1.425μg/mL). Docking studies of compounds 10 and 12 on the active site of DNA gyrase confirmed their ability to form stable complexes with the target enzyme. According to ADME data, the bioavailability profile of compound 12 was high, and its physicochemical and pharmacological characteristics were consistent with Lipinski's RO5 anticipated constraints. Collectively, these data strongly highlight the efficiency of our multidisciplinary approach in the field of novel potent antimicrobial DNA gyrase inhibitors.

Identification of potential DNA gyrase inhibitors: virtual screening, extra-precision docking and molecular dynamics simulation study

DNA gyrase brings negative supercoils into DNA and loosens up certain positive supercoils that collect during replication and transcription and is a notable antibacterial target. To fight against the menace of antibiotic-resistant bacterial infections, we have employed various computational tools like high throughput virtual screening (HTVS), standard precision (SP) docking, extra precision (XP) docking, and molecular dynamics (MD) simulation studies to identify some potential DNA gyrase inhibitors. A focused library of 5968 anti-bacterial compounds was screened using the HTVS docking protocol of the glide module of Maestro. The top 200 docked compounds were further filtered using SP and XP docking protocols, and their free binding energies were calculated using MM-GBSA studies. The binding and stability of the top two compounds which showed better docking scores than the co-crystallized ligand (Clorobiocin) of DNA gyrase (PDB ID: 1KZN) were further probed by MD simulation of 100 ns using GROMACS. MD simulation study suggested that the compounds AM1 and AM5 form a stable complex with DNA gyrase with a good number of hydrogen bonds. XP docking study showed that interaction with the crucial amino acids for compounds AM1 and AM5 was like the co-crystallized ligand. These compounds were also predicted to be drug-like molecules with good water solubility and excellent absorption profiles. Based on the above studies, herein we report compounds AM1 (1R,3S)-1-(2-((3-(ammoniomethyl)phenyl)amino)-2-oxoethyl)-3-carbamoylpiperidin-1-ium and AM5 (1'S,2 s,4R)-4-ammonio-6-ethyl-1'-methylspiro[chromane-2,4'-piperidin]-1'-ium as potential DNA gyrase inhibitors which can be further developed as a potential lead against the menace of antibiotic resistance.

Isoflavonoid and Furanochromone Natural Products as Potential DNA Gyrase Inhibitors: Computational, Spectral, and Antimycobacterial Studies.

In pursuit of new antitubercular agents, we here report the antimycobacterial (H37Rv) and DNA gyrase inhibitory potential of daidzein and khellin natural products (NPs). We procured a total of 16 NPs based on their pharmacophoric similarities with known antimycobacterial compounds. The H37Rv strain of M. tuberculosis was found to be susceptible to only two out of the 16 NPs procured; specifically, daidzein and khellin each exhibited an MIC of 25 μg/mL. Moreover, daidzein and khellin inhibited the DNA gyrase enzyme with IC50 values of 0.042 and 0.822 μg/mL, respectively, compared to ciprofloxacin with an IC50 value of 0.018 μg/mL. Daidzein and khellin were found to have lower toxicity toward the vero cell line, with IC50 values of 160.81 and 300.23 μg/mL, respectively. Further, molecular docking study and MD simulation of daidzein indicated that it remained stable inside the cavity of DNA GyrB domain for 100 ns.

Development of pharmacophore model to identify potential DNA gyrase inhibitors

There is great concern in the medical community due to rapid increase in antibiotic resistance, causing 700,000 deaths annually worldwide. Therefore, there is paramount need to develop novel and innovative antibacterial agents active against resistant bacterial strains. DNA gyrase is a crucial enzyme in bacterial replication that is absent in eukaryotes, making it effective curative target for antibacterials. To identify potential DNA gyrase inhibitors by virtual screening of NCI database using a 3-step approach. A total of 271 compounds with known IC50 values against Escherichia coli DNA GyrA were selected to develop a pharmacophore model for dual screening approach to identify new potential hits from the NCI database. In the second step, the NCI database was also screened using in-house built NN-QSAR model. Molecular docking of common 5298 compounds screened from both methods were performed against E. coli DNA GyrA (PDB id- 6RKU), and 3004 compounds are reported to exhibit lower binding energies than ciprofloxacin (−6.77 Kcal/mol). The top three compounds (NCI371878, NCI371876 and NCI142159) reported with binding energy of −13.5, −13.19 and −13.03 Kcal/mol were further subjected to MD simulation studies for 100 ns supporting the stability of the docked complexes.

Molecular Docking and Pharmacokinetic Studies of Some New pyridyl and hydrazinyl bearing thiazole Derivatives as Potential DNA gyrase Inhibitors

Molecular Docking and Pharmacokinetic Studies of Some New pyridyl and hydrazinyl bearing thiazole Derivatives as Potential DNA gyrase Inhibitors

Potent Inhibition of Bacterial DNA Gyrase by Digallic Acid and Other Gallate Derivatives.

Bacterial DNA gyrase, an essential enzyme, is a validated target for discovering and developing new antibiotics. Here we screened a pool of polyphenols and discovered that digallic acid is a potent DNA gyrase inhibitor. We also found that several food additives based on gallate, such as dodecyl gallate, potently inhibit bacterial DNA gyrase. Interestingly, the IC50 of these gallate derivatives against DNA gyrase is correlated with the length of hydrocarbon chain connecting to the gallate. These new bacterial DNA gyrase inhibitors are ATP competitive inhibitors of DNA gyrase. Our results also show that digallic acid and certain gallate derivatives potently inhibit E. coli DNA topoisomerase IV. Several gallate derivatives have strong antimicrobial activities against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA). This study provides a solid foundation for the design and synthesis of gallate-based DNA gyrase inhibitors that may be used to combat antibacterial resistance.

Concentration-Dependent Activity of Pazufloxacin against Pseudomonas aeruginosa: An In Vivo Pharmacokinetic/Pharmacodynamic Study.

The bacterium Pseudomonas aeruginosa is known to be associated with nosocomial infections around the world. Pazufloxacin, a potent DNA gyrase inhibitor, is known to be an effective drug candidate. However, it has not been clarified whether the pharmacokinetic (PK)/pharmacodynamic (PD) of pazufloxacin was effective against P. aeruginosa. Herein, we demonstrated that the PK/PD index of pazufloxacin against P. aeruginosa infection is used to optimize the dosing regiments. We constructed an in vivo infection model by infecting P. aeruginosa into the thigh of a mouse to determine the PD, and we measured the serum concentration of pazufloxacin to construct the PK model using high-performance liquid chromatography. The therapeutic efficacy of pazufloxacin was correlated with the ratio of the area under the free concentration time curve at 24 h to the minimum inhibitory concentration (fAUC24/MIC), and the maximum free concentration to the MIC (fCmax/MIC). Each contribution rate (R2) was 0.72 and 0.65, respectively, whereas the time at which the free drug concentration remained above the MIC (R2 = 0.28). The target value of pazufloxacin fAUC24/MIC for stasis was 46.1, for 1 log10 it was 63.8, and for 2 log10 it was 100.8. Moreover, fCmax/MIC for stasis was 5.5, for 1 log10 it was 7.1, and for 2 log10 it was 10.8. We demonstrated that the in vivo concentration-dependent activity of pazufloxacin was effective against the P. aeruginosa infection, and successfully made the PK/PD model sufficiently bactericidal. The PK/PD model will be beneficial in preventing the spread of nosocomial infections.

Identification of Potent DNA Gyrase Inhibitors Active against Mycobacterium tuberculosis.

Mycobacterium tuberculosis DNA gyrase manipulates the DNA topology using controlled breakage and religation of DNA driven by ATP hydrolysis. DNA gyrase has been validated as the enzyme target of fluoroquinolones (FQs), second-line antibiotics used for the treatment of multidrug-resistant tuberculosis. Mutations around the DNA gyrase DNA-binding site result in the emergence of FQ resistance in M. tuberculosis; inhibition of DNA gyrase ATPase activity is one strategy to overcome this. Here, virtual screening, subsequently validated by biological assays, was applied to select candidate inhibitors of the M. tuberculosis DNA gyrase ATPase activity from the Specs compound library (www.specs.net). Thirty compounds were identified and selected as hits for in vitro biological assays, of which two compounds, G24 and G26, inhibited the growth of M. tuberculosis H37Rv with a minimal inhibitory concentration of 12.5 μg/mL. The two compounds inhibited DNA gyrase ATPase activity with IC50 values of 2.69 and 2.46 μM, respectively, suggesting this to be the likely basis of their antitubercular activity. Models of complexes of compounds G24 and G26 bound to the M. tuberculosis DNA gyrase ATP-binding site, generated by molecular dynamics simulations followed by pharmacophore mapping analysis, showed hydrophobic interactions of inhibitor hydrophobic headgroups and electrostatic and hydrogen bond interactions of the polar tails, which are likely to be important for their inhibition. Decreasing compound lipophilicity by increasing the polarity of these tails then presents a likely route to improving the solubility and activity. Thus, compounds G24 and G26 provide attractive starting templates for the optimization of antitubercular agents that act by targeting DNA gyrase.

The Antibacterial Activity of 1,2,3-triazole- and 1,2,4-Triazole-containing Hybrids against Staphylococcus aureus: An Updated Review (2020- Present).

Staphylococcus aureus (S. aureus), a prominent, highly contagious nosocomial and community- acquired bacterial pathogen, can cause a broad spectrum of diseases. Antibiotic-resistant S. aureus strains, which pose potential causes of morbidity and mortality, have continuously emerged in recent years, calling for novel anti-S. aureus agents. 1,2,3-triazole and 1,2,4-triazole, the bioisostere of amides, esters, and carboxylic acids, are potent inhibitors of DNA gyrase, topoisomerase IV, efflux pumps, filamentous temperature-sensitive protein Z, and penicillin-binding protein. In particular, 1,2,3-triazole- and 1,2,4-triazole-containing hybrids have the potential to exert dual or multiple antibacterial mechanisms of action. Moreover, 1,2,3-triazole-cephalosporin hybrid cefatrizine, 1,2,3- triazole-oxazolidinone hybrid radezolid, and 1,2,4-triazolo[1,5-a]pyrimidine hybrid essramycin, have already been used in clinical practice to treat bacterial infections. Hence, 1,2,3-triazole- and 1,2,4- triazole-containing hybrids possess promising broad-spectrum antibacterial activity against diverse clinically significant organisms, including drug-resistant forms. This review is an update on the latest development of 1,2,3-triazole- and 1,2,4-triazole-containing hybrids with anti-S. aureus activity, covering articles published between January 2020 and July 2021.

Design, Synthesis and Molecular Docking of New Benzimidazole Derivatives of Potential Antimicrobial Activity as DNA Gyrase and Topoisomerase IV Inhibitors

A new series of benzimidazole derivatives 3a-3d, 4a-4c, 8a-8d, 9a,9b, 10a-10d and 11 was synthesized and evaluated as antimicrobial agents against various gram-positive, gram-negative bacteria and fungi using vibramycin and fluconazole as positive controls for the antibacterial and antifungal activities, respectively. The examined microbial strains showed variable sensitivities against the target compounds.The examined microbial strains showed variable sensitivities against the target compounds. The minimum inhibitory concentration (MIC) was determined for the compounds showed zone of inhibition ≥ 16 mm (4a, 4c, 8a, 10a). The latter derivatives were also examined as S. aureus DNA gyrase/topoisomerase IV inhibitors. The compounds 4a, and 8a represented the most promising activity for both enzymes in ATPase assay (IC50 4a 0.39, 0.52 and 8a 0.66, 0.28 µM respectively) as well as the safest profile against the human normal WI38 cells upon comparing with Ciprofloxacin and Novobiocin. Compounds 8a showed dual inhibitory effect against both targets DNA gyrase and topoisomerase IV in supercoiling and decatenation assay (IC50 0.443 and 1.15 µM respectively). Both compounds 4a and 8a can be considered as lead compounds for further structural modifications to obtain more potent DNA gyrase and topoisomerase inhibitors as antibacterial agents. Molecular docking study was performed for the most promising compounds to explore the pharmacophoric moieties that governed their binding with amino acid residues of DNA gyrase and topoisomerase IV using MOE software. The results revealed a binding mode and docking scores comparable to those of a reference ligand and consistent with their DNA gyrase and topoisomerase IV inhibition activity.

Acetylenic Replacement of Albicidin's Methacrylamide Residue Circumvents Detrimental E/Z Photoisomerization and Preserves Antibacterial Activity.

The natural product albicidin is a highly potent inhibitor of bacterial DNA gyrase. Its outstanding activity, particularly against Gram‐negative pathogens, qualifies it as a promising lead structure in the search for new antibacterial drugs. However, as we show here, the N‐terminal cinnamoyl moiety of albicidin is susceptible to photochemical E/Z isomerization. Moreover, the newly formed Z isomer exhibits significantly reduced antibacterial activity, which hampers the development and biological evaluation of albicidin and potent derivatives thereof. Hence, we synthesized 13 different variants of albicidin in which the vulnerable para‐coumaric acid moiety was replaced; this yielded photostable analogues. Biological activity assays revealed that diaryl alkyne analogues exhibited virtually undiminished antibacterial efficacy. This promising scaffold will therefore serve as a blueprint for the design of a potent albicidin‐based drug.

Toward Catalytic Antibiotics: Redesign of Fluoroquinolones to Catalytically Fragment Chromosomal DNA.

A library of ciprofloxacin-nuclease conjugates was designed and synthesized to investigate their potential as catalytic antibiotics. The Cu(II) complexes of the new designer compounds (i) showed excellent in vitro hydrolytic and oxidative DNase activity, (ii) showed good antibacterial activity against both Gram-negative and Gram-positive bacteria, and (iii) proved to be highly potent bacterial DNA gyrase inhibitors via a mechanism that involves stabilization of the fluoroquinolone-topoisomerase-DNA ternary complex. Furthermore, the Cu(II) complexes of two of the new designer compounds were shown to fragment supercoiled plasmid DNA into linear DNA in the presence of DNA gyrase, demonstrating a "proof of concept" in vitro. These ciprofloxacin-nuclease conjugates can therefore serve as models with which to develop next-generation, in vivo functioning catalytic antimicrobials.

Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds

Novel bacterial type II topoisomerase inhibitors (NBTIs) stabilize single-strand DNA cleavage breaks by DNA gyrase but their exact mechanism of action has remained hypothetical until now. We have designed a small library of NBTIs with an improved DNA gyrase-binding moiety resulting in low nanomolar inhibition and very potent antibacterial activity. They stabilize single-stranded cleavage complexes and, importantly, we have obtained the crystal structure where an NBTI binds gyrase–DNA in a single conformation lacking apparent static disorder. This directly proves the previously postulated NBTI mechanism of action and shows that they stabilize single-strand cleavage through asymmetric intercalation with a shift of the scissile phosphate. This crystal stucture shows that the chlorine forms a halogen bond with the backbone carbonyls of the two symmetry-related Ala68 residues. To the best of our knowledge, such a so-called symmetrical bifurcated halogen bond has not been identified in a biological system until now.

In-silico driven design and development of spirobenzimidazo-quinazolines as potential DNA gyrase inhibitors

DNA gyrase and Topoisomerase IV are promising antibacterial drug targets as they regulate bacterial DNA replication and topology. In a quest for novel DNA topoisomerase inhibitors, a multidisciplinary approach was adopted that involves computational prediction of binding sites and molecular modelling followed by green synthesis and biological evaluation of antibacterial activity of spirobenzimidazo quinazolines derivatives. Using basic quantum chemistry principles, we evaluated spirobenzimidazo quinazolines derivatives with their pharmacokinetic profiles. Based on the results of the aforesaid in-silico studies, we synthesized a series of titled compounds using green synthetic methodology that were validated as potential antimicrobial agents. Quantum chemoinformatics based predicted activity for the synthesized compounds 9b, 9c, and 9j was concomitant with biological evaluation of broadspectrum antibacterial activity. Biological evaluation revealed that inhibition of biofilm formation was due to their potential antibacterial activity. We believe that the novel spirobenzimidazo quinazolines have the potential to be alternatives to aminocoumarins and classical quinazolines upon detailed target specific biological studies.

Identification of 4-diphenylamino 3-iodo coumarin as a potent inhibitor of DNA gyrase B of S. aureus

A necessity of therapeutics against antibiotic-resistant bacteria has led to a search for novel antibacterial compounds. The strategy to isolate compounds from non-microbial sources is the key to prevent antibiotic resistance. Here, we report isolation and characterization of an antibacterial coumarin derivative, 4-diphenylamino 3-iodo coumarin (4-DPA3IC) from a traditional drug formulation. The compound elicited high activity against MDR strains of S. aureus. Targets were identified through computational methods encompassing modules of Schrodinger 10.4. The 4-DPA3IC targeted S. aureus DNA gyrase enzyme B subunit. Amino acid residues and interactions involved here are totally different from those of novobiocin and clorobiocin. The validation was done by in vitro DNA gyrase supercoiling inhibition assay. This study proved 4-DPA3IC could potentially act against novobiocin and cholorbiocin resistant strains of S. aureus. Thus, the 4-DPA3IC is a unique inhibitor of bacterial DNA gyrase due to its plant origin as compared to other reported inhibitors.