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Graphic abstract COVID-19 is an unprecedented pandemic threatening global health, and variants were discovered rapidly after the pandemic. The two variants, namely the SARS-CoV-2 B.1.1.7 (Alpha) and P.1 (Gamma), were formed by the mutations in the receptor binding domain of spike glycoprotein (SGP). These two variants are known to possess a high binding affinity with the angiotensin-converting enzyme 2. Amidst the rapid spread of these mutant strains, research and development of novel molecules become tedious and labour-intensive. Imidazole and benzimidazole scaffolds were selected in this study based on their unique structural features and electron-rich environment, resulting in increased affinity against a variety of therapeutic targets. In the current study, imidazole- and benzimidazole-based anti-parasitic drugs are repurposed against SARS-CoV-2 Alpha and Gamma variant spike glycoproteins using computational strategies. Out of the screened 15 molecules, flubendazole and mebendazole have exhibited promising binding features to the two receptors (PDB ID: 7NEH and 7NXC), as evidenced by their glide score and binding free energy. The results are compared with that of the two standard drugs, remdesivir and hydroxychloroquine. Flubendazole and mebendazole have become convenient treatment options against mutant lineages of SARS-CoV-2. The edge of the flubendazole was further established by its stability in MD simulation conducted for 100 ns employing GROMACS software. Further, in vitro and in vivo studies are essential to understand, if flubendazole and mebendazole indeed hold the promise to manage SARS-CoV-2 mutant stains. Supplementary Information The online version contains supplementary material available at 10.1007/s11696-021-01900-8.

Bacterial resistance to antibiotics is rising to dangerously high levels globally making it one of the most urgent public health problems. Hence, there is an urgent need to develop new and potent antibacterial agents. ATP-dependent bacterial GyrB enzyme is crucial for the maintenance of DNA topology and survival of bacterial cells. GyrB is ubiquitous in bacterial cells but absent in human making it an attractive target for the development of antibacterial agents. Several GyrB inhibitors are described in the literature including coumarins, synthetic coumarins, triazine derivatives, benzimidazole ureas, benzothiazole ureas, pyrimidine-based analogues, pyrrolopyrimidines, 9H-pyrimido[4,5-b]indoles, thiazole-aminopiperidine hybrid analogue, pyrimido[4,5-b]indol-8-amine, aminopyrazinamide, thiazolyl pyrazole carboxamides, 3-(thiazol-2-yl)-1H-indazole derivatives, natural flavonoid quercetin and phytotoxin albicidin. etc. In the present review, we present structural information on different GyrB enzyme inhibitors and update status which may be used for the design and development of potent inhibitors against this enzyme.

In the present work, we carried out hydroxybenzotriazole (HOBT) and 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDCl)-mediated synthesis of new N'-(1,3-benzothiazol-2-yl)-arylamides C1-18 in high yields under relatively milder reaction conditions using dimethyl formamide as solvent. Synthesized compounds were characterized by FTIR, 1H-NMR, 13C-NMR and HRMS spectral data. The MIC values of synthesized compounds C1-18 were determined by the broth microdilution method using Mueller Hinton medium. Tested compounds showed variable activity against the tested Gram-positive and Gram-negative bacterial strains. Compounds C3, C5, C9, C13-15 and C17 exhibited promising activity against Staphylococcus aureus NCIM 5021 with MIC values in the range of 19.7–24.2 μM. Among all tested compounds, C13 possessing thiophene ring attached to the benzothiazole moiety via amide linkage exhibited maximum activity against S. aureus NCIM 5022 with MIC of 13.0 μM. Compound C13 showed maximum activity against S. aureus ATCC 43300 with MIC of 15.0 μM and exhibited bactericidal activity against this strain in minimum bactericidal concentration determination. This compound also eliminated S. aureus ATCC 43300 strain after 24-h exposure indicating its bactericidal activity. ADMET calculation showed favourable pharmacokinetic profile of synthesized compounds C1-18.

In the present work we synthesized a new series of phenoxyacetohydrazide functional compounds 4a-k and characterized by spectral data. Synthesized compounds were screened in vitro for their antibacterial activity. Compounds 4a, 4j and 4k exhibited inhibitory activity against S. aureus NCIM 5022 with MIC value of 64 µg/ml These compounds also exhibited activity against methicillin resistant S. aureus ATCC 43300 with MIC of 128 µg/ml. Among all the tested compounds 4c and 4j showed highest activity, respectively against B. subtilis NCIM 2545 and K. pneumoniae NCIM 2706. Only one compound i.e. 4d showed activity against another Gram-negative bacteria P. aeruginosa NCIM 2036 with MIC value of 64 µg/ml. Among three tested compounds, 4k exhibited highest inhibitory activity against S. aureus MurD enzyme with IC50 value of 35.80 µM. Further binding interactions of 4a-k with the modelled S. aureus MurD catalytic pocket residues is investigated with the extra-precision molecular docking and binding free energy calculation by MM-GBSA approach. The van der Waals energy term was observed to be the driving force for binding. Further, 50 ns molecular dynamics simulations were performed to validate the stabilities of 4j- and 4k-modelled S. aureus MurD.

Peptidoglycan, an essential component of the bacterial cell wall plays a critical role in protecting bacteria against osmotic lysis. The ATP-dependent MurC-F ligases are crucial for the early stages of peptidoglycan biosynthesis. MurE ligase is third in the series and catalyzes the addition of l-Lysine (l-Lys) in Gram-positive bacteria or meso-diaminopimelic acid (meso-A2pm) in most Gram-negative bacteria to form UDP-N-acetylmuramoyl-l-Ala-d-Glu-l-Lys/A2pm. The high substrate specific for l-Lys or meso-A2pm makes this enzyme an attractive target for the development of antibacterial agents. Several MurE inhibitors have been reported including phosphinates, peptidosulfonamides, napthylfuran-2-ones, benzene-1,3-dicarboxylic acids, phosphorylatedhydroxyethylamines, natural compounds, 5-benzylidenethiazolidin-4-ones, N-alkyl-2-alkynyl-4(1H)-quinolones, rhodanine substituted d-glutamic acids, 2,5-dimethyl pyrroles, 2,5-disubstitued furans, tetrahydroisoquinolines etc. In the present review we present an update status and structural information of MurE enzyme inhibitors which may be utilized for the design of potent inhibitors against this enzyme.

ParE, a subunit of topoisomerase IV, is involved in the management of DNA topology and validated to be an attractive target for the development of antibacterial agents. Availability of the crystal structure of Francisella tularensis in combination with one of the pyrrolo [2,3-d] pyrimidine-2-thiolinhibitor facilitated us to emphasize the combined computational approach for discovering the presumed binding mode of selected inhibitors into the binding pocket of ParE (pdb. 4HY1). In the current study, pharmacophore modelling and 3D-QSAR studies were performed using 33 reported F. tularensis ParE inhibitors having pKi ranging from 5.06 to 9.00. The developed five featured pharmacophore model, DHHRR_1 was statistically validated with different parameters like Q2 (0.66), R2 (0.99) and F value (682) at four-component partial least squares factor. Enrichment analysis was performed to validate the generated pharmacophore model. Extra-precision molecular docking, binding free energy calculation using PRIME MM-GBSA were performed for the selected inhibitors. Induced fit docking was performed for the highest active inhibitor 16. The highest-ranked induced fit docked complex 16/4HY1 was used to run a 50 ns molecular dynamic simulation to validate the stability. Further, in silico High Throughput Virtual Screening was performed using 22 lakhs chemical database molecules to identify the potential virtual hits and predicted activity was found for the virtual hits. These results provide promising strategies for the development of novel molecules with better inhibitory activity against F. tularensis ParE.

Peptidoglycan is an essential component of the bacterial cell wall and is required for the survival of bacteria. ATP-dependent MurC–F ligases are responsible for the early stages of peptidoglycan biosynthesis. Second in the series, MurD catalyzes the addition of d-glutamic acid to UDP-MurNAc-l-Ala which involves acyl-phosphate and tetrahedral intermediates. Due to its high specificity for d-glutamic acid substrate and its absence in mammalian cells, MurD is considered as an attractive target for the design of novel antibacterial agents. Several MurD inhibitors have been designed and tested for their activity. These include phosphinates, N-acetylmuramic acids, pulvinones, phosphinodipeptide, cyclic nonapeptides, macrocyclic compounds, benzene-1,3-dicarboxylic acid, naphthalene sulphonamides, 2-thioxothiazolidin-4-ones, benzylidene-2,4-thiazolidindiones, etc. In the present review, an updated status of MurD enzyme inhibitors is presented which will serve as a useful source of structural information and may be utilized for the design of potent inhibitors against this enzyme.

Antibacterial resistance (ABR) is a major life-threatening problem worldwide. Rampant dissemination of ABR always exemplified the need for the discovery of novel compounds. However, to circumvent the disease, a molecular target is required, which will lead to the death of the bacteria when acted upon by a compound. One group of enzymes that have proved to be an effective target for druggable candidates is bacterial DNA topoisomerases (DNA gyrase and ParE). In our present work, phenylacetamide and benzohydrazides derivatives were screened for their antibacterial activity against a selected panel of pathogens. The tested compounds displayed significant antibacterial activity with MIC values ranging from 0.64 to 5.65 μg/mL. Amongst 29 title compounds, compounds 5 and 21 exhibited more potent and selective inhibitory activity againstEscherichia coliwith MIC values at 0.64 and 0.67 μg/mL, respectively, and MBC at onefold MIC. Furthermore, compounds exhibited a post-antibiotic effect of 2 h at 1× MIC in comparison to ciprofloxacin and gentamicin. These compounds also demonstrated the concentration-dependent bactericidal activity againstE. coliand synergized with FDA-approved drugs. The compounds are screened for their enzyme inhibitory activity againstE. coliParE, whose IC50values range from 0.27 to 2.80 μg/mL. Gratifyingly, compounds, namely 8 and 25 belonging to the phenylacetamide series, were found to inhibit ParE enzyme with IC50values of 0.27 and 0.28 μg/mL, respectively. In addition, compounds were benign to Vero cells and displayed a promising selectivity index (169.0629–951.7240). Moreover, compounds 1, 7, 8, 21, 24, and 25 (IC50: 200) exhibited potent activity in reducing theE. colibiofilm in comparison with ciprofloxacin, erythromycin, and ampicillin. These astonishing results suggest the potential utilization of phenylacetamide and benzohydrazides derivatives as promising ParE inhibitors for treating bacterial infections.

A new series of benzothiazol-2-ylcarbamodithioate functional compounds 5a-f has been designed, synthesized and characterized by spectral data. These compounds were screened for their in vitro antibacterial activity against strains of Staphylococcus aureus (NCIM 5021, NCIM 5022 and methicillin-resistant isolate 43300), Bacillus subtilis (NCIM 2545), Escherichia coli (NCIM 2567), Klebsiella pneumoniae (NCIM 2706) and Psudomonas aeruginosa (NCIM 2036). Compounds 5a and 5d exhibited significant activity against all the tested bacterial strains. Specifically, compounds 5a and 5d showed potent activity against K. pneumoniae (NCIM 2706), while compound 5a also displayed potent activity against S. aureus (NCIM 5021). Compound 5d showed minimum IC50 value of 13.37 μM against S. aureus MurD enzyme. Further, the binding interactions of compounds 5a-f in the catalytic pocket have been investigated using the extra-precision molecular docking and binding free energy calculation by MM-GBSA approach. A 30 ns molecular dynamics simulation of 5d/modeled S. aureus MurD enzyme was performed to determine the stability of the predicted binding conformation.

The alarming rise of bacterial resistance is occurring worldwide and endangering the efficacy of antibiotics. Therefore, development of new and efficient antibacterial agents remains paramount. In the present work, we designed and synthesized a series of N'-(1,3-benzothiazol-2-yl)-substituted aryl/aralkyl hydrazides C1-C27 and evaluated them in vitro for their antibacterial activity. Among all tested compounds, C10, C15, and C24 showed potent activity against Staphylococcus aureus ATCC 43300 (MRSA). Minimum bactericidal concentration studies of synthesized compounds are performed against selected bacterial strains. Time kill kinetics showed that the compounds C10 and C15 possess bactericidal activity against MRSA ATCC 43300, while compound C24 possess bactericidal activity against S. aureus NCIM 5022. In the extra-precision docking, compounds C1-C27 exhibited interactions mainly with the N-terminal and central domains of S. aureus GyrB catalytic pocket. Binding free energy (ΔGbind ) of compounds C1-C27/3U2K complexes were computed by MM-GBSA approach. Free energy components indicated Coulomb energy term as favorable for binding, while van der Waals and electrostatic solvation energy terms strongly disfavored the binding. ADMET properties of synthesized compounds C1-C27 are also computed.

A new class of 2-aryloxy-N-phenylacetamide and N'-(2-aryloxyoxyacetyl) benzohydrazide derivatives with different active moieties were synthesized and screened for their antibacterial activity. Structural characterization of synthesized compounds was performed using HR-MS, 1 H-NMR, and 13 C-NMR spectral data. Amongst the synthesized compounds, 4-{2-[2-(2-chloroacetamido)phenoxy]acetamido}-3-nitrobenzoic acid (3h) and 2-chloro-N-(2-{2-[2-(2-chlorobenzoyl)hydrazinyl]-2-oxoethoxy}phenyl)acetamide (3o) have shown good antibacterial activity against a selected panel of bacteria. Besides, compounds also exhibited bactericidal activity against P. aeruginosa (3h, 0.69 μg/mL) and S. aureus (3o, 0.62 μg/mL) as evident by MBC and time-kill kinetics studies. In silico molecular docking and ADMET properties of newly synthesized compounds revealed that compounds could be considered as promising antibacterial agents.

Alar, a Pyridoxal 5′-phosphate (PLP)-dependent bacterial enzyme is responsible for the racemisation of L-alanine into D-alanine which is essential for the peptidoglycan biosynthesis in both...

Staphylococcus aureus MurE enzyme catalyzes the addition of l-lysine as third residue of the peptidoglycan peptide moiety. Due to the high substrate specificity and its ubiquitous nature among bacteria, MurE enzyme is considered as one of the potential target for the development of new therapeutic agents. In the present work, induced fit docking (IFD), binding free energy calculation, and molecular dynamics (MD) simulation were carried out to elucidate the inhibition potential of 2-thioxothiazolidin-4-one based inhibitor 1 against S. aureus MurE enzyme. The inhibitor 1 formed majority of hydrogen bonds with the central domain residues Asn151, Thr152, Ser180, Arg187, and Lys219. Binding free-energy calculation by MM-GBSA approach showed that van der Waals (ΔGvdW, −57.30 kcal/mol) and electrostatic solvation (ΔGsolv, −36.86 kcal/mol) energy terms are major contributors for the inhibitor binding. Further, 30-ns MD simulation was performed to validate the stability of ligand–protein complex and also to get structural insight into mode of binding. Based on the IFD and MD simulation results, we designed four new compounds D1–D4 with promising binding affinity for the S. aureus MurE enzyme. The designed compounds were subjected to the extra-precision docking and binding free energy was calculated for complexes. Further, a 30-ns MD simulation was performed for D1/4C13 complex.

ATP dependent ParE enzyme is as an attractive target for the development of antibacterial agents. Atom based 3D-QSAR model AADHR.187 was developed based on the thirty eight Escherichia coli ParE inhibitors. The generated model showed statistically significant coefficient of determinations for the training (R2 = 0.985) and test (R2 = 0.86) sets. The cross-validated correlation coefficient (q2) was 0.976. The utility of the generated model was validated by the enrichment study. The model was also validated with structurally diverse external test set of ten compounds. Contour plot analysis of the generated model unveiled the chemical features necessary for the E. coli ParE enzyme inhibition. Extra-precision docking result revealed that hydrogen bonding and ionic interactions play a major role in ParE protein-ligand binding. Binding free energy was computed for the data set inhibitors to validate the binding affinity. A 30-ns molecular dynamics simulation showed high stability and effective binding of inhibitor 34 within the active site of ParE enzyme. Using the best fitted model AADHR.187, pharmacophore-based high-throughput virtual screening was performed to identify virtual hits. Based on the above studies three new molecules are proposed as E. coli ParE inhibitors with high binding affinity and favourable ADME properties.

GyrB and ParE are type IIA topoisomerases and found in most bacteria. Its function is vital for DNA replication, repair and decatenation. The highly conserved ATP-binding subunits of DNA GyrB and ParE are structurally related and have been recognized as prime candidates for the development of dual-targeting antibacterial agents with broad-spectrum potential. However, no natural product or small molecule inhibitors targeting ATPase catalytic domain of both GyrB and ParE enzymes have succeeded in the clinic. Moreover, no inhibitors of these enzymes with broad-spectrum antibacterial activity against Gram-negative pathogens have been reported. Availability of high resolution crystal structures of GyrB and ParE made it possible for the design of many different classes of inhibitors with dual mechanism of action. Among them benzimidazoles, benzothiazoles, thiazolopyridines, imidiazopyridazoles, pyridines, indazoles, pyrazoles, imidazopyridines, triazolopyridines, pyrrolopyrimidines, pyrimidoindoles as well as related structures are disclosed in literatures. Unfortunately most of these inhibitors are found to be active against Gram-positive pathogens. In the present review we discuss about studies on novel dual targeting ATPase inhibitors.

Alanine racemase is a fold type III PLP-dependent amino acid racemase enzyme catalysing the conversion of l-alanine to d-alanine utilised by bacterial cell wall for peptidoglycan synthesis. As there are no known homologs in humans, it is considered as an excellent antibacterial drug target. The standard inhibitors of this enzyme include O-carbamyl-d-serine, d-cycloserine, chlorovinyl glycine, alaphosphin, etc. d-Cycloserine is indicated for pulmonary and extra pulmonary tuberculosis but therapeutic use of drug is limited due to its severe toxic effects. Toxic effects due to off-target affinities of cycloserine and other substrate analogs have prompted new research efforts to identify alanine racemase inhibitors that are not substrate analogs. In this review, an updated status of known inhibitors of alanine racemase enzyme has been provided which will serve as a rich source of structural information and will be helpful in generating selective and potent inhibitor of alanine racemase.

The discovery of clinically relevant inhibitors against MurF enzyme has proven to be a challenging task. In order to get further insight into the structural features required for the MurF inhibitory activity, we performed pharmacophore and atom-based three-dimensional quantitative structure–activity relationship studies for novel thiophene-3-carbonitriles based MurF inhibitors. The five-feature pharmacophore model was generated using 48 inhibitors having IC50 values ranging from 0.18 to 663 μm. The best-fitted model showed a higher coefficient of determination (R2 = 0.978), cross-validation coefficient (Q2 = 0.8835) and Pearson coefficient (0.9406) at four component partial least-squares factor. The model was validated with external data set and enrichment study. The effectiveness of the docking protocol was validated by docking the co-crystallized ligand into the catalytic pocket of MurF enzyme. Further, binding free energy calculated by the molecular mechanics generalized Born surface area approach showed that van der Waals and non-polar solvation energy terms are the main contributors to ligand binding in the active site of MurF enzyme. A 10-ns molecular dynamic simulation was performed to confirm the stability of the 3ZM6-ligand complex. Four new molecules are also designed as potent MurF inhibitors. These results provide insights regarding the development of novel MurF inhibitors with better binding affinity.

The binding modes of well known MurD inhibitors have been studied using molecular docking and molecular dynamics (MD) simulations. The docking results of inhibitors 1-30 revealed similar mode of interaction with Escherichia coli-MurD. Further, residues Thr36, Arg37, His183, Lys319, Lys348, Thr321, Ser415 and Phe422 are found to be important for inhibitors and E. coli-MurD interactions. Our docking procedure precisely predicted crystallographic bound inhibitor 7 as evident from root mean square deviation (0.96 A). In addition inhibitors 2 and 3 have been successfully cross-docked within the MurD active site, which was pre-organized for the inhibitor 7. Induced fit best docked poses of 2, 3, 7 and 15/2Y1O complexes were subjected to 10 ns MD simulations to determine the stability of the predicted binding conformations. Induce fit derived docked complexes were found to be in a state of near equilibrium as evident by the low root mean square deviations between the starting complex structure and the energy minimized final average MD complex structures. The results of molecular docking and MD simulations described in this study will be useful for the development of new MurD inhibitors with high potency.

2-Mercaptobenzothiazoles are an important class of bioactive and industrially important organic compounds. These compounds are reported for their antimicrobial and antifungal activities, and are subsequently highlighted as a potent mechanism-based inhibitor of several enzymes like acyl coenzyme A cholesterol acyltransferase, monoamine oxidase, heat shock protein 90, cathepsin D, and c-Jun N-terminal kinases. These derivatives are also known to possess antitubercular, anti-inflammatory, antitumor, amoebic, antiparkinsonian, anthelmintic, antihypertensive, antihyperlipidemic, antiulcer, chemoprotective, and selective CCR3 receptor antagonist activity. This present review article focuses on the pharmacological profile of 2-mercaptobenzothiazoles with their potential activities.