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Abstract: ATP dependent MurC-F ligases are essential for the biosynthesis of peptidoglycan, an essential bacterial cell wall component that is required for bacterial cell survival. Last, in the series, MurF catalyzes the ATP-dependent addition of D-Ala-D-Ala dipeptide to UDP-N-acetylmuramyl-tripeptide to form the UDP-N-acetylmuramy-pentapeptide monomeric precursor of peptidoglycan. Owing to its critical essentiality in peptidoglycan biosynthesis and absence in eukaryotic counterparts, MurF is considered a promising target for the design and development of potent antibacterial agents. Several MurF inhibitors have been designed and evaluated for their MurF inhibitory and antibacterial activity. These include aminoalkylphosphinates, sulfonamides, diarylquinolones, hydroxylamines, phosphorylated hydroxylamines, thiazolylaminopyrimidines, 2,4,6-trisubstituted 1,3,5-triazines, etc. However, most of the inhibitors developed till date lack potent antibacterial activity against both Gram-positive and Gram-negative bacteria. In the present review, an updated status of MurF ligase inhibitors is presented that may provide a useful source for the design of novel MurF inhibitors with potent and broad-spectrum antibacterial activity.

Alanine racemase is a pyridoxal-5´-phosphate dependent bacterial enzyme that provides the essential peptidoglycan precursor D-alanine, utilized for cell wall synthesis. This enzyme is ubiquitous throughout bacteria, including Mycobacterium tuberculosis, making it an attractive target for antibacterial drug discovery. We investigated the binding mode of twenty five reported Mycobacterium tuberculosis alanine racemase inhibitors. The results obtained from molecular docking studies emphasized the importance of inhibitor interaction with Lys42, Tyr46, Arg140, His172 and Tyr175 residues at the catalytic binding pocket of alanine racemase enzyme. The predicted binding free energies showed that van der Waals and nonpolar solvation interactions are the driving force for binding of inhibitors. Molecular dynamics simulation studies of four such inhibitor-alanine racemase systems were further explored to study the inhibition mechanism. The quantum chemical parameters calculated at the B3LYP/6-31G**++ level of theory indicated that the inhibitors must have low values of the lowest unoccupied molecular orbital energy and high values of electrostatic potential for stronger interactions. We expect that this study can provide significant theoretical guidance for design of potent Mycobacterium tuberculosis alanine racemase inhibitors in future.

Background: The frightening rise of bacterial resistance is occurring worldwide and endangering the efficacy of antibiotics. Hence, the development of novel and potent antibacterial is a need of the day. Objective: In this study, we designed and synthesized compounds C1-C11. These compounds are characterized by their FT-IR, NMR and MS spectral data and examined in vitro for their antibacterial activity. Methods: Compounds C1-C11 were synthesized by reacting 2-mercaptobenzothiazole with appropriate chloroacetamide in the presence of anhydrous potassium carbonate and dry acetone at room temperature. To assess the antibacterial activity, minimum inhibitory and minimum bactericidal concentrations were examined by broth microdilution method against the selected strains of both Gram-positive and Gram-negative bacteria. Time-kill kinetics study was also performed as per CLSI guidelines. Results: Compounds C6 and C7 displayed promising activity against Staphylococcus aureus ATCC 43300 with MICs of 9.43 and 7.73 μM, respectively. These two compounds also displayed promising antibacterial activity against S. aureus 5021 with MIC values of 7.53 and 9.68 µM, respectively. In MBC determination, these two compounds (tested in the concentration range of 7.53 to 262.3 μM) displayed bactericidal activity against methicillin resistant S. aureus ATCC 43300, S. aureus NCIM 5021 and S. aureus NCIM 5022. In time-kill kinetics study, compounds C6 and C7 also exhibited bactericidal activity against S. aureus NCIM 5021 and S. aureus ATCC 43300 after 12 h of exposure. In general, all tested compounds exhibited poor activity against Mycobacterium sp. NCIM 2984 and also against tested Gram-negative bacteria Klebsiella pneumoniae NCIM 2706, Escherichia coli NCIM 2065 and Pseudomonas aeruginosa NCIM 2036. Further, computed ADMET properties of C1-C11 showed a favourable pharmacokinetic profile with zero violation of Lipinski’s rule of five. Conclusion: The result showed that in phenylacetamides C6 and C7 presence of phenyl ring substituted with -CF3 group is responsible for their high antibacterial activity against S. aureus ATCC 43300 (MICs, 9.43 and 7.73 μM, respectively). These two compounds also exhibited bactericidal activity respectively against S. aureus NCIM 5021 in time kill kinetics study. other: Template of compound C7 can further be used to develop more potent antibacterial agents.

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.

Background: The increased emergence of multidrug resistant bacterial strains is a continuous life-threatening global problem. The best approach to prevent the reproduction and invasion of the pathogenic bacteria is to inhibit the replication stage. The untapped molecular machinery involved in the replication is ParE subunit of topoisomerase IV. The compounds active against the ParE were chosen for the study. Objective: To analyze the electronic parameters, chemical stability, kinetic stability, and binding modes of the compounds. Methods: Density functional theory (DFT) and molecular electrostatic potential (MESP) calculations were computed using Jaguar with a basis set 6-31G**++ (B3LYP) in the gas phase. MD simulation was performed for the 100 ns using Desmond available in Maestro to determine the stability and to get insight into the molecular mechanism of E. coli ParE docked complexes. Results: From the DFT calculations, the energy gap ∆E 7.58 and 7.75 eV between the HOMO and LUMO of both the compounds P1 (4-(2-(2-(2-chloroacetamido)phenoxy)acetamido)-3-nitrobenzoic acid) and P2 (4-(2-(benzo[d]thiazol-2-ylthio)acetamido)-3-nitrobenzoic acid) explained the chemical and kinetic stability of the system. MD results demonstrated the minimum fluctuations and conformational stability of the protein structures. Conclusion: The P1 and P2 compounds were chemically and kinetically stable. Further, MD results demonstrated the stability and inhibitory action of the ligands were dependent on hydrophobic, ionic and water bridges than that of hydrogen-bonding interactions.

Background: The south Indian Telugu states will celebrate a new year called ‘Ugadi’ which is a south Indian traditional festival. The ingredients used in ugadi pachadi have often also been used in food as well as traditional Ayurveda and Siddha medicinal preparations. Coronaviruses (CoVs) are a diverse family of enveloped positive-sense single-stranded RNA viruses which can infect humans and have the potential to cause large-scale outbreaks. Objective: Considering the benefits of ugadi pachadi, we investigated the binding modes of various phytochemical constituents reported from its ingredients against five targets of SARS-CoV-2. Methods: Flexible-ligand docking simulations were achieved through AutoDock version 1.5.6. Following 50ns of molecular dynamics simulation using GROMACS 2018.1 software and binding free energy (ΔGbind) of the protein-ligand complexes were calculated using the g_mmpbsa tool. ADME prediction was done using Qikprop of Schrodinger. Results: From the molecular docking and MM/PBSA results compound Eriodictin exhibited the highest binding energy when complexed with nucleocapsid N protein (6M3M) (-6.8 kcal/mol, - 82.46 kJ/mol), bound SARS-CoV-2-hACE2 complex (6M0J) (-7.4 kcal/mol, -71.10 kJ/mol) and Mpro (6XR3) (-8.6 kcal/mol, -140.21 kJ/mol). Van der Waal and electrostatic energy terms highly favored total free energy binding. Conclusion: The compounds Eriodictin, Vitexin, Cycloart-3, 24, 27-triol, Agigenin, Mangiferin, Mangiferolic acid, Schaftoside, 27-Hydroxymangiferonic acid, Quercetin, Azadirachtol, Cubebin, Isomangiferin, Isoquercitrin, Malicarpin, Orientin and procyanidin dimer exhibited satisfactory binding energy values when compared with standard molecules. The further iterative optimization of high-ranked compounds following validation by in vitro and in vivo techniques assists in discovering therapeutic anti-SARS-CoV-2 molecules.

Abstract: Bacterial infections are a major cause of mortality and morbidity in humans throughout the world. Infections due to resistant bacterial strains such as methicillin-resistant Staphyloccocusaureus vancomycin, resistant Enterococci, Klebsiella pneumoniae, Staphylococcus aureus, and Mycobacterium are alarming. Hence the development of new antibacterial agents, which act via a novel mechanism of action, became a priority in antibacterial research. One such approach to overcome bacterial resistance is to target novel protein and develop antibacterial agents that act via different mechanisms of action. Bacterial GlmU is one such bifunctional enzyme that catalyzes the two consecutive reactions during the biosynthesis of uridine 5′-diphospho-Nacetylglucosamine, an essential precursor for the biosynthesis of bacterial cell wall peptidoglycan. This enzyme comprises two distinct active sites; acetyltransferase and uridyltransferase and both these active sites act independently during catalytic reactions. GlmU is considered an attractive target for the design and development of newer antibacterial agents due to its important role in bacterial cell wall synthesis and the absence of comparable enzymes in humans. Availability of three dimensions X-crystallographic structures of GlmU and their known catalytic mechanism from different bacterial strains have instigated research efforts for the development of novel antibacterial agents. Several GlmU inhibitors belonging to different chemical classes like 2- phenylbenzofuran derivative, quinazolines, aminoquinazolines, sulfonamides, arylsulfonamide, D-glucopyranoside 6-phosphates, terreic acid, iodoacetamide, N-ethyl maleimide, and Nethylmaleimide etc., have been reported in the literature. In the present review, we present an update on GlmU inhibitors and their associated antibacterial activities. This review may be useful for the design and development of novel GlmU inhibitors with potent antibacterial activity.

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.

Enterococcus faecium MurF (EfMurF) enzyme catalyzes the addition of d-alanyl-d-alanine to form murein UDP-N-acetylmuramoyl-pentapeptide. This is the last cytoplasmic step of peptidoglycan synthesis and is essential for bacterial cell wall integrity. Due to the specificity of d-amino acid utilization and its absence in eukaryotic counterpart, this enzyme is considered as an attractive target for new antibacterial discovery. In the present investigation, we prepared the 3D structure of the EfMurF catalytic pocket by homology modelling. A combined molecular modelling approach was used to get insight into the binding mode of diarylquinoline-based inhibitor 1 against EfMurF. In extra-precision (XP) docking, inhibitor 1 exhibited hydrogen bonding and π-π stacking interactions mainly with the residues of N-terminal and central domains. In the molecular mechanics/generalized born surface area (MM-GBSA) binding free energy calculation, Coulomb and the non-polar solvation energy terms are observed to be major contributors for the inhibitor binding. To gain further insight into the binding mode and inhibition potential, the inhibitor 1/EfMurF enzyme complex was analyzed with 100-ns molecular dynamics simulation. Based on the docking and MD results, we designed three new compounds D1-D3 with a high binding affinity against EfMurF. These three designed compounds were subjected to the XP docking and the binding free energy calculation. A 50-ns MD simulation was also performed for the D1/EfMurF complex.

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.

The antibacterial resistance (ABR) is a growing phenomenon and global threat to mankind. To circumvent the ABR, many approaches have been put forth, but none of them meet the pre-requisites associated with the resistance mechanisms. In this review, we focused on the importance of unexploited enzyme, ParE, a topoisomerase responsible for the bacterial survival. The bacterial topoisomerases maintain the topological state of DNA. The gyrases and topoisomerases IV are validated targets for the antibacterial activity. Both these enzymes are structurally similar and possess high degree conservation in the catalytic domain of the N-terminal region, which make them appealing targets for broad spectrum antibacterial activity. Despite being an attractive target for the development of new antibacterials, there are currently no antibiotics targeting gyrases and topoisomerase (topo) IV in the market. Availability of the high-resolution crystal structure data for ParE made it possible to design new classes of antibacterials. Here, we discuss the importance of targeting topo IV enzyme as it is less prone to bacterial resistance which has been disclosed in the literature.

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.

Additional file 1. Shows few items that were used in online formative OBE.

Additional file 2. Shows table of item analysis results of online formative OBE.

The atomic and molecular properties of the title compounds were calculated by Jaguar using a basis set B3LYP/6-31G**++ with hybrid DFT in the gas phase, to determine the chemical reactivity. Analysis of Quantum chemical features such as HOMO and LUMO explained that the electronic charge transfer occurred within the system through conjugated paths of the selected compounds. The nucleophilic and electrophilic reactive sites are recognized from the molecular electrostatic potential plot. Electrophilic and nucleophilic attack-prone molecular sites were predicted by mapping ALIE and ALEA values to the molecular surface. The bond dissociation energy of the high active compound 15 (2-chloro-N-(2-(2-(2-(2-chlorobenzoyl)hydrazineyl)-2-oxoethoxy)phenyl)acetamide) was calculated to assess the probability of compounds autoxidation or degradation. Further, molecular docking, binding free energy calculations, and ADMET profile of the degradation products (DPs) of compound 15 was carried out to determine the binding affinity and toxicity profile of the formed DPs compared with the parent compound. A 150 ns molecular dynamics (MD) simulation was performed to evaluate the binding stability of the compound 15/4URL complex using Desmond. Binding free energy and binding affinity of the complex were computed for 100 trajectory frames using the MM-GBSA approach.

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 sulphatase inhibitor 667 COUMATE is in clinical trials for estrogen-positive breast cancer therapy for postmenopausal women, while there are a number of similar sulphatase inbitors are under development. Schiff's bases are versatile pharmacophores in which the N atom involves in hydrogen bonding with active cell centers interfering in normal cell biology. A library of novel coumate analogues with Schiff bases were designed, and structural based drug design was performed with human estrogen receptor (PDB ID: 2IOG) (Already reported). Based on the in-silico outcomes, seven coumate-schiff bases were synthesized. The compounds were obtained in good yield. The novelty had been ascertained by sci finder software. The synthesized molecules were consistent with their assigned spectra such as IR, Mass and NMR spectral data which confirmed their formation. The cytotoxicity study was performed by MTT assay for all the synthesized compounds. Most of the compounds have good IC50 values (below 100 µg/ml).Two of the synthesized compounds COU-2 and COU-5 have shown good IC50 values such as 19µg/ml and 39µg/ml, respectively. They suppressed the proliferation of estrogen receptor overexpressed MCF-7 cells.

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 MurD enzyme of Staphylococcus aureus is an attractive drug target as it is essential and ubiquitous in bacteria but absent in mammalian cells. In the present study, we performed in silico high-throughput virtual screening with small molecule library of 1.60 million compounds to identify potential hits. We used S. aureus modeled MurD protein for this purpose and to find the best leads, dock complexes were further subjected to the extra-precision docking and binding free energy calculations by MM-GBSA approach. It is evident that van der Waals and Coulomb energy terms are major favorable contributors while electrostatic solvation energy term strongly disfavors the binding of ligands to the S. aureus MurD enzyme. The inhibitory activity of two selected virtual hits H5 and H10 was performed against S. aureus MurD enzyme using malachite green assay. In in vitro antibacterial screening, compound H5 inhibited the growth of S. aureus NCIM 5021, S. aureus NCIM 5022, and methicillin-resistant S. aureus (MRSA strain 43300) at high concentrations while the other tested compound H10 was inactive against all the tested strains. In order to validate the stability of inhibitor-protein complex, compound H5 with the highest inhibitory against S. aureus MurD and lowest binding free energy was subjected to 30-ns molecular dynamics simulation. Further, ADMET predictions showed the favorable pharmacokinetic profile of compounds H5 and H10.

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.

Background: Reverse transcriptase is an important therapeutic target to treat AIDS caused by the Human Immunodeficiency Virus (HIV). Despite many effective anti-HIV drugs, reverse transcriptase (RT) inhibitors remain the cornerstone of the drug regimen to treat AIDS. In the present work, we have expedited the use of different computational modules and presented an easy, cost-effective and high throughput screening method to identify potential reverse transcriptase inhibitors. Methods: A congeneric series of 4-Arylthio & 4-Aryloxy-3- Iodopyridine-2(1H)-one analogs having anti-HIV activity were subjected to structure-based 2D, 3D QSAR, Pharmacophore Modeling, and Molecular Docking to elucidate the structural properties required for the design of potent HIV-RT inhibitors. Prediction of preliminary Pharmacokinetic and the Drug Likeliness profile was performed for these compounds by in silico ADME study. Results: The 2D and 3D- QSAR models were developed by correlating two and three-dimensional descriptors with activity (pIC50) by sphere exclusion method and k-nearest neighbor molecular field analysis approach, respectively. The significant 2D- QSAR model developed by Partial Least Square is associated with the Sphere Exclusion method (PLS-SE), having r2 and q2 values 0.9509 and 0.8038, respectively. The 3D-QSAR model by Step Wise variable selection method (SW-kNN MFA) is more significant, which has a cross-validated squared correlation coefficient q2= 0.8509 and a non-crossvalidated correlation coefficient pred_r2= 0.8102. The pharmacophore hypothesis was developed, which comprised 5 features includes 3 aliphatic regions (Ala), 1 H-bond donor (HDr) and 1 H-bond acceptor (HAc). Docking studies of the selected inhibitors with the active site of reverse transcriptase enzyme showed hydrogen bond and π - π interaction with LYS-101, LYS-103, TYR- 181, TYR-188 and TRP-229 residues present at the active site. All the candidates with good bioavailability and ADMET drug likeliness properties. Conclusion: The results of the present work provide more useful information and important structural insights for the discovery, design of novel and potent reverse transcriptase inhibitors with high therapeutic windows in the future.

Background: The widespread hazardous issue of antibiotics resistance can be overcome by the development of target based potent antibacterial agents. Filamentous temperature-sensitive mutant Z (FtsZ), a simpler structural prokaryotic homolog of eukaryotic cytoskeletal tubulin, was considered as a competent target in antibacterial drug discovery. Objective: The purpose of present work is to evaluate the antitubercular activity of virtual hits by funnel-shaped filtering with glide docking followed by MM-GBSA binding energy and molecular dynamics simulation. Pharmacokinetics and biochemical activity of the computationally screened virtual hits have been studied to focus their potential to inhibit the bacterial cell division. Method: The docking study was performed against the crystal structure of Staphylococcus aureus and Mycobacterium tuberculosis FtsZ protein with the hits obtained from High Throughput Virtual Screening using Glide module in Schrodinger. ADME profile and 50 ns molecular dynamics simulationstudies were performed using the Schrödinger suite. The minimal inhibitory concentration of the test compounds were determined bythe colorimetric method by Resazurin Microtiter plate Assay. Results: The binding of hit molecules T5427054 and 6M356S were mainly supported by van der Waals interaction and an electrostatic component of solvation energycomputed by MM-GBSA method. 50 ns MD simulation built stability and dynamic property of the best-docked complex T5427054/2Q1Y. Both the hit molecules displayed antimycobacterial activity with minimal inhibitory concentration 500 μg/mL. Conclusion: In this study, it is found that new screened hit molecules with better theoretical results could be preferred to use as antimycobacterial agents and further their structural modification might be improved antimycobacterial properties of hit molecules.

Additional file 1.

The ATP-dependent bacterial MurD enzyme catalyses the formation of the peptide bond between cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine and D-glutamic acid. This is essential for bacterial cell wall peptidoglycan synthesis in both Gram-positive and Gram-negative bacteria. MurD is recognized as an important target for the development of new antibacterial agents. In the present study we prepared the 3D-stucture of the catalytic pocket of the Staphylococcus aureus MurD enzyme by homology modelling. Extra-precision docking, binding free energy calculation by the MM-GBSA approach and a 40 ns molecular dynamics (MD) simulation of 2-thioxothiazolidin-4-one based inhibitor $1 was carried out to elucidate its inhibition potential for the S. aureus MurD enzyme. Molecular docking results showed that Lys19, Gly147, Tyr148, Lys328, Thr330 and Phe431 residues are responsible for the inhibitor-protein complex stabilization. Binding free energy calculation revealed electrostatic solvation and van der Waals energy components as major contributors for the inhibitor binding. The inhibitor-modelled S. aureus protein complex had a stable conformation in response to the atomic flexibility and interaction, when subjected to MD simulation at 40 ns in aqueous solution. We designed some molecules as potent inhibitors of S. aureus MurD, and to validate the stability of the designed molecule D1-modelled protein complex we performed a 20 ns MD simulation. Results obtained from this study can be utilized for the design of potent S. aureus MurD inhibitors.

Background: In view of the estrogenic receptor inhibitory properties of coumarin nucleus, long chain nature of fatty acid and anti-breast cancer activity of fatty acids, it was proposed to attach long chain fatty acids at 3rd,4th and 7th position of coumarin nucleus and evaluate for their anti-breast cancer activity through suitable in-vitro methods. Methods: The present study focuses a library of fatty acid coumarin conjugates as ligands to the ligand-binding domain of the human estrogen receptor α (PDB ID 2IOG) and their binding affinities using GLIDE module of Schrodinger after ascertaining their drug-likeness with QIKPROP. The compounds LNAC 8, SAC 1 and OAC 5 are the best hits based on their docking scores as well as the Prime MM-GBSA free energy of binding. Based on the in-silico results and synthetic feasibility the compounds SAC 1 PAC 1 and OAC 1 are synthesized, characterized and investigated for their time interval growth inhibitory effect on MCF-7 which is an ER positive breast cancer cell lines. Results: SAC 1, showed better in vitro growth inhibitory effect in sub micromolar range as compared to Tamoxifen, a standard estrogen receptor modulator. Conclusion: Conclusively, in silico molecular docking studies have been very useful in predicting the pharmacokinetic profiles and the binding affinities of new hits before a detailed preclinical and clinical evaluation.