In Silico and In Vitro Screening of Natural Compounds as Broad-Spectrum ß-Lactamase Inhibitors against Acinetobacter baumannii New Delhi Metallo-ß-lactamase-1 (NDM-1).

Antibiotic resistance is one of the significant problems globally; there is an increase in resistance with introducing every new class of antibiotics. Further, this has become one of the reasons for arising of new resistance mechanisms in Acinetobacter baumannii. In this study, we have screened natural compounds as a possible inhibitor against the NDM-1 ß-lactamase enzyme from A. baumannii using a combination of in silico methods and in vitro evaluation. The database of natural compounds was screened against NDM-1 protein, using Glide docking, followed by QM-polarised ligand docking (QPLD). When the screened hits were validated in vitro, withaferin A and mangiferin had good IC50 values in reducing the activity of NDM-1 enzymes, and their fractional inhibitory concentration index (FICI) was ascertained in combination with imipenem. The withaferin A and mangiferin-NDM-1 docking complexes were analyzed for structural stability by molecular dynamic simulation analysis using GROMACS for 100 ns. The molecular properties of the natural compounds were then calculated using density functional theory (DFT). Withaferin A and mangiferin showed promising inhibitory activity and can be a natural compound candidate inhibitor synergistically used along with carbapenems against NDM-1 producing A. baumannii.

Inhibition of Aldose Reductase by Novel Phytocompounds: A Heuristic Approach to Treating Diabetic Retinopathy.

Aldose reductase (ALR2) activation in the polyol pathway has been implicated as the primary mechanism for the progression of diabetic retinopathy. Most of the aldose reductase inhibitors (ARIs), used for the treatment of diabetic complications, were withdrawn due to ineffective treatment and adverse side effects caused by nonspecificity. Epalrestat, a carboxylic acid inhibitor, is the only ARI used for the treatment of diabetic neuropathy, though associated with minor side effects to 8% of the treated population. Our study exploited the interactions of Epalrestat-ALR2 crystal structure for the identification of specific phytocompounds that could inhibit human lens ALR2. 3D structures of plant compounds possessing antidiabetic property were retrieved from PubChem database for inhibition analysis, against human lens ALR2. Among the shortlisted compounds, Agnuside and Eupalitin-3-O-galactoside inhibited lens ALR2 with IC50 values of 22.4 nM and 27.3 nM, respectively, compared to the drug Epalrestat (98 nM), indicating high potency of these compounds as ALR2 inhibitors. IC50 concentration of the identified ARIs was validated in vitro using ARPE-19 cells. The in silico and in vitro approaches employed to identify and validate specific and potent ALR2 inhibitors resulted in the identification of phytocompounds with potency equal to or better than the ALR2 inhibiting drug, Epalrestat.

A non-invasive, multi-target approach to treat diabetic retinopathy.

Hyperglycemia invoke number of pathways resulting in development of diabetic retinopathy (DR), including protein kinase C activation, increased expression of VEGF, advanced glycation end product (AGEs) formation and activation of polyol pathway, among which the pathophysiology of aldose reductase (ALR2) of the polyol pathway is evident by more than a decade of research. Subtle involvement of ALR2 in invoking various pathways of diabetic complications has caused an increase in attention towards the identification of novel aldose reductase inhibitors (ARIs). Numerous ARIs of different classes were employed in the treatment of diabetic complications initially, but few came into light as drugs. Though no ALR2 inhibitor has been used for the treatment or control of DR, Epalrestat has been used worldwide for treating diabetic neuropathy. This review critically analyses different treatments available for diabetic retinopathy, their limitations and the importance of the development of novel inhibitors of ALR2 that could prevent progression of DR, by causing a direct or indirect effect on controlling factors associated with DR.

Ligand Based-Pharmacophore Modeling and Extended Bi oactivity Prediction for Salinosporamide A, B and C from Marine Actino mycetes Salinispora tropica.

AIM AND OBJECTIVE: Actinomycetes produce structurally unique secondary metabolites with pharmaceutically essential bioactivities. Salinispora, an obligate marine actinomycete, produces structurally varied and unique secondary metabolites. There is plenty of scope for development of drugs from the novel compounds isolated from Salinispora. Anticancer, antibacterial and anti-protozoa activities have been shown for Salinosporamides A, B and C, the secondary metabolites identified from Salinispora, which make them interesting subjects for further extended biological activity prediction. MATERIAL AND METHODS: An in silico ligand based-pharmacophore approach was used for the prediction of extended biological targets for salinosporamide A, B and C. Pharmacophore models of salinosporamide A, B and C were generated individually and screened against known drug databases. The drugs with best fitness score were shortlisted, and their respective targets pertaining to their bioactivity were retrieved. The predicted biological drug targets were docked with salinosporamide A, B and C for validation. RESULTS: The glucocorticoid receptor and methionine aminopeptidase 2 showed good docking score and binding energy with salinosporamide A, B and C. Molecular dynamics studies of the protein-ligand complexes showed stable interactions suggesting that the predicted new targets for salinosporamides might be promising. CONCLUSIONS: The glucocorticoid receptor and methionine aminopeptidase 2 could be possible new drug targets of bioactivity of salinosporamides. These proteins could be the druggable targets for antiinflammatory and anticancer activity of salinosporamides.

Pterostilbene-mediated Nrf2 activation: Mechanistic insights on Keap1:Nrf2 interface.

The discovery of Keap1-Nrf2 protein-protein interaction (PPI) inhibitors has become a promising strategy to develop novel lead molecules against variety of stress. Hence, Keap1-Nrf2 system plays an important role in oxidative/electrophilic stress associated disorders. Our earlier studies identified pterostilbene (PTS), a natural analogue of resveratrol, as a potent Nrf2 activator and Keap1-Nrf2 PPI inhibitor as assessed by luciferase complementation assay. In this study, we further identified the potential of PTS in Nrf2 activation and ARE-driven downstream target genes expression by nuclear translocation experiments and ARE-luciferase reporter assay, respectively. Further, the luciferase complementation assay identified that PTS inhibits Keap1-Nrf2 PPI in both dose and time-dependent manner. Computational studies using molecular docking and dynamic simulation revealed that PTS directly interacts with the basic amino acids of kelch domain of Keap1 and perturb Keap1-Nrf2 interaction pattern. This manuscript not only shows the binding determinants of Keap1-Nrf2 proteins but also provides mechanistic insights on Nrf2 activation potential of PTS.

Inhibition of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis: in silico screening and in vitro validation.

Tuberculosis, caused by Mycobacterium tuberculosis, remains a serious global health threat, highlighting the urgent need for novel antituberculosis drugs. The shikimate pathway, responsible for aromatic amino acid biosynthesis, is required for the growth of Mycobacterium tuberculosis and is a potential drug target. 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (mtDAH7Ps) catalyzes the first step in shikimate pathway. E-pharmacophore models for inhibitors of mtDAH7Ps - tyrosine, phenylalanine, phosphoenolpyruvate and (2S)-2,7-bis(phosphonooxy)heptanoic acid were screened against ZINC synthetic and natural compounds databases. The shortlisted compounds were subjected to induce fit docking and validated by Prime/Molecular Mechanics Generalized Born Surface Area calculation to predict ligand binding energy and ligand strain energy for ligand and receptor. The lead compounds were screened for their inhibitory activity against purified mtDAH7Ps enzyme. Lead compounds inhibited mtDAH7Ps in a concentration-dependent manner; with an IC50 value of 21 µM, 42 µM and 54 µM for α-Tocopherol, rutin and 3-Pyridine carboxyaldehyde respectively. Molecular Dynamics analysis for 50 ns of the active compounds-mtDAH7Ps complexes showed that the backbone of mtDAH7Ps was stable. These results suggest that α-tocopherol, 3 - Pyridine carboxyaldehyde and rutin could be novel drug leads to inhibit mtDAH7Ps in M. tuberculosis.

Identification of natural compound inhibitors for multidrug efflux pumps of Escherichia coli and Pseudomonas aeruginosa using in silico high-throughput virtual screening and in vitro validation.

Pseudomonas aeruginosa and Escherichia coli are resistant to wide range of antibiotics rendering the treatment of infections very difficult. A main mechanism attributed to the resistance is the function of efflux pumps. MexAB-OprM and AcrAB-TolC are the tripartite efflux pump assemblies, responsible for multidrug resistance in P. aeruginosa and E. coli respectively. Substrates that are more susceptible for efflux are predicted to have a common pharmacophore feature map. In this study, a new criterion of excluding compounds with efflux substrate-like features was used, thereby refining the selection process and enriching the inhibitor identification process. An in-house database of phytochemicals was created and screened using high-throughput virtual screening against AcrB and MexB proteins and filtered by matching with the common pharmacophore models (AADHR, ADHNR, AAHNR, AADHN, AADNR, AAADN, AAADR, AAANR, AAAHN, AAADD and AAADH) generated using known efflux substrates. Phytochemical hits that matched with any one or more of the efflux substrate models were excluded from the study. Hits that do not have features similar to the efflux substrate models were docked using XP docking against the AcrB and MexB proteins. The best hits of the XP docking were validated by checkerboard synergy assay and ethidium bromide accumulation assay for their efflux inhibition potency. Lanatoside C and diadzein were filtered based on the synergistic potential and validated for their efflux inhibition potency using ethidium bromide accumulation study. These compounds exhibited the ability to increase the accumulation of ethidium bromide inside the bacterial cell as evidenced by these increase in fluorescence in the presence of the compounds. With this good correlation between in silico screening and positive efflux inhibitory activity in vitro, the two compounds, lanatoside C and diadzein could be promising efflux pump inhibitors and effective to use in combination therapy against drug resistant strains of P. aeruginosa and E. coli.

Biologically active ligands for yersinia outer protein H (YopH): feature based pharmacophore screening, docking and molecular dynamics studies.

Yersinia pestis, a Gram negative bacillus, spreads via lymphatic to lymph nodes and to all organs through the bloodstream, causing plague. Yersinia outer protein H (YopH) is one of the important effector proteins, which paralyzes lymphocytes and macrophages by dephosphorylating critical tyrosine kinases and signal transduction molecules. The purpose of the study is to generate a three-dimensional (3D) pharmacophore model by using diverse sets of YopH inhibitors, which would be useful for designing of potential antitoxin. In this study, we have selected 60 biologically active inhibitors of YopH to perform Ligand based pharmacophore study to elucidate the important structural features responsible for biological activity. Pharmacophore model demonstrated the importance of two acceptors, one hydrophobic and two aromatic features toward the biological activity. Based on these features, different databases were screened to identify novel compounds and these ligands were subjected for docking, ADME properties and Binding energy prediction. Post docking validation was performed using molecular dynamics simulation for selected ligands to calculate the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF). The ligands, ASN03270114, Mol_252138, Mol_31073 and ZINC04237078 may act as inhibitors against YopH of Y. pestis.

Biological activity of sporolides A and B from Salinispora tropica: in silico target prediction using ligand-based pharmacophore mapping and in vitro activity validation on HIV-1 reverse transcriptase.

Sporolides A and B are novel polycyclic macrolides from the obligate marine actinomycetes, Salinispora tropica. The unique and novel structure of sporolides makes them interesting candidates for targeting diverse biological activities. Biological target prediction of sporolides was carried out using ligand-based pharmacophore screening against known inhibitors and drugs. Validation of pharmacophore screening was carried out for the identified hits. New biological targets predicted for sporolides using this method were HIV-1 reverse transcriptase, adenosine A3 receptor, endothelin receptor ET-A, oxytocin receptor, voltage-gated L-type calcium channel α-1C subunit/calcium channel α/Δ subunit 1. Drug-likeness properties were predicted for the selected compounds using QikProp module. Sporolides A and B showed maximum docking score with HIV-1 reverse transcriptase. Structural interaction fingerprints analysis indicated similar binding pattern of the sporolides with the HIV-1 reverse transcriptase. Sporolide B exhibited good inhibitory activity against HIV-1 reverse transcriptase in in vitro fluorescent assay.

Comprehensive database of Chorismate synthase enzyme from shikimate pathway in pathogenic bacteria.

BACKGROUND: Infectious diseases are major public health problem. It is increasingly affecting more than 50 million people worldwide. Targeting shikimate pathway could be efficiently used for the development of broad spectrum antimicrobial compound against variety of infectious diseases. Chorismate synthase is an enzyme in shikimate pathway that catalyzes Phosphoenol pyruvate to chorismate in most of the prokaryotic bacteria. This step is crucial for its growth, since Chorismate acts as a precursor molecule for the synthesis of aromatic amino acids. Hence, we present a comprehensive database of Chorismate Synthase Database (CSDB) which is a manually curated database. It provides information on the sequence, structure and biological activity of chorismate synthase from shikimate pathway of pathogenic bacteria. Design of suitable inhibitors for this enzyme, hence could be a probable solution to destroy its proteomic machinery and thereby inhibit the bacterial growth. DESCRIPTION: The aim of this study was to characterise chorismate synthase enzyme belonging to pathogenic bacteria to analysis the functional and structural characterization of chorismate synthase is very important for both structure-based and ligand based drug design. CONCLUSIONS: The broad range of data easy to use user interface makes csdb.in a useful database for researchers in designing drugs.

High-throughput virtual screening and docking studies of matrix protein vp40 of ebola virus.

Ebolavirus, a member of the Filoviridae family of negative-sense RNA viruses, causes severe haemorrhagic fever leading up to 90% lethality. Ebolavirus matrix protein VP40 is involved in the virus assembly and budding process. The RNA binding pocket of VP40 is considered as the drug target site for structure based drug design. High Throughput Virtual Screening and molecular docking studies were employed to find the suitable inhibitors against VP40. Ten compounds showing good glide score and glide energy as well as interaction with specific amino acid residues were short listed as drug leads. These small molecule inhibitors could be potent inhibitors for VP40 matrix protein by blocking virus assembly and budding process.

In vitro antimicrobial activity on clinical microbial strains and antioxidant properties of Artemisia parviflora.

BACKGROUND: Artemisia parviflora leaf extracts were evaluated for potential antimicrobial and antioxidant properties. Antimicrobial susceptibility assay was performed against ten standard reference bacterial strains. Antioxidant activity was analyzed using the ferric thiocyanate and 2, 2-Diphenyl-1-Picrylhydrazyl (DPPH) assays. Radical scavenging activity and total phenolic content were compared. Phytochemical analyses were performed to identify the major bioactive constitution of the plant extract. RESULTS: Hexane, methanol and ethyl acetate extracts of A. parviflora leaves exhibited good activity against the microorganisms tested. The n-hexane extract of A. parviflora showed high inhibition of the growth of Pseudomonas aeruginosa, Escherichia coli and Shigella flexneri. Methanol extract showed strong radical scavenging and antioxidant activity, other extracts showed moderate antioxidant activity. The major derivatives present in the extracts are of terpenes, steroids, phenols, flavonoids, tannins and volatile oil. CONCLUSIONS: The results obtained with n-hexane extract were particularly significant as it strongly inhibited the growth of P. aeruginosa, E. coli and S. flexneri. The major constituent of the n-hexane extract was identified as terpenes. Strong antioxidant activity could be observed with all the individual extracts. The antimicrobial and antioxidant property of the extracts were attributed to the secondary metabolites, terpenes and phenolic compounds present in A. parviflora and could be of considerable interest in the development of new drugs.

In vitro antifungal activity of indirubin isolated from a South Indian ethnomedicinal plant Wrightia tinctoria R. Br.

ETHNOPHARMACOLOGICAL RELEVANCE: Acalypha indica, Cassia alata, Lawsonia inermis, Punica granatum, Thespesia populnea and Wrightia tinctoria are folklore medicines extensively used in the treatment of ringworm infections and skin related diseases in Tamil Nadu, India. AIM: The present study was designed to investigate the in vitro antifungal activity of certain medicinal plants and the pure compound indirubin isolated from Wrightia tinctoria. MATERIALS AND METHODS: The hexane, chloroform, methanol and ethanol extracts of six different plants were investigated against dermatophytes, non-dermatophytes and yeasts. Chloroform extract of Wrightia tinctoria leaf was fractionated using column chromatography and the major compound was identified using spectroscopic techniques. Antifungal activity was studied by spore germination test using agar dilution method. The minimum inhibitory concentration (MIC) was determined using broth microdilution method. RESULTS: Wrightia tinctoria showed promising activity against dermatophytic and non-dermatophytic fungi. Leaf chloroform extract showed activity at 0.5 mg/ml against Trichophyton rubrum, Epidermophyton floccosum, Aspergillus niger and Scopulariopsis brevicaulis. The major compound, identified as indirubin, exhibited activity against dermatophytes such as Epidermophyton floccosum (MIC=6.25 µg/ml); Trichophyton rubrum and Trichophyton tonsurans (MIC=25 µg/ml); Trichophyton mentagrophytes and Trichophyton simii (MIC=50 µg/ml). It was also active against non-dermatophytes (Aspergillus niger, Candida albicans and Cryptococcus sp.) within a MIC range of 0.75-25 µg/ml. CONCLUSION: The indole compound indirubin from Wrightia tinctoria showed antifungal activity and may be useful in the treatment of dermatophytosis.

Antibacterial activity of Artemisia nilagirica leaf extracts against clinical and phytopathogenic bacteria.

BACKGROUND: The six organic solvent extracts of Artemisia nilagirica were screened for the potential antimicrobial activity against phytopathogens and clinically important standard reference bacterial strains. METHODS: The agar disk diffusion method was used to study the antibacterial activity of A. nilagirica extracts against 15 bacterial strains. The Minimum Inhibitory Concentration (MIC) of the plant extracts were tested using two fold agar dilution method at concentrations ranging from 32 to 512 microg/ml. The phytochemical screening of extracts was carried out for major phytochemical derivatives in A. nilagirica. RESULTS: All the extracts showed inhibitory activity for gram-positive and gram-negative bacteria except for Klebsiella pneumoniae, Enterococcus faecalis and Staphylococcus aureus. The hexane extract was found to be effective against all phytopathogens with low MIC of 32 microg/ml and the methanol extract exhibited a higher inhibition activity against Escherichia coli, Yersinia enterocolitica, Salmonella typhi, Enterobacter aerogenes, Proteus vulgaris, Pseudomonas aeruginosa (32 microg/ml), Bacillus subtilis (64 microg/ml) and Shigella flaxneri (128 microg/ml). The phytochemical screening of extracts answered for the major derivative of alkaloids, amino acids, flavonoids, phenol, quinines, tannins and terpenoids. CONCLUSION: All the extracts showed antibacterial activity against the tested strains. Of all, methanol and hexane extracts showed high inhibition against clinical and phytopathogens, respectively. The results also indicate the presence of major phytochemical derivatives in the A. nilagirica extracts. Hence, the isolation and purification of therapeutic potential compounds from A. nilagirica could be used as an effective source against bacterial diseases in human and plants.

Utilization of catechin and its metabolites by Bradyrhizobium japonicum.

Catechin, a condensed tannin was utilized as sole carbon source by Bradyrhizobium japonicum. Protocatechuic acid, phloroglucinolcarboxylic acid, phloroglucinol, resorcinol and hydroxyquinol were identified as intermediates of catechin degradation. The aromatic substrates favoured good growth up to 5 or 10 mM: . B. japonicum tolerated up to 50 mM: catechin and phloroglucinolcarboxylic acid, 40 mM: phloroglucinol and resorcinol, 30mM: protocatechuic acid and 10 mM: hydroxyquinol. Catechin-induced cells oxidized catechin more rapidly than uninduced cells. The two final ring compounds of the catechin catabolic pathway, protocatechuic acid and hydroxyquinol, were oxidized differentially. The enzymes of the catechin degradative pathway were inducible in B. japonicum.