Rukmankesh Mehra

Capsaicin, a novel inhibitor of the NorA efflux pump, reduces the intracellular invasion of Staphylococcus aureus

OBJECTIVES To delineate the role of capsaicin (8-methyl-N-vanillyl-6-nonenamide) as an inhibitor of the NorA efflux pump and its impact on invasion of macrophages by Staphylococcus aureus. METHODS Capsaicin in combination with ciprofloxacin was tested for activity against S. aureus SA-1199B (NorA overproducing), SA-1199 (wild-type) and SA-K1758 (norA knockout). The role of NorA in the intracellular invasion of S. aureus and the ability of capsaicin to inhibit this invasion was established in J774 macrophage cell lines. The three-dimensional structure of NorA was predicted using an in silico approach and docking studies of capsaicin were performed. RESULTS Capsaicin significantly reduced the MIC of ciprofloxacin for S. aureus SA-1199 and SA-1199B. Furthermore, capsaicin also extended the post-antibiotic effect of ciprofloxacin by 1.1 h at MIC concentration. There was a decrease in mutation prevention concentration of ciprofloxacin when combined with capsaicin. Inhibition of ethidium bromide efflux by NorA-overproducing S. aureus SA-1199B confirmed the role of capsaicin as a NorA efflux pump inhibitor (EPI). The most significant finding of this study was the ability of capsaicin to reduce the intracellular invasion of S. aureus SA-1199B (NorA overproducing) in J774 macrophage cell lines by 2 log(10). CONCLUSIONS This study, for the first time, has shown that capsaicin, a novel EPI, not only inhibits the NorA efflux pump of S. aureus but also reduces the invasiveness of S. aureus, thereby reducing its virulence.

Molecular characterization of UGT94F2 and UGT86C4, two glycosyltransferases from Picrorhiza kurrooa: comparative structural insight and evaluation of substrate recognition.

Uridine diphosphate glycosyltransferases (UGTs) are pivotal in the process of glycosylation for decorating natural products with sugars. It is one of the versatile mechanisms in determining chemical complexity and diversity for the production of suite of pharmacologically active plant natural products. Picrorhiza kurrooa is a highly reputed medicinal herb known for its hepato-protective properties which are attributed to a novel group of iridoid glycosides known as picrosides. Although the plant is well studied in terms of its pharmacological properties, very little is known about the biosynthesis of these important secondary metabolites. In this study, we identified two family-1 glucosyltransferases from P. kurrooa. The full length cDNAs of UGT94F4 and UGT86C4 contained open reading frames of 1455 and 1422 nucleotides, encoding polypeptides of 484 and 473 amino acids respectively. UGT94F2 and UGT86C4 showed differential expression pattern in leaves, rhizomes and inflorescence. To elucidate whether the differential expression pattern of the two Picrorhiza UGTs correlate with transcriptional regulation via their promoters and to identify elements that could be recognized by known iridoid-specific transcription factors, upstream regions of each gene were isolated and scanned for putative cis-regulatory elements. Interestingly, the presence of cis-regulatory elements within the promoter regions of each gene correlated positively with their expression profiles in response to different phytohormones. HPLC analysis of picrosides extracted from different tissues and elicitor-treated samples showed a significant increase in picroside levels, corroborating well with the expression profile of UGT94F2 possibly indicating its implication in picroside biosynthesis. Using homology modeling and molecular docking studies, we provide an insight into the donor and acceptor specificities of both UGTs identified in this study. UGT94F2 was predicted to be an iridoid-specific glucosyltransferase having maximum binding affinity towards 7-deoxyloganetin while as UGT86C4 was predicted to be a kaempferol-specific glucosyltransferase. These are the first UGTs being reported from P. kurrooa.

Computationally Guided Identification of Novel Mycobacterium tuberculosis GlmU Inhibitory Leads, Their Optimization, and in Vitro Validation

Mycobacterium tuberculosis (Mtb) infections are causing serious health concerns worldwide. Antituberculosis drug resistance threatens the current therapies and causes further need to develop effective antituberculosis therapy. GlmU represents an interesting target for developing novel Mtb drug candidates. It is a bifunctional acetyltransferase/uridyltransferase enzyme that catalyzes the biosynthesis of UDP-N-acetyl-glucosamine (UDP-GlcNAc) from glucosamine-1-phosphate (GlcN-1-P). UDP-GlcNAc is a substrate for the biosynthesis of lipopolysaccharide and peptidoglycan that are constituents of the bacterial cell wall. In the current study, structure and ligand based computational models were developed and rationally applied to screen a drug-like compound repository of 20,000 compounds procured from ChemBridge DIVERSet database for the identification of probable inhibitors of Mtb GlmU. The in vitro evaluation of the in silico identified inhibitor candidates resulted in the identification of 15 inhibitory leads of this target. Literature search of these leads through SciFinder and their similarity analysis with the PubChem training data set (AID 1376) revealed the structural novelty of these hits with respect to Mtb GlmU. IC50 of the most potent identified inhibitory lead (5810599) was found to be 9.018 ± 0.04 μM. Molecular dynamics (MD) simulation of this inhibitory lead (5810599) in complex with protein affirms the stability of the lead within the binding pocket and also emphasizes on the key interactive residues for further designing. Binding site analysis of the acetyltransferase pocket with respect to the identified structural moieties provides a thorough analysis for carrying out the lead optimization studies.

Anti-asthmatic activity of azepino [2, 1-b] quinazolones, synthetic analogues of vasicine, an alkaloid from Adhatoda vasica

Asthma is characterized by persistent airway inflammation caused by over expression of pro-inflammatory immune response, predominantly by eosinophils and lymphocytes. Lymphocytes (CD4+ Th2) have been documented to be responsible for the pathogenesis of asthma by secreting Th2 cytokines and activating eosinophils, leading to airway hypersensitivity. Secretion of Th2 cytokines has been shown critical for the induction of the characteristic airway inflammation in humans and animal models of asthma. These cytokines influence the inflammatory response and lead to the pathological changes associated with asthma. In the present study, 10 azepino [2,1-b] quinazolone derivatives (R1 to R10) were synthesised and evaluated for their anti-asthmatic activity using a murine model of asthma. The compounds R2, R4, R6, R7 and R8 caused a notable decrease Th2 cytokine secretion and eosinophilia in asthma-induced animals. However, the decrease was highly significant in case of R8-treated animals. Crystal structure of R8 was made by X-ray crystallography. Molecular modelling studies were done for the compound R8 with transcription factors STAT6 and GATA3 which are the main transcription factors responsible for Th2 cell differentiation. Also the pharmacokinetics of R8 was carried out in mice after oral and intravenous administrations.

Identification and optimization of Escherichia coli GlmU inhibitors: an in silico approach with validation thereof.

Bacterial infections are causing havoc on the populace. Continuous rising of antibiotic resistance in bacteria causes pressing requirement of new drugs and drug therapies that are effective against these multidrug resistance bacteria. GlmU, which is a bifunctional acetyltransferase/uridyltransferase enzyme, is novel target to treat bacterial infections. An effort has been made to identify and develop novel inhibitors of acetyltransferase activity of Escherichia coli (Ec) GlmU protein. In silico approach has been applied to screen chemical library of 50,000 drug-like compounds procured from ChemBridge and ChemDiv databases. This chemical library was screened by using a combination of ligand guided and structure guided techniques. In vitro evaluation of the in silico identified hits helped in the discovery of 8 promising inhibitors of acetyltransferase activity of Ec GlmU. Structure guided lead optimization strategy was adopted based on the acetyltransferase binding site analysis, that presented the scope of modification around three different structural moieties identified through in vitro hits. In addition, molecular dynamics studies revealed the stability of the protein-inhibitor complexes of the two most promising inhibitors identified in this study.

Benzothiazole Derivative as a Novel Mycobacterium tuberculosis Shikimate Kinase Inhibitor: Identification and Elucidation of Its Allosteric Mode of Inhibition

Mycobacterium tuberculosis shikimate kinase (Mtb-SK) is a key enzyme involved in the biosynthesis of aromatic amino acids through the shikimate pathway. Since it is proven to be essential for the survival of the microbe and is absent from mammals, it is a promising target for anti-TB drug discovery. In this study, a combined approach of in silico similarity search and pharmacophore building using already reported inhibitors was used to screen a procured library of 20,000 compounds of the commercially available ChemBridge database. From the in silico screening, 15 hits were identified, and these hits were evaluated in vitro for Mtb-SK enzyme inhibition. Two compounds presented significant enzyme inhibition with IC50 values of 10.69 ± 0.9 and 46.22 ± 1.2 μM. The best hit was then evaluated for the in vitro mode of inhibition where it came out to be an uncompetitive and noncompetitive inhibitor with respect to shikimate (SKM) and ATP, respectively, suggesting its binding at an allosteric site. Potential binding sites of Mtb-SK were identified which confirmed the presence of an allosteric binding pocket apart from the ATP and SKM binding sites. The docking simulations were performed at this pocket in order to find the mode of binding of the best hit in the presence of substrates and the products of the enzymatic reaction. Molecular dynamics (MD) simulations elucidated the probability of inhibitor binding at the allosteric site in the presence of ADP and shikimate-3-phosphate (S-3-P), that is, after the formation of products of the reaction. The inhibitor binding may prevent the release of the product from Mtb-SK, thereby inhibiting its activity. The binding stability and the key residue interactions of the inhibitor to this product complex were also revealed by the MD simulations. Residues ARG43, ILE45, and PHE57 were identified as crucial that were involved in interactions with the best hit. This is the first report of an allosteric binding site of Mtb-SK, which could largely address the selectivity issue associated with kinase inhibitors.

Synthesis and biological evaluation of substituted N-alkylphenyl-3,5-dinitrobenzamide analogs as anti-TB agents

Here, a medicinal chemistry study of an N-alkylphenyl-3,5-dinitrobenzamide (DNB) scaffold as a potent anti-TB agent is presented. A series of chemical modifications were performed and forty-three new molecules were synthesized to study the structure–activity relationship (SAR) by evaluating against a sensitive strain (H37Rv) of Mycobacterium tuberculosis (MTB). Potent DNB analogs 4b, 7a, 7c, 7d, 7j, 7r and 9a were further tested against resistant strains of MTB. Their intracellular as well as bactericidal potential was also evaluated. Cytotoxicity and in vivo pharmacokinetic studies suggested that DNB analogs have an acceptable safety index, in vivo stability and bio-availability. From the present work, two compounds 7a and 7d have shown nanomolar to sub micro-molar MIC in extracellular and intracellular assays.

Discovery of novel small molecule EGFR inhibitory leads by structure and ligand-based virtual screening

In modern drug discovery, virtual screening is an attractive and cost-effective approach, which is widely applied to filter chemical compound libraries for the identification of novel inhibitors. Epidermal growth factor receptor protein is a well reported anticancer molecular target due to its over expression and mutation in many solid tumours. The decline in epidermal growth factor receptor activity by small molecules has proved to be an effective treatment for cancer. To design inhibitors for this target, the crystal structures information of epidermal growth factor receptors, co-crystallized with its inhibitors, provide a gateway to perform receptor-based drug designing studies, whereas the inhibitors with their biological activity reported in literature provide information to carry out ligand-based drug designing studies. In the present study, the drug designing methods were strategically combined and used parallely on a library of 50,000 drug-like compounds from ChemDiv and ChemBridge database, for the selection of potential inhibitors of epidermal growth factor receptor. This resulted in the identification of 200 common hits, which were further pruned down to 87, based on the knowledge about the key interaction of known epidermal growth factor receptor inhibitors with Met793. These 87 hits were clustered into 12 different structural moieties. In vitro studies of some of these hits were also carried out in order to validate the screening approach. Further, the lead optimization studies were performed by analyzing the binding poses of all the identified structural moieties in order to ascertain the scope of modifications around these moieties. Molecular dynamics simulation studies further revealed some important residues of the target which may be helpful for providing stability to the enzyme-inhibitor complex. These findings could be very much helpful for a medicinal chemist to design a novel potent inhibitor of epidermal growth factor receptor.

Anti-tubercular drug discovery: in silico implications and challenges

Abstract Tuberculosis (TB) has been reported as a major public health concern, especially in the developing countries. WHO report on tuberculosis 2016 shows a high mortality rate caused by TB leading to 1.8 million deaths worldwide (including deaths due to TB in HIV positive individuals), which is one of the top 10 causes of mortality in 2015. However, the main therapy used for the treatment of TB is still the Direct Observed Therapy Short‐course (DOTS) that consists of four main first‐line drugs. Due to the prolonged and unorganized use of these drugs, Mycobacterium tuberculosis (Mtb) has developed drug‐resistance against them. To overcome this drug‐resistance, efforts are continuously being made to develop new therapeutics. New drug‐targets of Mtb are pursued by the researchers to develop their inhibitors. For this, new methodologies that comprise of the computational drug designing techniques are vigorously applied. A major limitation that is found with these techniques is the inability of the newly identified target‐based inhibitors to inhibit the whole cell bacteria. A foremost factor for this limitation is the inability of these inhibitors to penetrate the bacterial cell wall. In this regard, various strategies to overcome this limitation have been discussed in detail in this review, along with new targets and new methodologies. A bunch of in silico tools available for the prediction of physicochemical properties that need to be explored to deal with the permeability issue of the Mtb inhibitors has also been discussed. Graphical abstract Figure. No Caption available.