Rupinder Tewari

Panjab University, Chandīgarh, Union Territory of Chandigarh, India

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Publications (42)98.4 Total impact

  • [show abstract] [hide abstract]
    ABSTRACT: Optimization of cultural conditions for enhanced cellulase production by Aspergillus niger NS-2 were studied under solid-state fermentation. Significant increase in yields (CMCase 463.9 ± 20.1 U/g, FPase 101.1 ± 3.5 U/g and β-glucosidase 99 ± 4.0 U/g) were obtained under optimized conditions. Effect of different nutritional parameters was studied to induce the maximum production of cellulase complex. Scale-up studies for enzyme production process were carried out. Characterization studies showed that enzymes produced by A. niger NS-2 were highly temperature- and pH stable. At 50 °C, the half life for CMCase, FPase, β-glucosidase were approximately 240 h. Cellulases from A. niger NS-2 were stable at 35 °C for 24 h over a broader pH range of 3.0-9.0. We examined the feasibility of using steam pretreatment to increase the saccharification yields from various lignocellulosic residues for sugar release which can potentially be used in bioethanol production. Saccharification of pretreated dry potato peels, carrot peels, composite waste mixture, orange peels, onion peels, banana peels, pineapple peels by crude enzyme extract from A. niger NS-2, resulted in very high cellulose conversion efficiencies of 92-98 %.
    Applied biochemistry and biotechnology 09/2013; · 1.94 Impact Factor
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    ABSTRACT: The emergence of multi-drug-resistant bacterial pathogens along with labor-intensive and time-consuming drug discovery methods has put an emphasis on alternative approaches which can overcome these drawbacks. One such approach is in silico identification of novel bacterial inhibitors using structure-based drug design methodology. In the present study, novel inhibitors have been proposed against two essential enzymes (MurA and MurZ) involved in the biosynthesis of cell wall of Enterococcus faecalis, a serious nosocomial bacterial pathogen. Homology models of MurA and MurZ of E. faecalis were constructed using template MurA of Enterobacter cloacae and Haemophilus influenza, respectively. The validation of the refined models, using Ramachandran, Errat and ProSA energy plots, showed that constructed models were reliable and of good quality. The active site amino acid residues, as predicted by CASTp server, were in accordance with the residues identified from MurA crystal structures available for other bacteria. The present study revealed for the first time the importance of two additional amino acid residues (Thr305 and Tyr329) in MurA and MurZ enzymes, which might be crucial for the binding of ligands/inhibitors with the target. Based on the GLIDE score and interaction profile, 5-sulfonoxyanthranilic acid derivatives, T6361 and T6362 were found to be the potential inhibitors of MurA and MurZ enzymes.
    Medicinal Chemistry Research 09/2013; · 1.61 Impact Factor
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    ABSTRACT: Emergence of the multidrug-resistant pathogens has rendered the current therapies ineffective thereby, resulting in the need for new drugs and drug targets. The accumulating protein sequence data has initiated a drift from classical drug discovery protocols to structure-based drug designing. In the present study, in silico subtractive genomics approach was implemented to find a set of potential drug targets present in an opportunist bacterial pathogen, Acinetobacter baumannii (A. baumannii). Out of the 43 targets identified, further studies for protein model building and lead-inhibitor identification were carried out on two cell-essential targets, MurA and MurB enzymes (of A. baumannii designated as MurAAb and MurBAb) involved in the peptidoglycan biosynthesis pathway of bacteria. The homology model built for each of them was further refined and validated using various available programs like PROCHECK, Errat, ProSA energy plots, etc. Compounds showing activity against MurA and MurB enzymes of other organisms were collected from the literature and were docked into the active site of MurAAb and MurBAb enzymes. Three inhibitors namely, T6361, carbidopa, and aesculin, showed maximum Glide score, hydrogen bonding interactions with the key amino acid residues of both the enzymes and acceptable ADME properties. Furthermore, molecular dynamics simulation studies on MurAAb-T6361 and MurBAb-T6361 complexes suggested that the ligand has a high binding affinity with both the enzymes and the hydrogen bonding with the key residues were stable in the dynamic condition also. Therefore, these ligands have been propsed as dual inhibitors and promising lead compounds for the drug design against MurAAb and MurBAb enzymes.
    Applied biochemistry and biotechnology 07/2013; · 1.94 Impact Factor
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    ABSTRACT: BACKGROUND: Mycobacterium tuberculosis (M.tb) is the causative agent of tuberculosis, killing ~1.7 million people annually. The remarkable capacity of this pathogen to escape the host immune system for decades and then to cause active tuberculosis disease, makes M.tb a successful pathogen. Currently available anti-mycobacterial therapy has poor compliance due to requirement of prolonged treatment resulting in accelerated emergence of drug resistant strains. Hence, there is an urgent need to identify new chemical entities with novel mechanism of action and potent activity against the drug resistant strains. RESULTS: This study describes novel computational models developed for predicting inhibitors against both replicative and non-replicative phase of drug-tolerant M.tb under carbon starvation stage. These models were trained on highly diverse dataset of 2135 compounds using four classes of binary fingerprint namely PubChem, MACCS, EState, SubStructure. We achieved the best performance Matthews correlation coefficient (MCC) of 0.45 using the model based on MACCS fingerprints for replicative phase inhibitor dataset. In case of non-replicative phase, Hybrid model based on PubChem, MACCS, EState, SubStructure fingerprints performed better with maximum MCC value of 0.28. In this study, we have shown that molecular weight, polar surface area and rotatable bond count of inhibitors (replicating and non-replicating phase) are significantly different from non-inhibitors. The fragment analysis suggests that substructures like hetero_N_nonbasic, heterocyclic, carboxylic_ester, and hetero_N_basic_no_H are predominant in replicating phase inhibitors while hetero_O, ketone, secondary_mixed_amine are preferred in the non-replicative phase inhibitors. It was observed that nitro, alkyne, and enamine are important for the molecules inhibiting bacilli residing in both the phases. In this study, we introduced a new algorithm based on Matthews correlation coefficient called MCCA for feature selection and found that this algorithm is better or comparable to frequency based approach. CONCLUSION: In this study, we have developed computational models to predict phase specific inhibitors against drug resistant strains of M.tb grown under carbon starvation. Based on simple molecular properties, we have derived some rules, which would be useful in robust identification of tuberculosis inhibitors. Based on these observations, we have developed a webserver for predicting inhibitors against drug tolerant M.tb H37Rv available at http://crdd.osdd.net/oscadd/mdri/.
    Chemistry Central Journal 03/2013; 7(1):49. · 1.31 Impact Factor
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    ABSTRACT: Aims: In view of the changing sensitivity pattern of Salmonella, this study was carried out to investigate the current antibiogram and clonal relatedness among the drug-resistant Salmonella enterica serovar Typhi in Northern India. Results: Re-emergence in the sensitivity to chloramphenicol and cotrimoxazole with increase in the resistance to various quinolones has been observed. The efficacy of nalidixic acid resistance to be used as a marker for decrease in sensitivity to ciprofloxacin may vary. Clonal differences on the basis of amplification of repetitive elements (rep-PCR) were found in the two different areas within the same region. Conclusions: The present study creates a paramount baseline for rationalizing the judicious use of quinolones and re-examine the use of chloramphenicol and cotrimoxazole. Molecular analysis of clinical Salmonella isolates depicts the clonal expansion of the isolates that may serve as a reference to which newer outbreak strains can be compared. rep-PCR techniques may be useful in molecular discrimination of isolates for better understanding of the Salmonella epidemiology and as a basis for development of rational control strategies.
    Microbial drug resistance (Larchmont, N.Y.) 01/2013; · 1.99 Impact Factor
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    ABSTRACT: Like any other enteric pathogen, Salmonella also encounters acidic stress in the stomach as well as within the host macrophage milieu. However, the pathogen is reported to combat this stress through acid tolerance response (ATR), expressing a number of genes and eventually the proteins. Recently, an acid induced outer membrane phenotype encoded by fliC gene in Salmonella enterica serovar Typhi has been identified. In the present study, fliC gene was cloned to study its biological implications. The recombinant FliC (rFliC) protein was observed to stimulate the production of antibodies. These antibodies could also recognize the FliC protein (antigen) in the clinical samples i.e. blood samples from typhoid patents as well as healthy blood samples spiked with serovar Typhi. Moreover, the rFliC also reacted with the sera from patients suffering with typhoid fever indicating its in-vivo immunogenicity. Ex-vivo study revealed that rFliC has the potential to stimulate the macrophages to generate higher levels of inflammatory mediators such as malondialdehyde (MDA) and nitrite. The inflammatory potential of FliC was also confirmed in-vivo, by the paw oedema test as well as by flicking response of the inflamed paw indicating hyperalgesia occurring during inflammatory response. The findings of the present study indicate that acid induced FliC might be one of the factors enhancing the virulence of serovar Typhi under the host acidic conditions and may prove to be helpful in designing the prophylactic measures.
    AMB Express. 10/2012; 2(1):55.
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    ABSTRACT: Aspartate-semialdehyde dehydrogenase (Asd; ASADH; EC 1.2.1.11) is the enzyme that lies at the first branch point in the biosynthetic pathway of important amino acids including lysine and methionine and the cell-wall component diaminopimelate (DAP). The enzymatic reaction of ASADH is the reductive dephosphorylation of aspartyl-β-phosphate (ABP) to aspartate β-semialdehyde (ASA). Since the aspartate pathway is absolutely essential for the survival of many microbes and is absent in humans, the enzymes involved in this pathway can be considered to be potential antibacterial drug targets. In this work, the structure of ASADH from Mycobacterium tuberculosis H37Rv (Mtb-ASADH) has been determined in complex with glycerol and sulfate at 2.18 Å resolution and in complex with S-methyl-L-cysteine sulfoxide (SMCS) and sulfate at 1.95 Å resolution. The overall structure of Mtb-ASADH is similar to those of its orthologues. However, in the Mtb-ASADH-glycerol complex structure the glycerol molecule is noncovalently bound to the active-site residue Cys130, while in the Mtb-ASADH-SMCS complex structure the SMCS (Cys) is covalently linked to Cys130. The Mtb-ASADH-SMCS complex structurally mimics one of the intermediate steps in the proposed mechanism of ASADH enzyme catalysis. Comparison of the two complex structures revealed that the amino acids Glu224 and Arg249 undergo conformational changes upon binding of glycerol. Moreover, the structures reported here may help in the development of species-specific antibacterial drug molecules against human pathogens.
    Acta Crystallographica Section D Biological Crystallography 06/2012; 68(Pt 6):671-9. · 12.67 Impact Factor
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    ABSTRACT: Various agricultural and kitchen waste residues were assessed for their ability to support the production of a complete cellulase system by Aspergillus niger NS-2 in solid state fermentation. Untreated as well as acid and base-pretreated substrates including corn cobs, carrot peelings, composite, grass, leaves, orange peelings, pineapple peelings, potato peelings, rice husk, sugarcane bagasse, saw dust, wheat bran, wheat straw, simply moistened with water, were found to be well suited for the organism's growth, producing good amounts of cellulases after 96 h without the supplementation of additional nutritional sources. Yields of cellulases were higher in alkali treated substrates as compared to acid treated and untreated substrates except in wheat bran. Of all the substrates tested, wheat bran appeared to be the best suited substrate producing appreciable yields of CMCase, FPase and β-glucosidase at the levels of 310, 17 and 33 U/g dry substrate respectively. An evaluation of various environmental parameters demonstrated that appreciable levels of cellulases could be produced over a wide range of temperatures (20-50 °C) and pH levels (3.0-8.0) with a 1:1.5 to 1:1.75 substrate to moisture ratio.
    Waste Management 04/2012; 32(7):1341-6. · 2.49 Impact Factor
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    ABSTRACT: The effect of four phosphate solubilizing bacteria (PSB) was studied on growth and aloin-A content of Aloe barbadensis in soil containing tricalcium phosphate (TCP). PSB were identified based on 16S rRNA gene sequencing as Pseudomonas synxantha, Burkholderia gladioli, Enterobacter hormaechei and Serratia marcescens. These PSB solubilized 25-340 μg ml(-1) of TCP into the liquid phase. The treatment of plants with individual PSB or mixture of these increased soil available P, P uptake in plants and plant growth. The increase in aloin-A content due to higher plant biomass and unit biomass production was 673%, 294%, 276%, 119% and 108% in plants treated with a PSB consortium, P. synxantha, S. marcescens, B. gladioli, and E. hormaechei in TCP amended soil, respectively.
    Microbiological Research 03/2012; 167(6):358-63. · 1.99 Impact Factor
  • Acta Crystallographica Section D Biological Crystallography 02/2012; · 14.10 Impact Factor
  • Ankur Gautam, Praveen Rishi, Rupinder Tewari
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    ABSTRACT: The emergence of antibiotic resistance in bacterial pathogens has foxed the health organizations which are actively scrambling for solutions. The available data indicate an increased morbidity in infections often leading to mortality among patients where drug-resistant pathogens have negated the effect of the medicines. In the context of developing "novel bacterial inhibitors" for killing or arresting the growth of drug-resistant pathogens, UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is an enzyme that provides hope for the future. This enzyme catalyzes the first committed step in the biosynthesis of peptidoglycan, an integral and essential component of the bacterial cell wall. MurA enzyme is neither present nor required by mammals and shows poor homology with human proteins. Therefore, it is an ideal target for antibacterial chemotherapy. Till date, 18 structures of MurA (in native and ligand-bound forms) from different bacterial pathogens have been solved. In the last 2 years, eight structures of bacterial MurA have been submitted to the Protein Data Bank and many inhibitors discovered. The present review discusses the structural and functional features of MurA of bacterial pathogens along with the development of MurA-targeted inhibitors.
    Applied Microbiology and Biotechnology 08/2011; 92(2):211-25. · 3.69 Impact Factor
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    ABSTRACT: Biofertilizers offer alternative means to pro-moting cultivation of medicinal plants less dependent on chemical fertilizers. Present study was aimed at evaluating the potential of phosphate-solubilizing bacteria (PSB) Burkholderia gladioli MTCC 10216, B. gladioli MTCC 10217, Enterobacter aerogenes MTCC 10208 and Serratia marcescens MTCC 10238 for utilizing Mussoorie rock phosphate (MRP) to enhance plant growth, and stevioside (ST) and rebaudioside-A (R-A) contents of Stevia rebau-diana. The solubilization of MRP by PSB strains varied from 1.4 to 15.2 lg ml -1 , with the highest solubilization by Enterobacter aerogenes 10208. The PSB treatment increased the growth and ST and R-A contents of plants. Plant growth and stevioside contents were more pro-nounced with plants treated with a mixture of strains and grown in MRP amended soil compared to the unamended soil. The increment in shoot length (47.8%), root length (17.4%), leaf dry weight (164%), stem dry weight (116%), total shoot biomass (136%) resulted in enhanced produc-tivity of ST (291%) and R-A (575%) in plants inoculated with mixture of PSB as compared to the uninoculated plants. The soils of PSB treated plants contained more available P than the soils of uninoculated plants (increase of 86–576%). PSB inoculated plants also recorded higher P content (64–273% increase) compared to uninoculated plants. The PSB strains differed in the extent of rhizosphere colonization, carbon source utilization pattern and whole cell fatty acids methyl esters composition.
    Plant Growth Regulation 08/2011; 65(3-ISSN: 0167-6903 (Print) 1573-5087 (Online)):449-457. · 1.67 Impact Factor
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    Sanjeev Kumar, Rohit Sharma, Rupinder Tewari
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    ABSTRACT: The pharmaceutically important compound N-acetylglucosamine (NAG), is used in various therapeutic formulations, skin care products and dietary supplements. Currently, NAG is being produced by an environment-unfriendly chemical process using chitin, a polysaccharide present in abundance in the exoskeleton of crustaceans, as a substrate. In the present study, we report the potential of an eco-friendly biological process for the production of NAG using recombinant bacterial enzymes, chitinase (CHI) and chitobiase (CHB). The treatment of chitin with recombinant CHI alone produced 8% NAG and 72% chitobiose, a homodimer of NAG. However, supplementation of the reaction mixture with another recombinant enzyme, CHB, resulted in approximately six fold increase in NAG production. The product, NAG, was confirmed by HPLC, TLC and ESI-MS studies. Conditions are being optimized for increased production of NAG from chitin.
    Indian Journal of Microbiology 07/2011; 51(3):319-25. · 0.46 Impact Factor
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    ABSTRACT: The intracellular enzyme dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52) from Pseudomonas aeruginosa is a potential drug target because it is essential for the growth of bacteria while it is absent in humans. Therefore, in order to design new compounds using structure based approach for inhibiting the function of DHDPS from P. aeruginosa (Ps), we have cloned, characterized biochemically and biophysically and have determined its three-dimensional structure. The gene encoding DHDPS (dapA) was cloned in a vector pET-28c(+) and the recombinant protein was overexpressed in the Escherichia coli host. The K(m) values of the recombinant enzyme estimated for the substrates, pyruvate and (S)-aspartate-β-semialdehyde [(S)-ASA] were found to be 0.90±0.13 mM and 0.17±0.02 mM, respectively. The circular dichroism studies showed that the enzyme adopts a characteristic β/α conformation which is retained up to 65°C. The fluorescence data indicated the presence of exposed tryptophan residues in the enzyme. The three-dimensional structure determination showed that DHDPS forms a homodimer which is stabilized by several hydrogen bonds and van der Waals forces at the interface. The active site formed with residues Thr44, Tyr107 and Tyr133 is found to be stereochemically suitable for catalytic function. It may be noted that Tyr107 of the catalytic triad belongs to the partner molecule in the dimer. The structure of the complex of PsDHDPS with (S)-lysine determined at 2.65 Å resolution revealed the positions of three lysine molecules bound to the protein.
    International journal of biological macromolecules 03/2011; 48(5):779-87. · 2.37 Impact Factor
  • Archives of Agronomy and Soil Science. 01/2011;
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    ABSTRACT: Salmonella enterica has been reported to have evolved different strategies to subvert normal host cellular functions which allow it to enter into and proliferate within the host cells. Although low pH of stomach is a formidable barrier to infections, but majority of the Enterobacteriaceae family members exhibit strong innate resistance to low pH by expressing certain gene products involved in acid tolerance responses (ATR). In this brief report, we have isolated and characterized an over expressed outer membrane protein of Salmonella enterica serovar Typhi Ty2 grown under acidic conditions (pH 4.5). The protein band was excised and subjected to peptide mass fingerprinting (MALDI-TOF). The fragments obtained were BLAST using MASCOT search engine and it was identified as flagellin (fliC) gene product (53.2 kDa) consisting of 506 amino acid residues. Up-regulation of flagellin protein may influence the functional capacity of Salmonella enterica during the course of infection. Further, an attempt to knockout this gene may help in confirming the exclusive role of fliC gene product in the biological implications such as apoptosis, inflammation, cytokine production, adhesion and invasion which would help in better understanding of the host-pathogen interactions.
    Am. J. Biomed. Sci. Am. J. Biomed. Sci. 01/2011; 3(3):23-30.
  • Ankur Gautam, Rajan Vyas, Rupinder Tewari
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    ABSTRACT: The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade.
    Critical Reviews in Biotechnology 11/2010; 31(4):295-336. · 5.10 Impact Factor
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    Aarti Garg, Rupinder Tewari, Gajendra P S Raghava
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    ABSTRACT: Identification of novel drug targets and their inhibitors is a major challenge in the field of drug designing and development. Diaminopimelic acid (DAP) pathway is a unique lysine biosynthetic pathway present in bacteria, however absent in mammals. This pathway is vital for bacteria due to its critical role in cell wall biosynthesis. One of the essential enzymes of this pathway is dihydrodipicolinate synthase (DHDPS), considered to be crucial for the bacterial survival. In view of its importance, the development and prediction of potent inhibitors against DHDPS may be valuable to design effective drugs against bacteria, in general. This paper describes a methodology for predicting novel/potent inhibitors against DHDPS. Here, quantitative structure activity relationship (QSAR) models were trained and tested on experimentally verified 23 enzyme's inhibitors having inhibitory value (Ki) in the range of 0.005-22(mM). These inhibitors were docked at the active site of DHDPS (1YXD) using AutoDock software, which resulted in 11 energy-based descriptors. For QSAR modeling, Multiple Linear Regression (MLR) model was engendered using best four energy-based descriptors yielding correlation values R/q2 of 0.82/0.67 and MAE of 2.43. Additionally, Support Vector Machine (SVM) based model was developed with three crucial descriptors selected using F-stepping remove-one approach, which enhanced the performance by attaining R/q2 values of 0.93/0.80 and MAE of 1.89. To validate the performance of QSAR models, external cross-validation procedure was adopted which accomplished high training/testing correlation values (q2/r2) in the range of 0.78-0.83/0.93-0.95. Our results suggests that ligand-receptor binding interactions for DHDPS employing QSAR modeling seems to be a promising approach for prediction of antibacterial agents. To serve the experimentalist to develop novel/potent inhibitors, a webserver "KiDoQ" has been developed http://crdd.osdd.net/raghava/kidoq, which allows the prediction of Ki value of a new ligand molecule against DHDPS.
    BMC Bioinformatics 03/2010; 11:125. · 3.02 Impact Factor
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    BMC Bioinformatics. 01/2010; 11:53.
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    BMC Bioinformatics. 01/2010; 11:125.

Publication Stats

546 Citations
12k Downloads
5k Views
98.40 Total Impact Points

Institutions

  • 2000–2013
    • Panjab University
      • • Centre for Microbial Biotechnology
      • • Department of Biotechnology
      • • Department of Microbiology
      Chandīgarh, Union Territory of Chandigarh, India
  • 2010–2011
    • Bioinformatics Institute of India
      Noida, Uttar Pradesh, India
    • Institute of Microbial Technology
      • Bioinformatics Centre (IMTECH)
      Chandīgarh, Union Territory of Chandigarh, India
  • 2006
    • National Institute of Immunology
      New Dilli, NCT, India
  • 2001
    • Central University of Punjab
      BUP, Punjab, India