Pranav Kumar

Publications of Pranav Kumar

• In silico screening, structure-activity relationship, and biologic evaluation of selective pteridine reductase inhibitors targeting visceral leishmaniasis.

  Authors: Jaspreet Kaur, Pranav Kumar, Sargam Tyagi, Richa Pathak, Sanjay Batra, Prashant Singh, Neeloo Singh

  Antimicrobial agents and chemotherapy. 02/2011; 55(2):659-66.

  In this study we utilized the concept of rational drug design to identify novel compounds with optimal selectivity, efficacy and safety, which would bind to the target enzyme pteridine reductase 1In this study we utilized the concept of rational drug design to identify novel compounds with optimal selectivity, efficacy and safety, which would bind to the target enzyme pteridine reductase 1 (PTR1) in Leishmania parasites. Twelve compounds afforded from Baylis-Hillman chemistry were docked by using the QUANTUM program into the active site of Leishmania donovani PTR1 homology model. The biological activity for these compounds was estimated in green fluorescent protein-transfected L. donovani promastigotes, and the most potential analogue was further investigated in intracellular amastigotes. Structure-activity relationship based on homology model drawn on our recombinant enzyme was substantiated by recombinant enzyme inhibition assay and growth of the cell culture. Flow cytometry results indicated that 7-(4-chlorobenzyl)-3-methyl-4-(4-trifluoromethyl-phenyl)-3,4,6,7,8,9-hexahydro-pyrimido[1,2-a]pyrimidin-2-one (compound 7) was 10 times more active on L. donovani amastigotes (50% inhibitory concentration [IC(50)] = 3 μM) than on promastigotes (IC(50) = 29 μM). Compound 7 exhibited a K(i) value of 0.72 μM in a recombinant enzyme inhibition assay. We discovered that novel pyrimido[1,2-a]pyrimidin-2-one systems generated from the allyl amines afforded from the Baylis-Hillman acetates could have potential as a valuable pharmacological tool against the neglected disease visceral leishmaniasis.

• An orally effective dihydropyrimidone (DHPM) analogue induces apoptosis-like cell death in clinical isolates of Leishmania donovani overexpressing pteridine reductase 1.

  Authors: Neeloo Singh, Jaspreet Kaur, Pranav Kumar, Swati Gupta, Nasib Singh, Angana Ghosal, Avijit Dutta, Ashutosh Kumar, RamaPati Tripathi, Mohammad Siddiqi, Chitra Mandal, Anuradha Dube

  Parasitology research. 08/2009;

  The protozoan parasite Leishmania donovani is the causative agent of visceral leishmaniasis. The enzyme pteridine reductase 1 (PTR1) of L. donovani acts as a metabolic bypass for drugs targetingThe protozoan parasite Leishmania donovani is the causative agent of visceral leishmaniasis. The enzyme pteridine reductase 1 (PTR1) of L. donovani acts as a metabolic bypass for drugs targeting dihydrofolate reductase (DHFR); therefore, for successful antifolate chemotherapy to be developed against Leishmania, it must target both enzyme activities. Leishmania cells overexpressing PTR1 tagged at the N-terminal with green fluorescent protein were established to screen for proprietary dihydropyrimidone (DHPM) derivatives of DHFR specificity synthesised in our laboratory. A cell-permeable molecule with impressive antileishmanial in vitro and in vivo oral activity was identified. Structure activity relationship based on homology model drawn on our recombinant enzyme established the highly selective inhibition of the enzyme by this analogue. It was seen that the leishmanicidal effect of this analogue is triggered by programmed cell death mediated by the loss of plasma membrane integrity as detected by binding of annexin V and propidium iodide (PI), loss of mitochondrial membrane potential culminating in cell cycle arrest at the sub-G0/G1 phase and oligonucleosomal DNA fragmentation. Hence, this DHPM analogue [(4-fluoro-phenyl)-6-methyl-2-thioxo-1, 2, 3, 4-tetrahydropyrimidine-5-carboxylic acid ethyl ester] is a potent antileishmanial agent that merits further pharmacological investigation.

• Leishmania donovani pteridine reductase 1: Biochemical properties and structure-modeling studies.

  Authors: Pranav Kumar, Ashutosh Kumar, Shyam Sundar Verma, Namrata Dwivedi, Nasib Singh, Mohammad Imran Siddiqi, Rama Pati Tripathi, Anuradha Dube, Neeloo Singh

  Experimental parasitology. 07/2008;

  Pteridine reductase 1 (PTR1, EC 1.5.1.33) is a NADPH dependent short-chain reductase (SDR) responsible for the salvage of pterins in the protozoan parasite Leishmania. This enzyme acts as a metabolicPteridine reductase 1 (PTR1, EC 1.5.1.33) is a NADPH dependent short-chain reductase (SDR) responsible for the salvage of pterins in the protozoan parasite Leishmania. This enzyme acts as a metabolic bypass for drugs targeting dihydrofolate reductase, therefore, for successful antifolate chemotherapy to be developed against Leishmania, it must target both enzyme activities. Based on homology model drawn on recombinant pteridine reductase isolated from a clinical isolate of L. donovani, we carried out molecular modeling and docking studies with two compounds of dihydrofolate reductase specificity showing promising antileishmanial activity in vitro. Both the inhibitors appeared to fit well in the active pocket revealing the tight binding of the carboxylic acid ethyl ester group of pyridine moiety to pteridine reductase and identify the important interactions necessary to assist the structure based development of novel pteridine reductase inhibitors.

• Degradation of pteridine reductase 1 (PTR1) enzyme during growth phase in the protozoan parasite Leishmania donovani.

  Authors: Pranav Kumar, Shyam Sundar, Neeloo Singh

  Experimental parasitology. 07/2007; 116(2):182-9.

  Pteridine reductase 1 (PTR1) is an essential enzyme of pterin and folate metabolism in the protozoan parasite Leishmania. The present work is focused on the degradation of PTR1 during growth phase inPteridine reductase 1 (PTR1) is an essential enzyme of pterin and folate metabolism in the protozoan parasite Leishmania. The present work is focused on the degradation of PTR1 during growth phase in Leishmania donovani. Western blot analysis with PTR1-GFP transfected promastigotes revealed that PTR1 protein was degraded in the stationary phase of growth at the time when the parasites were undergoing metacyclogenesis. Fluorescence microscopy revealed cytoplasmic localization of GFP tagged protein extending to the flagellum in these stationary phase promastigotes, implying that degradation of the protein was not by the usual multivesicular tubule lysosome (MVT) pathway. A probable destruction box of nine amino acids Q63ADLSNVAK71 and possible lysine residue K156 was identified in L. donovani PTR1 to be the site for ubiquitin conjugation. This suggests that PTR1 degradation during the stationary phase of growth is mediated by the proteasome. This leads to lower levels of H4-biopterin, which favors metacyclogenesis, and subsequently results in a highly infective stage of the parasite. Therefore, this finding has importance to identify new target molecule like the proteasome for therapeutic intervention.

• Possibility of membrane modification as a mechanism of antimony resistance in Leishmania donovani.

  Authors: Hema Kothari, Pranav Kumar, Shyam Sundar, Neeloo Singh

  Parasitology international. 04/2007; 56(1):77-80.

  Resistance to antimonials has become a clinical threat in the treatment of visceral leishmaniasis (VL). Unravelling the resistance mechanism needs attention to circumvent the problem of drugResistance to antimonials has become a clinical threat in the treatment of visceral leishmaniasis (VL). Unravelling the resistance mechanism needs attention to circumvent the problem of drug resistance. In one of the resistant isolates, we earlier identified a gene (PG1) implicated in antimony resistance whose localization in the present study was confirmed on the pellicular plasma membrane of the parasite thereby indicating towards membrane modification as a mechanism of resistance in this resistant isolate.

• Translation of open reading frame in kinetoplast DNA minicircles of clinical isolates of L. donovani.

  Authors: Hema Kothari, Pranav Kumar, Rohit Saluja, Shyam Sundar, Neeloo Singh

  Parasitology research. 04/2007; 100(4):893-7.

  Till today, it remains an enigma whether the open reading frames said to be transcribed in minicircle sequences are indeed translated into protein products or not. We establish a protein-coding geneTill today, it remains an enigma whether the open reading frames said to be transcribed in minicircle sequences are indeed translated into protein products or not. We establish a protein-coding gene in minicircle variable region of kinetoplast DNA from clinical isolates of Leishmania donovani. The protein was expressed as an N-tagged green fluorescent protein (GFP) fusion protein in leishmanial expression system. Fluorescence microscopy of the transfectants carrying recombinant GFP construct showed the protein to be localized on the plasmalemma of the parasite. This shows that the minicircle transcript is indeed translated into a protein product in the parasite cell and further points toward probable biological function of minicircles in kinetoplastids.

• Prokaryotic expression, purification, and polyclonal antibody production against a novel drug resistance gene of Leishmania donovani clinical isolate.

  Authors: Hema Kothari, Pranav Kumar, Neeloo Singh

  Protein expression and purification. 02/2006; 45(1):15-21.

  Diseases produced by protozoan parasites are one of the main causes of morbidity and mortality around the world, affecting millions of people. Among these, leishmaniasis has become the second mostDiseases produced by protozoan parasites are one of the main causes of morbidity and mortality around the world, affecting millions of people. Among these, leishmaniasis has become the second most common cause of death and the problem is further complicated by the expansion of parasite resistance to the conventional drugs. The high rate of therapeutic failure thus calls for new rational approaches to develop alternative drugs. Understanding resistance mechanisms may help identify new targets for drug development. So we present here the cloning, expression, purification, and antibody production of a gene implicated in imparting resistance to pentavalent antimony (SbV) in clinical isolates of kala azar with a view to gain insight into the novel mechanism of its drug resistance.

• Overexpression in Escherichia coli and purification of pteridine reductase (PTR1) from a clinical isolate of Leishmania donovani.

  Authors: Pranav Kumar, Hema Kothari, Neeloo Singh

  Protein expression and purification. 01/2005; 38(2):228-36.

  Pteridine reductase 1 (PTR1) is part of a novel metabolic pathway in Leishmania associated with folate metabolism. Its main function is to salvage pterins but a second one is to reduce folates. ThePteridine reductase 1 (PTR1) is part of a novel metabolic pathway in Leishmania associated with folate metabolism. Its main function is to salvage pterins but a second one is to reduce folates. The novelty and possible uniqueness of the pathway in which PTR1 is involved opens the possibility of developing specific inhibitors, which in combination with dihydrofolate reductase inhibitors could be highly effective against Leishmania. In order to increase our understanding of this putative important chemotherapeutic target, we present here the cloning, overexpression and purification of this enzyme from a clinical isolate of Leishmania donovani causing kala azar in India. This recombinant enzyme will set the basis for inhibition studies as well as for structure-function relationships.

• Possibility of membrane modification as a mechanism of antimony resistance in Leishmania donovani

  Authors: Hema Kothari, Pranav Kumar, Shyam Sundar, Neeloo Singh

  Parasitology International.

  Resistance to antimonials has become a clinical threat in the treatment of visceral leishmaniasis (VL). Unravelling the resistance mechanism needs attention to circumvent the problem of drugResistance to antimonials has become a clinical threat in the treatment of visceral leishmaniasis (VL). Unravelling the resistance mechanism needs attention to circumvent the problem of drug resistance. In one of the resistant isolates, we earlier identified a gene (PG1) implicated in antimony resistance whose localization in the present study was confirmed on the pellicular plasma membrane of the parasite thereby indicating towards membrane modification as a mechanism of resistance in this resistant isolate.

• Leishmania donovani pteridine reductase 1: Biochemical properties and structure-modeling studies

  Authors: Pranav Kumar, Ashutosh Kumar, Shyam Sundar Verma, Namrata Dwivedi, Nasib Singh, Mohammad Imran Siddiqi, Rama Pati Tripathi, Anuradha Dube, Neeloo Singh

  Experimental Parasitology.

  Pteridine reductase 1 (PTR1, EC 1.5.1.33) is a NADPH dependent short-chain reductase (SDR) responsible for the salvage of pterins in the protozoan parasite Leishmania. This enzyme acts as a metabolicPteridine reductase 1 (PTR1, EC 1.5.1.33) is a NADPH dependent short-chain reductase (SDR) responsible for the salvage of pterins in the protozoan parasite Leishmania. This enzyme acts as a metabolic bypass for drugs targeting dihydrofolate reductase, therefore, for successful antifolate chemotherapy to be developed against Leishmania, it must target both enzyme activities. Based on homology model drawn on recombinant pteridine reductase isolated from a clinical isolate of L. donovani, we carried out molecular modeling and docking studies with two compounds of dihydrofolate reductase specificity showing promising antileishmanial activity in vitro. Both the inhibitors appeared to fit well in the active pocket revealing the tight binding of the carboxylic acid ethyl ester group of pyridine moiety to pteridine reductase and identify the important interactions necessary to assist the structure based development of novel pteridine reductase inhibitors.

• Overexpression in Escherichia coli and purification of pteridine reductase (PTR1) from a clinical isolate of Leishmania donovani

  Authors: Pranav Kumar, Hema Kothari, Neeloo Singh

  Protein Expression and Purification.

  Pteridine reductase 1 (PTR1) is part of a novel metabolic pathway in Leishmania associated with folate metabolism. Its main function is to salvage pterins but a second one is to reduce folates. ThePteridine reductase 1 (PTR1) is part of a novel metabolic pathway in Leishmania associated with folate metabolism. Its main function is to salvage pterins but a second one is to reduce folates. The novelty and possible uniqueness of the pathway in which PTR1 is involved opens the possibility of developing specific inhibitors, which in combination with dihydrofolate reductase inhibitors could be highly effective against Leishmania. In order to increase our understanding of this putative important chemotherapeutic target, we present here the cloning, overexpression and purification of this enzyme from a clinical isolate of Leishmania donovani causing kala azar in India. This recombinant enzyme will set the basis for inhibition studies as well as for structure–function relationships.