Prajwal Paudel - Academia.edu (original) (raw)

Papers by Prajwal Paudel

Comprehensive Natural Products III, 2020

is a small (8.6 kDa) regulatory protein of 76 amino acids that adopts a b-grasp fold. Ub is highl... more is a small (8.6 kDa) regulatory protein of 76 amino acids that adopts a b-grasp fold. Ub is highly conserved in eukaryotic organisms. The conjugation of ubiquitin to a target protein is called ubiquitination or ubiquitylation. 1 Typically, Ub is attached to proteins through an isopeptide linkage between the C-terminal carboxylate of ubiquitin (glycine 76) and an e-amino group of a lysine residue in the acceptor proteins. Ubiquitination is an important, reversible post-translational modification (PTM) in eukaryotic cells. Since its discovery in the late 1970s and early 1980s, the modification by ubiquitin has emerged as an essential regulatory mechanism in almost all cellular processes in eukaryotes. Ubiquitination affects substrate proteins in many different ways including signaling, proteasomal degradation, altering cellular localization, modulating catalytic activity, and promoting or preventing protein interactions. 2,3 The cellular processes regulated by ubiquitination include cell cycle, transcription, trafficking, inflammation and DNA repair. Notably, many of the processes are independent of proteasome-mediated protein degradation. 4 Ubiquitination involves three main enzymatic steps catalyzed by ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s) (see Fig. 1). 5 First, ubiquitin is activated in a two-step reaction by an E1 (ubiquitinactivating enzyme) with the consumption of ATP, forming a ubiquitin adenylate intermediate and subsequently a thioester bond between the C-terminal carboxyl group of ubiquitin and the active site cysteine of E1. 6,7 The human genome contains two E1s, i.e. UBA1 and UBA6. 8 E2 catalyzes the transfer of Ub from the Ub-E1 conjugate to the active site cysteine of E2 and forms the Ub-E2 conjugate through a transthioesterification reaction. The human genome possesses more than 30 different E2 enzymes. 9 The E3 ubiquitin ligase catalyzes the final step of the ubiquitination cascade by transferring Ub from the Ub-E2 conjugate to the substrate protein. E3s have substrate specificity for the E2 enzymes. The cullin-RING ligases, which constitute the largest group of E3s (around 600 members), do not form a covalent bond with Ub. Two smaller groups of E3s, the HECT ligases (around 30 members) and RBR ligases (around 12 members), form a Ub-thioester intermediate with the E3 active site cysteine. 10 Notably, substrate proteins can be ubiquitinated at different lysine residues resulting in multi-monoubiquitination. Ub itself can be further ubiquitinated, namely polyubiquitination, giving rise to Ub chains. 11 This can occur through one of seven Ub Lys residues (K6, K11, K27, K29, K33, K48, and K63) or the Ub N-terminal methionine residue (M1). 3 Furthermore, mixed and branched Ub chains also exist in cells. 12 Different Ub chain linkages are associated with various cellular functions. For instance, the K48-linked polyubiquitination is the best studied Ub modification and it targets proteins to the proteasome for degradation. 13 The K63-linked polyubiquitination is mostly related to non-proteolytic processes such as endocytic trafficking, inflammation, translation, and DNA repair. 1,14 M1-linked (also called linear) Ub chains play a very important roles in immune response. 15 2 Deubiquitinases Deubiquitinating enzymes or deubiquitinases (DUBs) are isopeptidases that hydrolyze the isopeptide bond between a Ub C-terminal carboxyl group and a side-chain amine group of a lysine residue in the acceptor proteins. The receptor proteins can be a ubiquitinated target protein or a receptor Ub in a polyubiquitin chain. In the human genome there are close to 100 DUBs, which can be classified into two main categories, i.e. cysteine proteases and metalloproteases. 16 The cysteine proteases can be further divided into six families: ubiquitin-specific proteases (USPs), ubiquitin C-terminal hydrolases (UCHs), ovarian tumor proteases (OTU), Machado-Josephin domain DUBs (MJD), motif interacting with Ub-containing novel DUB family (MINDY) and the newly characterized zinc finger with UFM1-specific peptidase (ZUFSP). In the USP family, there are around 56 known DUBs (Fig.

American Journal of Essential Oils and Natural Products, 2015

The essential oil from the leaves of Psidium guajava, collected from Kathmandu, Nepal, was obtain... more The essential oil from the leaves of Psidium guajava, collected from Kathmandu, Nepal, was obtained by hydrodistillation and analyzed by GC-MS. A total of 53 compounds were identified, accounting for 100% of the oil composition. The major components of the essential oil were (E)-nerolidol (35.6%) and (E)-caryophyllene (15.8%), with lower concentrations of (2Z,6E)-farnesol (6.7%), and ledol (5.5%). A cluster analysis of the major components of P. guajava leaf oils has revealed at least nine chemotypes; the sample from Nepal belongs to the nerolidol/caryophyllene chemotype. P. guajava leaf oil showed notable larvicidal activity against Chaoborus plumicornis, marginal nematicidal (Caenorhabditis elegans) and insecticidal (Drosophila melanogaster) activities, and showed no antimicrobial or cytotoxic activity.

American Journal of Essential Oils and Natural Products, 2017

The essential oil from the aerial parts of Centella asiatica, collected from Kirtipur, Nepal, was... more The essential oil from the aerial parts of Centella asiatica, collected from Kirtipur, Nepal, was obtained by hydrodistillation and analyzed by gas chromatography – mass spectrometry (GC-MS). The essential oil was dominated by sesquiterpene hydrocarbons, including (E)-β-farnesene (26.5%), α-humulene (20.9%), and (E)-caryophyllene (13.3%). The essential oil was screened for in-vitro cytotoxic activity against MCF-7 cells and antimicrobial activity against Bacillus cereus, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Aspergillus niger. The C. asiatica essential oil showed no antimicrobial activity and was only marginally cytotoxic to MCF-7 cells.

Natural Product Communications, 2013

Four essential oils from the leaf (P23) and rhizomes (P19, P22, P24) of Acorus calamus L., collec... more Four essential oils from the leaf (P23) and rhizomes (P19, P22, P24) of Acorus calamus L., collected from various parts of Nepal, were obtained by hydrodistillation and analyzed by GC-MS. From a total of 61 peaks, 57 compounds were identified among the four essential oils accounting for 94.3%, 96.2%, 97.6%, and 94.1% of the oils, respectively. All of the essential oils were dominated by ( Z)-asarone (78.1%–86.9%). The essential oils also contained ( E)-asarone (1.9%–9.9%) and small amounts of γ-asarone (2.0–2.3%), ( Z)-methyl isoeugenol (1.5–2.0%), and linalool (0.2–4.3%). Allelopathic testing of the rhizome oil showed inhibition of seed germination of Lactuca sativa and Lolium perenne with IC50 values of 450 and 737 μg/mL, respectively. The rhizome essential oil demonstrated stronger seedling growth inhibition of L. perenne than of L. sativa, however. The rhizome oil also showed notable brine shrimp lethality ( LC50 = 9.48 μg/mL), cytotoxic activity (92.2% kill on MCF-7 cells at 10...

Natural Product Communications, 2012

The essential oils from the leaves of Artemisia dubia, A. indica, and A. vulgaris growing wild in... more The essential oils from the leaves of Artemisia dubia, A. indica, and A. vulgaris growing wild in Nepal were obtained by hydrodistillation and analyzed by GC-MS. The major components in A. dubia oil were chrysanthenone (29.0%), coumarin (18.3%), and camphor (16.4%). A. indica oil was dominated by ascaridole (15.4%), isoascaridole (9.9%), trans-p-mentha-2,8-dien-1-ol (9.7%), and trans-verbenol (8.4%). The essential oil of Nepalese A. vulgaris was rich in α-thujone (30.5%), 1,8-cineole (12.4%), and camphor (10.3%). The essential oils were screened for phytotoxic activity against Lactuca sativa (lettuce) and Lolium perenne (perennial ryegrass) using both seed germination and seedling growth, and all three Artemisia oils exhibited notable allelopathic activity. A. dubia oil showed in-vitro cytotoxic activity on MCF-7 cells (100% kill at 100 μg/mL) and was also marginally antifungal against Aspergillus niger (MIC = 313 μg/mL). DFT calculations (B3LYP/6-31G*) revealed thermal decomposition of ascaridole to be energetically accessible at hydrodistillation and GC conditions, but these are spin-forbidden processes. If decomposition does occur, it likely proceeds by way of homolytic peroxide bond cleavage rather than retro-Diels-Alder elimination of molecular oxygen.

Natural Product Communications, 2013

This work examines the biological activity of essential oils of Cinnamomum camphora leaves, C. gl... more This work examines the biological activity of essential oils of Cinnamomum camphora leaves, C. glaucescens fruit, and C. tamala root from Nepal. The oils were screened for phytotoxic activity against lettuce and perennial ryegrass, brine shrimp lethality, and antibacterial, antifungal, cytotoxic, insecticidal, and nematicidal activities. C. camphora leaf essential oil was phytotoxic to lettuce, antifungal to Aspergillus niger, and insecticidal, particularly toward midge and butterfly larvae, fruit flies, and fire ants. C. camphora oil was also toxic to brine shrimp and human breast tumor cells. C. glaucescens fruit essential oil showed notable nematicidal activity, as well as termiticidal and mosquito larvicidal activity. The root essential oil of C. tamala was toxic to mosquito larvae and fire ants.

Natural Product Communications, 2013

The essential oils from the leaves of Juglans regia, collected from Kathmandu, Nepal, and Juglans... more The essential oils from the leaves of Juglans regia, collected from Kathmandu, Nepal, and Juglans nigra from Huntsville, Alabama, USA, were obtained by hydrodistillation and analyzed by GC-MS. A total of 69 compounds were identified in the J. regia oil, accounting for 99.0% of the eluting components of the oil while three different samples of J. nigra were analyzed identifying a total of 99.3%, 99.4% and 99.7% of the oils. The leaf essential oil of J. regia was dominated by the aromatic compounds eugenol (27.5%) and methyl salicylate (16.2%), and the sesquiterpenes germacrene D (21.4%) and ( E)-β-farnesene (8.2%). The essential oils from three different samples of J. nigra contained ( E)-caryophyllene (17.3%–20.4%) and germacrene D (7.1%–22.5%) with smaller amounts of juglone (1.0%–8.8%), α-hydrojuglone (1.0–9.5%), and δ-cadinene (3.8%–8.7%). J. regia leaf oil, devoid of juglone, showed allelopathic activity, while J. nigra leaf oil was less phytotoxic. The presence of eugenol and m...

Journal of agricultural and food chemistry, Jan 24, 2016

Degradation of glyphosate in the presence of Mn oxide and UV light was analyzed using phosphate o... more Degradation of glyphosate in the presence of Mn oxide and UV light was analyzed using phosphate oxygen isotope ratios and density function theory (DFT). Preference of C-P or C-N bond cleavage was found to vary with changing glyphosate:Mn oxide ratios indicating the potential role of sorption-induced conformational changes on the composition of intermediate degradation products. Isotope data confirmed that one oxygen atom derived solely from water was incorporated into the released phosphate during glyphosate degradation and this might suggest similar nucleophilic substitution at P centers and C-P bond cleavage both in Mn oxide- and UV light-mediated degradation. The DFT results reveal that the C-P bond could be cleaved by water, OH- or ∙OH, with the energy barrier opposing bond dissociation being lowest in the presence of the radical species, and C-N bond cleavage is favored by the formation of both nitrogen and carbon centered radicals. Overall, these results highlight the factors ...

Journal of Essential Oil Bearing Plants, 2012

ABSTRACT The volatile oil from the stem bark of Vitellaria paradoxa (shea) has been obtained by h... more ABSTRACT The volatile oil from the stem bark of Vitellaria paradoxa (shea) has been obtained by hydrodistillation and analyzed by GC-MS. The oil is characterized by a high concentration of germacrene D (21.8 %), with smaller quantities of linalool (6.5 %), (E)-caryophyllene (6.3 %), (E)-phytol (4.9 %), and β-elemene (3.8 %). The V. paradoxa bark oil was screened for antibacterial activity but was inactive (MIC ≥ 625 μg/mL).

Journal of Essential Oil Bearing Plants, 2012

ABSTRACT The essential oil from the leaf of Kyllinga brevifolia Rottb., collected from Biratnagar... more ABSTRACT The essential oil from the leaf of Kyllinga brevifolia Rottb., collected from Biratnagar, Nepal, was obtained by hydrodistillation and analyzed by GC-MS. A total of 22 compounds were identified in the oil accounting for 96.1 % of the oil composition. The majority of the essential oil was identified to be occadinol (40.3 %),’L-τ-muurolol (19.5 %), and germacrene D-4-ol (12.5 %). The oil also contained smaller amounts of δ-cadinene (2.9 %), and germacrene D (4.0 %). Reports on the essential oil composition of K. brevifolia from Nepal were compared with a sample from Brazil, which showed that 13-epi-manoyl oxide (26.1 %) and manoyl oxide derivatives constituted the majority of composition with a-cadinol comprising only 0.4 %. However germacrene D was found in similar percentages between Nepal and Brazil samples (4.0 %and 4.2 %, respectively).

Pharmacognosy Research, 2013

Background: Pinus roxburghii Sarg. Is one of 3 species of pine found in Nepal, the oil of which i... more Background: Pinus roxburghii Sarg. Is one of 3 species of pine found in Nepal, the oil of which is traditionally used to treat cuts, wounds, boils, and blisters. Objective: To obtain, analyze, and examine the anti-microbial and cytotoxic activities of the essential oils of P. roxburghii. Materials and Methods: Three plant parts (cone, needle, and bark) of Pinus roxburghii were collected in Biratnagar, Nepal. The essential oils were obtained by hydrodistillation, and the chemical compositions were determined by GC-MS. The needle and cone essential oils were screened for anti-microbial activity against Bacillus cereus, Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Aspergillus niger; brine shrimp (Artemia salina) lethality; and in-vitro cytotoxicity against MCF-7 cells. Results: GC-MS analysis for the cone oil revealed 81 compounds with 78 components being identified (95.5% of the oil) while 98.3% of needle oil was identified to contain 68 components and 98.6% of the bark oil (38 components) was identified. The 3 essential oils were dominated by sesquiterpenes, particularly (E)-caryophyllene (26.8%-34.5%) and α-humulene (5.0%-7.3%) as well as monoterpene alcohols terpinen-4-ol (4.1%-30.1%) and α-terpineol(2.8%-5.0%). The monoterpene δ-3-carene was present only in needle and cone essential oils (2.3% and 6.8%, respectively). Bio-activity assays of the cone essential oil of P. roxburghii showed remarkable cytotoxic activity (100% killing of MCF-7 cells at 100 μg/ mL) along with notable brine shrimp lethality (LC 50 =11.8 μg/mL). The cone essential oil did not show anti-bacterial activity, but it did exhibit anti-fungal activity against Aspergillus niger (MIC=39 μg/mL). Conclusion: The bioactivity of P. roxburghii essential oil is consistent with its traditional medicinal use.

Pharmaceutical Biology, 2010

Context: Pycnostachys abyssinica Fresen and Pycnostachys eminii Gürke (Lamiaceae) are used in tra... more Context: Pycnostachys abyssinica Fresen and Pycnostachys eminii Gürke (Lamiaceae) are used in traditional Ethiopian medicine against eye and skin infections, "Mitch disease", and dysentery. Objective: Our study was aimed at characterizing essential oil (EO), phytochemical groups, and antimicrobial and anthelmintic activity of extracts to underscore the species' indigenous medicinal use. Materials and methods: Plant organs of Pycnostachys species were subjected to hydrodistillation, and essential oils (EO) analyzed by GC-MS. Phytochemical compounds, antimicrobial (diffusion assay) and anthelmintic activity (bioassay) of gradient solvent extracts of different polarity were studied. Results: In the stem and root EO of P. abyssinica, 25 (99%) and 30 (99.79%) compounds were detected respectively, with estragole (70.4%) (stem) and exo-fenchyl acetate (30.6%) (root) as the most abundant compounds. In leaf, stem and root EO of P. eminii, 30 (90.66%), 27 (90.59%) and 27 (99.96%) compounds were detected, respectively, with high levels of β-caryophyllene (from 18.08% to 28.85%) and germacrene D (from 15.1% to 22.06%). Alkaloids, saponins, phytosterols, flavonoids, polyphenols, diterpenoids and carotenoids were detected in Pycnostachys. Petroleum ether, chloroform and methanol extracts showed distinct antimicrobial effects with generally higher potential activity of lipophilic and semi-lipophilic fractions. Leaf and root methanol extracts of both species showed lethal activity against earthworms. Discussion: Identified EO constituents and phytochemical groups underscore the observed antifungal, antibacterial and anthelmintic activity of Pycnostachys gradient solvent extracts. Conclusion: EO analysis, phytochemical screening, and antimicrobial and anthelmintic assays indicate the biological potential of Pycnostachys species from Ethiopia, and emphasize their pharmacological and indigenous applications.

Natural Product Research, 2013

The essential oil from the parasitic vine Cuscuta reflexa Roxb., collected from Kirtipur, Kathman... more The essential oil from the parasitic vine Cuscuta reflexa Roxb., collected from Kirtipur, Kathmandu, Nepal, was obtained by hydrodistillation and analysed by gas chromatography-mass spectrometry. From a total of 62 peaks, 61 compounds were identified in the oil, accounting for 99.6% of the oil. The majority of the essential oil was dominated by the relatively rare component cis-3-butyl-4-vinylcyclopentane (26.4%). The oil also contained substantial amounts of limonene (5.1%) and (E)-nerolidol (9.5%). Biological screening for antimicrobial activities did not show appreciable activity against either Gram-positive (Bacillus cereus and Staphylococcus aureus) or Gram-negative (Escherichia coli and Pseudomonas aeruginosa) bacteria. However, marginal activity against Aspergillus niger was observed (minimum inhibitory concentration = 313 μg/mL).

Journal of Natural Pharmaceuticals, 2012

Letter to the Editor Microbiological activities of volatile constituents of Leucas aspera (Willd.... more Letter to the Editor Microbiological activities of volatile constituents of Leucas aspera (Willd.) Link from Nepal Leucas aspera (Willd.) Link [Synonym Leucas plukenetii (Roth) Spreng.] is a species of annual branched herb belonging to the Lamiaceae, and distributed throughout South Asia (India, Bangladesh, Nepal), Malaysia, and Mauritius. [1] L. aspera has been traditionally used as an antipyretic, insecticide, [2] and as a remedy for toothache; [3] its flowers are used as an expectorant, stimulant, diaphoretic, antirheumatic, and antipsoriatic, while its leaves are useful in treating snake bites. [4,5]

The essential oil from the leaves of Lawsonia inermis L. (collected from Biratnagar, Nepal) was o... more The essential oil from the leaves of Lawsonia inermis L. (collected from Biratnagar, Nepal) was obtained by hydrodistillation and analyzed by GC-MS. A total of 40 compounds were identified in the oil, accounting for 100.0% of the oil. The majority of the essential oil was composed of (E)-phytol (27.5%), while the remainder of the essential oil was dominated by monoterpenoids including: limonene (20.0%), 1,8-cineole (6.9%), and linalool (7.0%). The oil was screened for antimicrobial activity against Bacillus cereus, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Aspergillus niger and showed marginal activity (MIC = 625 μg/mL).

Proceedings of the National Academy of Sciences, 2019

USP9X is a conserved deubiquitinase (DUB) that regulates multiple cellular processes. Dysregulati... more USP9X is a conserved deubiquitinase (DUB) that regulates multiple cellular processes. Dysregulation of USP9X has been linked to cancers and X-linked intellectual disability. Here, we report the crystal structure of the USP9X catalytic domain at 2.5-Å resolution. The structure reveals a canonical USP-fold comprised of fingers, palm, and thumb subdomains, as well as an unusual β-hairpin insertion. The catalytic triad of USP9X is aligned in an active configuration. USP9X is exclusively active against ubiquitin (Ub) but not Ub-like modifiers. Cleavage assays with di-, tri-, and tetraUb chains show that the USP9X catalytic domain has a clear preference for K11-, followed by K63-, K48-, and K6-linked polyUb chains. Using a set of activity-based diUb and triUb probes (ABPs), we demonstrate that the USP9X catalytic domain has an exo-cleavage preference for K48- and endo-cleavage preference for K11-linked polyUb chains. The structure model and biochemical data suggest that the USP9X catalyti...

Comprehensive Natural Products III, 2020

is a small (8.6 kDa) regulatory protein of 76 amino acids that adopts a b-grasp fold. Ub is highl... more is a small (8.6 kDa) regulatory protein of 76 amino acids that adopts a b-grasp fold. Ub is highly conserved in eukaryotic organisms. The conjugation of ubiquitin to a target protein is called ubiquitination or ubiquitylation. 1 Typically, Ub is attached to proteins through an isopeptide linkage between the C-terminal carboxylate of ubiquitin (glycine 76) and an e-amino group of a lysine residue in the acceptor proteins. Ubiquitination is an important, reversible post-translational modification (PTM) in eukaryotic cells. Since its discovery in the late 1970s and early 1980s, the modification by ubiquitin has emerged as an essential regulatory mechanism in almost all cellular processes in eukaryotes. Ubiquitination affects substrate proteins in many different ways including signaling, proteasomal degradation, altering cellular localization, modulating catalytic activity, and promoting or preventing protein interactions. 2,3 The cellular processes regulated by ubiquitination include cell cycle, transcription, trafficking, inflammation and DNA repair. Notably, many of the processes are independent of proteasome-mediated protein degradation. 4 Ubiquitination involves three main enzymatic steps catalyzed by ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s) (see Fig. 1). 5 First, ubiquitin is activated in a two-step reaction by an E1 (ubiquitinactivating enzyme) with the consumption of ATP, forming a ubiquitin adenylate intermediate and subsequently a thioester bond between the C-terminal carboxyl group of ubiquitin and the active site cysteine of E1. 6,7 The human genome contains two E1s, i.e. UBA1 and UBA6. 8 E2 catalyzes the transfer of Ub from the Ub-E1 conjugate to the active site cysteine of E2 and forms the Ub-E2 conjugate through a transthioesterification reaction. The human genome possesses more than 30 different E2 enzymes. 9 The E3 ubiquitin ligase catalyzes the final step of the ubiquitination cascade by transferring Ub from the Ub-E2 conjugate to the substrate protein. E3s have substrate specificity for the E2 enzymes. The cullin-RING ligases, which constitute the largest group of E3s (around 600 members), do not form a covalent bond with Ub. Two smaller groups of E3s, the HECT ligases (around 30 members) and RBR ligases (around 12 members), form a Ub-thioester intermediate with the E3 active site cysteine. 10 Notably, substrate proteins can be ubiquitinated at different lysine residues resulting in multi-monoubiquitination. Ub itself can be further ubiquitinated, namely polyubiquitination, giving rise to Ub chains. 11 This can occur through one of seven Ub Lys residues (K6, K11, K27, K29, K33, K48, and K63) or the Ub N-terminal methionine residue (M1). 3 Furthermore, mixed and branched Ub chains also exist in cells. 12 Different Ub chain linkages are associated with various cellular functions. For instance, the K48-linked polyubiquitination is the best studied Ub modification and it targets proteins to the proteasome for degradation. 13 The K63-linked polyubiquitination is mostly related to non-proteolytic processes such as endocytic trafficking, inflammation, translation, and DNA repair. 1,14 M1-linked (also called linear) Ub chains play a very important roles in immune response. 15 2 Deubiquitinases Deubiquitinating enzymes or deubiquitinases (DUBs) are isopeptidases that hydrolyze the isopeptide bond between a Ub C-terminal carboxyl group and a side-chain amine group of a lysine residue in the acceptor proteins. The receptor proteins can be a ubiquitinated target protein or a receptor Ub in a polyubiquitin chain. In the human genome there are close to 100 DUBs, which can be classified into two main categories, i.e. cysteine proteases and metalloproteases. 16 The cysteine proteases can be further divided into six families: ubiquitin-specific proteases (USPs), ubiquitin C-terminal hydrolases (UCHs), ovarian tumor proteases (OTU), Machado-Josephin domain DUBs (MJD), motif interacting with Ub-containing novel DUB family (MINDY) and the newly characterized zinc finger with UFM1-specific peptidase (ZUFSP). In the USP family, there are around 56 known DUBs (Fig.

American Journal of Essential Oils and Natural Products, 2015

The essential oil from the leaves of Psidium guajava, collected from Kathmandu, Nepal, was obtain... more The essential oil from the leaves of Psidium guajava, collected from Kathmandu, Nepal, was obtained by hydrodistillation and analyzed by GC-MS. A total of 53 compounds were identified, accounting for 100% of the oil composition. The major components of the essential oil were (E)-nerolidol (35.6%) and (E)-caryophyllene (15.8%), with lower concentrations of (2Z,6E)-farnesol (6.7%), and ledol (5.5%). A cluster analysis of the major components of P. guajava leaf oils has revealed at least nine chemotypes; the sample from Nepal belongs to the nerolidol/caryophyllene chemotype. P. guajava leaf oil showed notable larvicidal activity against Chaoborus plumicornis, marginal nematicidal (Caenorhabditis elegans) and insecticidal (Drosophila melanogaster) activities, and showed no antimicrobial or cytotoxic activity.

American Journal of Essential Oils and Natural Products, 2017

The essential oil from the aerial parts of Centella asiatica, collected from Kirtipur, Nepal, was... more The essential oil from the aerial parts of Centella asiatica, collected from Kirtipur, Nepal, was obtained by hydrodistillation and analyzed by gas chromatography – mass spectrometry (GC-MS). The essential oil was dominated by sesquiterpene hydrocarbons, including (E)-β-farnesene (26.5%), α-humulene (20.9%), and (E)-caryophyllene (13.3%). The essential oil was screened for in-vitro cytotoxic activity against MCF-7 cells and antimicrobial activity against Bacillus cereus, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Aspergillus niger. The C. asiatica essential oil showed no antimicrobial activity and was only marginally cytotoxic to MCF-7 cells.

Natural Product Communications, 2013

Four essential oils from the leaf (P23) and rhizomes (P19, P22, P24) of Acorus calamus L., collec... more Four essential oils from the leaf (P23) and rhizomes (P19, P22, P24) of Acorus calamus L., collected from various parts of Nepal, were obtained by hydrodistillation and analyzed by GC-MS. From a total of 61 peaks, 57 compounds were identified among the four essential oils accounting for 94.3%, 96.2%, 97.6%, and 94.1% of the oils, respectively. All of the essential oils were dominated by ( Z)-asarone (78.1%–86.9%). The essential oils also contained ( E)-asarone (1.9%–9.9%) and small amounts of γ-asarone (2.0–2.3%), ( Z)-methyl isoeugenol (1.5–2.0%), and linalool (0.2–4.3%). Allelopathic testing of the rhizome oil showed inhibition of seed germination of Lactuca sativa and Lolium perenne with IC50 values of 450 and 737 μg/mL, respectively. The rhizome essential oil demonstrated stronger seedling growth inhibition of L. perenne than of L. sativa, however. The rhizome oil also showed notable brine shrimp lethality ( LC50 = 9.48 μg/mL), cytotoxic activity (92.2% kill on MCF-7 cells at 10...

Natural Product Communications, 2012

The essential oils from the leaves of Artemisia dubia, A. indica, and A. vulgaris growing wild in... more The essential oils from the leaves of Artemisia dubia, A. indica, and A. vulgaris growing wild in Nepal were obtained by hydrodistillation and analyzed by GC-MS. The major components in A. dubia oil were chrysanthenone (29.0%), coumarin (18.3%), and camphor (16.4%). A. indica oil was dominated by ascaridole (15.4%), isoascaridole (9.9%), trans-p-mentha-2,8-dien-1-ol (9.7%), and trans-verbenol (8.4%). The essential oil of Nepalese A. vulgaris was rich in α-thujone (30.5%), 1,8-cineole (12.4%), and camphor (10.3%). The essential oils were screened for phytotoxic activity against Lactuca sativa (lettuce) and Lolium perenne (perennial ryegrass) using both seed germination and seedling growth, and all three Artemisia oils exhibited notable allelopathic activity. A. dubia oil showed in-vitro cytotoxic activity on MCF-7 cells (100% kill at 100 μg/mL) and was also marginally antifungal against Aspergillus niger (MIC = 313 μg/mL). DFT calculations (B3LYP/6-31G*) revealed thermal decomposition of ascaridole to be energetically accessible at hydrodistillation and GC conditions, but these are spin-forbidden processes. If decomposition does occur, it likely proceeds by way of homolytic peroxide bond cleavage rather than retro-Diels-Alder elimination of molecular oxygen.

Natural Product Communications, 2013

This work examines the biological activity of essential oils of Cinnamomum camphora leaves, C. gl... more This work examines the biological activity of essential oils of Cinnamomum camphora leaves, C. glaucescens fruit, and C. tamala root from Nepal. The oils were screened for phytotoxic activity against lettuce and perennial ryegrass, brine shrimp lethality, and antibacterial, antifungal, cytotoxic, insecticidal, and nematicidal activities. C. camphora leaf essential oil was phytotoxic to lettuce, antifungal to Aspergillus niger, and insecticidal, particularly toward midge and butterfly larvae, fruit flies, and fire ants. C. camphora oil was also toxic to brine shrimp and human breast tumor cells. C. glaucescens fruit essential oil showed notable nematicidal activity, as well as termiticidal and mosquito larvicidal activity. The root essential oil of C. tamala was toxic to mosquito larvae and fire ants.

Natural Product Communications, 2013

The essential oils from the leaves of Juglans regia, collected from Kathmandu, Nepal, and Juglans... more The essential oils from the leaves of Juglans regia, collected from Kathmandu, Nepal, and Juglans nigra from Huntsville, Alabama, USA, were obtained by hydrodistillation and analyzed by GC-MS. A total of 69 compounds were identified in the J. regia oil, accounting for 99.0% of the eluting components of the oil while three different samples of J. nigra were analyzed identifying a total of 99.3%, 99.4% and 99.7% of the oils. The leaf essential oil of J. regia was dominated by the aromatic compounds eugenol (27.5%) and methyl salicylate (16.2%), and the sesquiterpenes germacrene D (21.4%) and ( E)-β-farnesene (8.2%). The essential oils from three different samples of J. nigra contained ( E)-caryophyllene (17.3%–20.4%) and germacrene D (7.1%–22.5%) with smaller amounts of juglone (1.0%–8.8%), α-hydrojuglone (1.0–9.5%), and δ-cadinene (3.8%–8.7%). J. regia leaf oil, devoid of juglone, showed allelopathic activity, while J. nigra leaf oil was less phytotoxic. The presence of eugenol and m...

Journal of agricultural and food chemistry, Jan 24, 2016

Degradation of glyphosate in the presence of Mn oxide and UV light was analyzed using phosphate o... more Degradation of glyphosate in the presence of Mn oxide and UV light was analyzed using phosphate oxygen isotope ratios and density function theory (DFT). Preference of C-P or C-N bond cleavage was found to vary with changing glyphosate:Mn oxide ratios indicating the potential role of sorption-induced conformational changes on the composition of intermediate degradation products. Isotope data confirmed that one oxygen atom derived solely from water was incorporated into the released phosphate during glyphosate degradation and this might suggest similar nucleophilic substitution at P centers and C-P bond cleavage both in Mn oxide- and UV light-mediated degradation. The DFT results reveal that the C-P bond could be cleaved by water, OH- or ∙OH, with the energy barrier opposing bond dissociation being lowest in the presence of the radical species, and C-N bond cleavage is favored by the formation of both nitrogen and carbon centered radicals. Overall, these results highlight the factors ...

Journal of Essential Oil Bearing Plants, 2012

ABSTRACT The volatile oil from the stem bark of Vitellaria paradoxa (shea) has been obtained by h... more ABSTRACT The volatile oil from the stem bark of Vitellaria paradoxa (shea) has been obtained by hydrodistillation and analyzed by GC-MS. The oil is characterized by a high concentration of germacrene D (21.8 %), with smaller quantities of linalool (6.5 %), (E)-caryophyllene (6.3 %), (E)-phytol (4.9 %), and β-elemene (3.8 %). The V. paradoxa bark oil was screened for antibacterial activity but was inactive (MIC ≥ 625 μg/mL).

Journal of Essential Oil Bearing Plants, 2012

ABSTRACT The essential oil from the leaf of Kyllinga brevifolia Rottb., collected from Biratnagar... more ABSTRACT The essential oil from the leaf of Kyllinga brevifolia Rottb., collected from Biratnagar, Nepal, was obtained by hydrodistillation and analyzed by GC-MS. A total of 22 compounds were identified in the oil accounting for 96.1 % of the oil composition. The majority of the essential oil was identified to be occadinol (40.3 %),’L-τ-muurolol (19.5 %), and germacrene D-4-ol (12.5 %). The oil also contained smaller amounts of δ-cadinene (2.9 %), and germacrene D (4.0 %). Reports on the essential oil composition of K. brevifolia from Nepal were compared with a sample from Brazil, which showed that 13-epi-manoyl oxide (26.1 %) and manoyl oxide derivatives constituted the majority of composition with a-cadinol comprising only 0.4 %. However germacrene D was found in similar percentages between Nepal and Brazil samples (4.0 %and 4.2 %, respectively).

Pharmacognosy Research, 2013

Background: Pinus roxburghii Sarg. Is one of 3 species of pine found in Nepal, the oil of which i... more Background: Pinus roxburghii Sarg. Is one of 3 species of pine found in Nepal, the oil of which is traditionally used to treat cuts, wounds, boils, and blisters. Objective: To obtain, analyze, and examine the anti-microbial and cytotoxic activities of the essential oils of P. roxburghii. Materials and Methods: Three plant parts (cone, needle, and bark) of Pinus roxburghii were collected in Biratnagar, Nepal. The essential oils were obtained by hydrodistillation, and the chemical compositions were determined by GC-MS. The needle and cone essential oils were screened for anti-microbial activity against Bacillus cereus, Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Aspergillus niger; brine shrimp (Artemia salina) lethality; and in-vitro cytotoxicity against MCF-7 cells. Results: GC-MS analysis for the cone oil revealed 81 compounds with 78 components being identified (95.5% of the oil) while 98.3% of needle oil was identified to contain 68 components and 98.6% of the bark oil (38 components) was identified. The 3 essential oils were dominated by sesquiterpenes, particularly (E)-caryophyllene (26.8%-34.5%) and α-humulene (5.0%-7.3%) as well as monoterpene alcohols terpinen-4-ol (4.1%-30.1%) and α-terpineol(2.8%-5.0%). The monoterpene δ-3-carene was present only in needle and cone essential oils (2.3% and 6.8%, respectively). Bio-activity assays of the cone essential oil of P. roxburghii showed remarkable cytotoxic activity (100% killing of MCF-7 cells at 100 μg/ mL) along with notable brine shrimp lethality (LC 50 =11.8 μg/mL). The cone essential oil did not show anti-bacterial activity, but it did exhibit anti-fungal activity against Aspergillus niger (MIC=39 μg/mL). Conclusion: The bioactivity of P. roxburghii essential oil is consistent with its traditional medicinal use.

Pharmaceutical Biology, 2010

Context: Pycnostachys abyssinica Fresen and Pycnostachys eminii Gürke (Lamiaceae) are used in tra... more Context: Pycnostachys abyssinica Fresen and Pycnostachys eminii Gürke (Lamiaceae) are used in traditional Ethiopian medicine against eye and skin infections, "Mitch disease", and dysentery. Objective: Our study was aimed at characterizing essential oil (EO), phytochemical groups, and antimicrobial and anthelmintic activity of extracts to underscore the species' indigenous medicinal use. Materials and methods: Plant organs of Pycnostachys species were subjected to hydrodistillation, and essential oils (EO) analyzed by GC-MS. Phytochemical compounds, antimicrobial (diffusion assay) and anthelmintic activity (bioassay) of gradient solvent extracts of different polarity were studied. Results: In the stem and root EO of P. abyssinica, 25 (99%) and 30 (99.79%) compounds were detected respectively, with estragole (70.4%) (stem) and exo-fenchyl acetate (30.6%) (root) as the most abundant compounds. In leaf, stem and root EO of P. eminii, 30 (90.66%), 27 (90.59%) and 27 (99.96%) compounds were detected, respectively, with high levels of β-caryophyllene (from 18.08% to 28.85%) and germacrene D (from 15.1% to 22.06%). Alkaloids, saponins, phytosterols, flavonoids, polyphenols, diterpenoids and carotenoids were detected in Pycnostachys. Petroleum ether, chloroform and methanol extracts showed distinct antimicrobial effects with generally higher potential activity of lipophilic and semi-lipophilic fractions. Leaf and root methanol extracts of both species showed lethal activity against earthworms. Discussion: Identified EO constituents and phytochemical groups underscore the observed antifungal, antibacterial and anthelmintic activity of Pycnostachys gradient solvent extracts. Conclusion: EO analysis, phytochemical screening, and antimicrobial and anthelmintic assays indicate the biological potential of Pycnostachys species from Ethiopia, and emphasize their pharmacological and indigenous applications.

Natural Product Research, 2013

The essential oil from the parasitic vine Cuscuta reflexa Roxb., collected from Kirtipur, Kathman... more The essential oil from the parasitic vine Cuscuta reflexa Roxb., collected from Kirtipur, Kathmandu, Nepal, was obtained by hydrodistillation and analysed by gas chromatography-mass spectrometry. From a total of 62 peaks, 61 compounds were identified in the oil, accounting for 99.6% of the oil. The majority of the essential oil was dominated by the relatively rare component cis-3-butyl-4-vinylcyclopentane (26.4%). The oil also contained substantial amounts of limonene (5.1%) and (E)-nerolidol (9.5%). Biological screening for antimicrobial activities did not show appreciable activity against either Gram-positive (Bacillus cereus and Staphylococcus aureus) or Gram-negative (Escherichia coli and Pseudomonas aeruginosa) bacteria. However, marginal activity against Aspergillus niger was observed (minimum inhibitory concentration = 313 μg/mL).

Journal of Natural Pharmaceuticals, 2012

Letter to the Editor Microbiological activities of volatile constituents of Leucas aspera (Willd.... more Letter to the Editor Microbiological activities of volatile constituents of Leucas aspera (Willd.) Link from Nepal Leucas aspera (Willd.) Link [Synonym Leucas plukenetii (Roth) Spreng.] is a species of annual branched herb belonging to the Lamiaceae, and distributed throughout South Asia (India, Bangladesh, Nepal), Malaysia, and Mauritius. [1] L. aspera has been traditionally used as an antipyretic, insecticide, [2] and as a remedy for toothache; [3] its flowers are used as an expectorant, stimulant, diaphoretic, antirheumatic, and antipsoriatic, while its leaves are useful in treating snake bites. [4,5]

The essential oil from the leaves of Lawsonia inermis L. (collected from Biratnagar, Nepal) was o... more The essential oil from the leaves of Lawsonia inermis L. (collected from Biratnagar, Nepal) was obtained by hydrodistillation and analyzed by GC-MS. A total of 40 compounds were identified in the oil, accounting for 100.0% of the oil. The majority of the essential oil was composed of (E)-phytol (27.5%), while the remainder of the essential oil was dominated by monoterpenoids including: limonene (20.0%), 1,8-cineole (6.9%), and linalool (7.0%). The oil was screened for antimicrobial activity against Bacillus cereus, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Aspergillus niger and showed marginal activity (MIC = 625 μg/mL).

Proceedings of the National Academy of Sciences, 2019

USP9X is a conserved deubiquitinase (DUB) that regulates multiple cellular processes. Dysregulati... more USP9X is a conserved deubiquitinase (DUB) that regulates multiple cellular processes. Dysregulation of USP9X has been linked to cancers and X-linked intellectual disability. Here, we report the crystal structure of the USP9X catalytic domain at 2.5-Å resolution. The structure reveals a canonical USP-fold comprised of fingers, palm, and thumb subdomains, as well as an unusual β-hairpin insertion. The catalytic triad of USP9X is aligned in an active configuration. USP9X is exclusively active against ubiquitin (Ub) but not Ub-like modifiers. Cleavage assays with di-, tri-, and tetraUb chains show that the USP9X catalytic domain has a clear preference for K11-, followed by K63-, K48-, and K6-linked polyUb chains. Using a set of activity-based diUb and triUb probes (ABPs), we demonstrate that the USP9X catalytic domain has an exo-cleavage preference for K48- and endo-cleavage preference for K11-linked polyUb chains. The structure model and biochemical data suggest that the USP9X catalyti...