Papers by Prof. Dinithi Peiris
Journal of Medical Virology
The coronavirus disease 2019 virus outbreak continues worldwide, with many variants emerging, som... more The coronavirus disease 2019 virus outbreak continues worldwide, with many variants emerging, some of which are considered variants of concern (VOCs). The WHO designated Omicron as a VOC and assigned it under variant B.1.1.529. Here, we used computational studies to examine the VOCs, including Omicron subvariants, and one variant of interest. Here we found that the binding affinity of human receptor angiotensin-converting enzyme 2 (hACE2) and receptor-binding domain (RBDs) increased in the order of wild type (Wuhan-strain) < Beta < Alpha < OmicronBA.5 < Gamma < Delta < Omicron BA.2.75 < BA.1 < BA.3 < BA.2. Interactions between docked complexes revealed that the RBD residue positions like 452, 478, 493, 498, 501, and 505 are crucial in creating strong interactions with hACE2. Omicron BA.2 shows the highest binding capacity to the hACE2 receptor among all the mutant complexes. The BA.5's L452R, F486V, and T478K mutation significantly impact the interaction network in the BA.5 RBD-hACE2 interface. Here for the first time, we report the His505, an active residue on the RBD forming a salt bridge in the BA.2, leading to increased mutation stability. When the active RBD residues are mutated, binding affinity and intermolecular interactions increase across all mutant complexes. By examining the differences in different variants, this study may provide a solid foundation for structure-based drug design for newly emerging variants.
Society of Environmental Toxicology and Chemistry Europe, Brussels, 2001
There is a common agreement that amphibian population is in danger due to environmental pollutant... more There is a common agreement that amphibian population is in danger due to environmental pollutants. However, pollutant effects on amphibian populations are not complete. Chlorpyrifos is toxic to many aquatic organisms but limited information is available on amphibian species. We assessed the susceptibility of JUDO50 (Chlorpyrifos) to Rana spp. early tadpole stages and eggs. Main aim was to determine LC50 value for tadpoles and to investigate effects of various sub lethal concentrations on hatching rate. Several concentrations of JUDO 50 (commercial name for Chlorpyrifos) ranging 10-30 ppm were used in the pilot study reveled that below 5ppm of Chlorpyrifos can be lethal to early stages of tadpoles. Therefore, this experiment used sub lethal concentrations. LC50 values of JUDO5O were 2.4-2.6 ppm at 24 hours and 2.0-2.3 ppm al48 hours. Hatching rate significantly decreased (Control; 90o/o, 0.01 ppm; 620/o, 0.03 ppm; 19o/o; and 0.05 ppm; 8%; P<0.05) with the concentration of Chlorpyrifos. Dead embryos showed arrested development. Delay in hatching as well as decreased percentage of hatching during the experimental period showed toxic effects of low concentrations of JUDO5O to fertilized eggs of the species studied. This is really important due to obligatory aquatic tendency of many amphibians during breeding. ln most cases tadpoles stay in the water body for longer periods. Therefore, decease in hatching percentage can affect on population size. The study confirms that tadpoles can be used as a potential species in toxicology studies. Effects on hatching rate and survival rates confirm that tadpoles may face risk due to pollutants, such as Chlorpyrifos in the field.
Natural Medicinal Plants, 2021
Marine seaweeds are a promising source of bioactive secondary metabolites that can be utilized in... more Marine seaweeds are a promising source of bioactive secondary metabolites that can be utilized in drug development and nutraceuticals. Diabetes mellitus is a leading non-communicable disease, and it is the third leading cause of death worldwide. Among the types of diabetes, type 2 became the major health problem as it is associated with severe health complications. Since available oral hypoglycemic drugs cause several adverse effects, it is worth searching for a natural cure with fewer or no side effects that may benefit patients with type 2 diabetes. Among the marine seaweeds, brown and red seaweeds are extensively studied for the anti-diabetic activity compared to the green seaweeds. Bioactive compounds present in marine seaweeds possess anti-diabetic potential through diverse mechanisms, mainly by reducing postprandial hyperglycemia and associated complication. Most of the studies emphasized that the marine seaweeds control the hyperglycemic condition by inhibiting carbohydrate h...
Cystatins, a superfamily of evolutionary related proteins are classified as housekeeping proteins... more Cystatins, a superfamily of evolutionary related proteins are classified as housekeeping proteins vital for the inhibition of Papain-like cysteine proteases. Over expression of cysteine proteases have been related to the development of diseases. These facts result in the realization of Cystatins importance as regulators of protease activity and their role in the body’s immune system. The Cystatin C protein understudy was identified from a pre-established transcriptomic database of D. rerio using the NCBI database and the NCBI-BLAST algorithm. Cystatin C belongs to the Type 2 Cystatin family and is the most powerful cysteine protease inhibitor effective against Papain like proteases. The research study aims to develop an economical in-silico based approach to analyze the structure and functionality of novel proteins with a comprehensive revelation of their clinical significance. Therefore, we report on novel in-silico tools to generate a model of the Cystatin C protein expressed by D...
Seaweeds, rich in bioactive compounds is important in development of drug leads and nutraceutical... more Seaweeds, rich in bioactive compounds is important in development of drug leads and nutraceuticals. Brown algae is known for their rich bioactive compounds with numerous biological activities. However, Sri Lankan marine algae are underexploited. Hence, the present study aimed to determine the bioactive compounds present in different fractions (hexane, chloroform and ethyl acetate) of phenolic rich methanol extract of a Sri Lankan brown algae Choonospora minima for the first time. De-polysaccharide methanolic extract of C. minima was partitioned with hexane, chloroform and ethyl acetate with increasing polarity. The GC-MS analysis was performed two times for the same fraction using an Agilent Technologies gas chromatograph model 5975C and HP-5MS capillary column to increase the reliability of the results obtained. Maximum number of active compounds were identified in ethyl acetate fraction of C. minima; alkenes, phenolic compounds, ketones, thiophene derivatives and benzene-carboxyli...
Previously we have shown that leaves of Passiflora suberosa L. (family Passifloraceae, commonly k... more Previously we have shown that leaves of Passiflora suberosa L. (family Passifloraceae, commonly known as devil pumpkin) can be sued to combat diabetes and high cholesterol levels. The present study evaluated in vitro antioxidant, antihaemolytic, cytotoxic and antimicrobial potentials of different extracts of P. suberosa leaves. Aqueous, methanol, chloroform and hexane extracts of leaves obtained under reflux conditions were subjected for phytochemical screening according to previously established methods. Aqueous and methanol extracts of P. suberosa leaves possessed more phytochemicals, thus those extracts were subjected for further evaluations. Antioxidant activity was determined using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay. Antihaemolytic activity was studied using cow blood, while cytotoxic activity was determined using the brine shrimp lethality assay. Antibacterial activity against three Gram-positive (Bacillus subtilis, Staphylococcus aureus and Enteroco...
Marine seaweeds are a renewable source that possess different biological activities. The current ... more Marine seaweeds are a renewable source that possess different biological activities. The current study investigated the total phenolic and flavonoid contents and selected biological activites of the polysaccharide fraction of methanol crude from Codium fragile (Family: Codiaceae). Dried seaweed was extracted with 70% methanol and the polysaccharide fraction was separated. Total phenolic (TPC), total flavonoid (TFC) contents were determined using standard methods. Anti-inflammatory activity was evaluated using albumin (protein) denaturation, trypsin (proteinase) inhibitory and membrane stabilisation assays, while antioxidant activity was conducted using DPPH radical scavenging assay and ferric reducing antioxidant power (FRAP) assay. TPC, TFC values were 21.01±0.90 μg GE/g, 24.14±4.50 μg QE/g, respectively. Ferric ion reducing power recorded as 10.84±0.58 μg TE/g and IC50 value of DPPH radical scavenging activity was 1685.3±4.4 μg/ml and less effective than Trolox standard (IC50=10.4...
Environmental Research, 2022
Consistent search of plants for green synthesis of silver nanoparticles (SNPs) is an important ar... more Consistent search of plants for green synthesis of silver nanoparticles (SNPs) is an important arena in Nanomedicine. The present study focuses on synthesis of SNPs using bioreduction of Silver Nitrate (AgNO 3) by aqueous root extract of Decalepis hamiltonii. The biosynthesis of SNPs was monitored by UV-Vis analysis at absorbance maxima 432 nm. The fluorescence emission spectra of SNPs illustrated the broad emission peak 450-483 nm at different excitation wavelength. The surface characteristics were studied by Scanning Electron Microscope (SEM) and Atomic Force Microscopy (AFM), showed spherical shape of SNPs and Dynamic Light Scattering (DLS) analysis confirmed the average particle size 32.5 nm and the presence of metallic silver was confirmed by Energy Dispersive X-ray (EDX). Face Centred Cubic (FCC) structure with crystal size 33.3 nm was revealed by Powder X-ray diffraction (XRD). Fourier transform infrared spectroscopy (FTIR) indicated the biomolecules involved in reduction mainly polyols and phenols present in root extracts were found to be responsible for the synthesis of SNPs. The stability and charge on SNPs was revealed by zeta potential analysis. Additionally, on therapeutic forum, the synthesized SNPs elicit antioxidant and antimicrobial activity against Bacillus cereus, Bacillus licheniformis, Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus.
Proceedings of International Forestry and Environment Symposium, 2015
Extracts of the genes Passiflora has been shown to compromises a therapeutic value to control gly... more Extracts of the genes Passiflora has been shown to compromises a therapeutic value to control glycemia and lipid levels. Raw leaves of Passiflora suberosa L. (Family: Passifloraceae) is used as a traditional remedy to manage diabetes. Yet, its ethnomedical usage is not scientifically proven. The present study was conducted to examine the hypoglyceamic effect of the aqueous leaf extract (ALE) of P. suberosa, using normoglycemic male mice. ALE was prepared and mice (n=9/group), were treated with 25, 50, 100, 200 mg/kg ALE and distilled water (DW; control). Fasting and random blood glucose levels were determined at 1 st , 3 rd and 5 th h post-treatment. Acute administration of 50 mg/kg of ALE significantly (p<0.01) reduced fasting blood glucose levels (BGL) by 10%, 20% and 24% respectively at 1 st , 3 rd and 5 th h post treatment. Similarly, 100 mg/kg of ALE significantly (p<0.01) reduced fasting BGL at 3 rd (24%) and 5 th (29%) h post treatment. However, it did not change the random BGL in non-fasted mice. To evaluate the chronic effect of ALE, 18 mice (n=9) were treated orally either with 50 mg/kg of ALE or DW for 30 consecutive days and on day 31, fasting BGL was measured after 1,3 and 5 hrs. A significant reduction in fasting BGL was observed, at 1 st (17%), 3 rd (18%) and 5 th (27%) h respectively. The same dose showed a significant (p<0.01) improvement in sucrose tolerance test (18%) after 5 hours. However, ALE did not show a significant improvement in glucose tolerance test following an oral glucose challenge. The findings from this study provide evidences for ethnomedical usage of P. suberosa as an anti-diabetic agent in the traditional Sri Lankan medicinal system.
Medicinal & Aromatic Plants, 2015
Asian journal of andrology, 2001
To evaluate the effects of acute and chronic doses of methoxy acetic acid (MAA) on in vitro ferti... more To evaluate the effects of acute and chronic doses of methoxy acetic acid (MAA) on in vitro fertilisation by hamster sperm and to correlate the data with the testicular damage. Adult male hamsters were gavaged with 3 single doses (0, 80, 160 and 650 mg/kg) and 3 chronic doses (0, 8, 32 and 64 mg/kg daily for 5 weeks) of MAA in distilled water. After treatment hamsters were killed at weekly intervals and spermatozoa recovered from the distal cauda epididymides were used to assess the fertilising capacity in vitro. The testes were processed for histological examination. Acute doses showed a significant reduction in sperm fertilising ability from week 3 and 4 after treatment and with the chronic doses, the effects were more extensive and persistent. The results were in correpondence with the testicular damages observed. It is evident that both acute and chronic doses of MAA can impair the sperm function by damaging one or more cell populations in the testis.
Journal of Biomolecular Structure and Dynamics, 2020
In this study, the antimicrobial properties of Plumbago indica root bark against bacterial strain... more In this study, the antimicrobial properties of Plumbago indica root bark against bacterial strains and a fungal strain were investigatedusing the disc diffusion and minimum inhibitory concentration assays. Gas chromatography/mass spectrometry, nuclear magnetic resonance spectrometry, and column chromatography analyses were conducted to identify and isolate the active compounds. A docking study was performed to identify possible interactions between the active compound and DNA gyrase using the Schr€ odinger Glide docking program. Both methanol extract and the ethyl acetate fraction of the root bark showed significant antimicrobial activity against the gram-positive bacteria than against the gram-negative bacteria and the fungal strain. The active compound was identified as plumbagin. A disc diffusion assay of plumbagin revealed potent antimicrobial activity against methicillin-resistant Staphylococcus aureus. Molecular docking of plumbagin revealed high specificity towards the DNA gyrase binding site with a high fitness score and a minimum energy barrier of À7.651 kcal/mol. These findings indicate that P. indica exhibits significant antimicrobial activity, primarily due to the presence of plumbagin. The specificity of plumbagin toward DNA gyrase in S. aureus indicates the feasibility of utilizing P. indica for developing new drug leads against drug resistant microbial strain.
Dose-Response, 2019
1,3-Dinitrobenzene (mDNB) is a widely used intermediate in commercial products and causes testicu... more 1,3-Dinitrobenzene (mDNB) is a widely used intermediate in commercial products and causes testicular injury. However, genotoxic effects upon low-level exposure are poorly understood. The present study evaluated the effects of very low-chronic doses of mDNB on sperm nuclear integrity. Male hamsters were treated with 1.5 mg/kg/d/4 wks (group A), 1.5 mg/kg/mDNB/d/week/4 weeks (group B), 1.0 mg/kg/mDNB/3 d/wk/4 wks (group C), or polyethylene glycol 600 (control). Nuclear integrity of distal cauda epididymal sperm was determined using the sperm chromatin structure assay and acridine orange staining (AOS). The germ cell nuclear integrity was assessed by the comet assay. Testicular histopathology was conducted to evaluate the sensitive stages. The comet assay revealed denatured nuclear DNA in group A (in diploid and polyploid cells from weeks 2-5); respectively at week 4 and weeks 3 to 4 in groups B and C. According to AOS, only group A animals exhibited denatured sperm DNA (weeks 1 and 3)...
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Papers by Prof. Dinithi Peiris