Exploring the interaction between tyrphostin 9 and human serum albumin using biophysical and computational methods

Abstract

Tyrphostin 9 (Tyr 9) is a potent platelet-derived growth factor receptor (PDGFR) inhibitor, which induces apoptosis in various cancer cell types. The binding of Tyr 9 to the major transport protein, human serum albumin (HSA) was investigated using several spectroscopic techniques and molecular docking method. Fluorescence quenching titration results showed progressive decrease in the protein fluorescence with increasing drug concentrations. A decreasing trend of the Stern-Volmer constant, K _sv with increasing temperature characterized the drug-induced quenching as static quenching, thus pointed towards the formation of Tyr 9–HSA complex. The binding constant of Tyr 9–HSA interaction was found to lie within the range 3.48–1.69?×?10⁵ M^?1 at three different temperatures, i.e. 15 °C, 25 °C and 35?°C, respectively and suggested intermediate binding affinity between Tyr 9 and HSA. The drug–HSA complex seems to be stabilized by hydrophobic forces, van der Waals forces and hydrogen bonds, as suggested from the thermodynamic data as well as molecular docking results. The far-UV and the near-UV CD spectral results showed slight alteration in the secondary and tertiary structures, respectively, of the protein upon Tyr 9 binding. Interaction of Tyr 9 with HSA also produced microenvironmental perturbations around protein fluorophores, as evident from the three-dimensional fluorescence spectral results but increased protein’s thermal stability. Both competitive drug binding results and molecular docking analysis suggested Sudlow’s Site I of HSA as the preferred Tyr 9 binding site.

Communicated by Ramaswamy H. Sarma     

Synthesis and characterization of polyacids from palm acid oil and sunflower oil via addition reaction

In this study aliphatic polyacids were synthesized using palm acid oil (PAO) and sunflower oil (SFO) via addition reaction technique. The synthesized materials were characterized using Fourier-transform infra-red (FTIR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS) and thermo-gravimetric analysis (TGA). Mixing formic acid and hydrogen peroxide with PAO or SFO at the ratio 3:10:1 produced the lowest iodine value of 10.57 and 9.24 respectively, indicating the increase in epoxidization of both oils. Adding adipic acid to the epoxidized oils at a ratio of 1:10 increases the acid values of SFO and PAO to 11.22 and 6.73 respectively. The existence of multi-acid groups present in synthesized polyacid was confirmed by MALD-ToF-MS. This feature indicates a possible value to the biomaterials development.     

Microsatellite-based evidences of genetic bottlenecks in the cryptic species “Andrographis paniculata Nees”: a potential anticancer agent

Andrographis paniculata (AP) is a medicinal plant species introduced into Malaysia. To address the genetic structure and evolutionary connectedness of the Malaysian AP with the Indian AP, a DNA sequence analysis was conducted based on 24 microsatellite markers. Out of the 24 primer sets, seven novel microsatellite primers were designed and amplified intra-specifically according to the available Indian AP sequences at the National Centre for Biotechnology Information (NCBI), where 17 of them were amplified using the cross-species strategy by employing the primers belonging to Acanthus ilicifolius Linn (Acanthaceae) and Lumnitzera racemosa Wild (Combretaceae). The primers were then applied on the Malaysian AP accessions. Sixteen of the new microsatellite loci were amplified successfully. Analysis of these microsatellite sequences, revealed some significant differences between the Indian and Malaysian AP accessions in terms of the size and type of the repeat motifs. These findings depicted the cryptic feature of this species. Despite identifying several heterozygous alleles no polymorphism was observed in the detected loci of the selected accessions. This situation was in concordance with the presence of “fixed heterozygosity” phenomenon in the mentioned loci. Accordingly, this was fully consistent with the occurrence of the genetic bottleneck and founder effect within Malaysian AP population. Apart from the amplification of new microsatellites in this species, our observations could be in agreement with the risk of genetic depletion and consequently extinction of this precious herb in Malaysia. This issue should be taken into consideration in the future studies.     

DNA damage and protein oxidation associated with ageing correlate with cognitive dysfunction in a Malaysian population

Abstract

Ageing is associated with increased oxidative stress accompanied by cognitive decline. The aim of this study was to evaluate oxidative stress biomarkers and their possible relationship with cognitive performances during ageing among the Malay population. Approximately 160 healthy Malay adults aged between 28 and 79 years were recruited around Selangor and Klang Valley. Cognitive function was assessed by Montreal Cognitive Assessment (MoCA), forward digit span (FDS), backward digit span (BDS), digit symbol, Rey Auditory Verbal Learning Test immediate recalled [RAVLT(I)] and delayed recalled [RAVLT(D)], and visual reproduction immediate recalled (VR-I) and delayed recalled (VR-II). DNA damage, plasma protein carbonyl and malondialdehyde (MDA) levels were also determined. Cognitive function test showed significant lower scores of MoCA, BDS, RAVLT(I), RAVLT(D), digit symbol, VR-I, and VR-II in the older age group (60 years old) compared with the 30-, 40-, and 50-year-old group. The extent of DNA damage was sequential with age: 60?>?50?>?40?>?30, whereas protein carbonyl was higher in 40-, 50-, and 60-year-old groups compared with the youngest group (30 years old). However, the MDA level was observed unchanged in all age groups. Approximately 21.88% of the participants had cognitive impairment. Multiple logistic regression analysis revealed that DNA damage and protein carbonyl levels are predictors for cognitive impairment in healthy Malays. In conclusion, cognitive decline occurred in healthy adult Malay population at an early age of 30 years old with corresponding higher DNA damage and protein oxidation.     

Synthesis of 2-methoxybenzoylhydrazone and evaluation of their antileishmanial activity

Compounds 1–25 showed varying degree of antileishmanial activities with IC₅₀ values ranging between 1.95 and 88.56 μM. Compounds 2, 10, and 11 (IC₅₀ = 3.29 ± 0.07 μM, 1.95 ± 0.04 μM, and 2.49 ± 0.03 μM, respectively) were found to be more active than standard pentamidine (IC₅₀ = 5.09 ± 0.04 μM). Compounds 7 (IC₅₀ = 7.64 ± 0.1 μM), 8 (IC₅₀ = 13.17 ± 0.46 μM), 18 (IC₅₀ = 13.15 ± 0.02 μM), and 24 (IC₅₀ = 15.65 ± 0.41 μM) exhibited good activities. Compounds 1, 3, 4, 5, 9, 12, 15, 18, and 19 were found to be moderately active. Compounds 13, 14, 16, 17, 20–25 showed weak activities with IC₅₀ values ranging between 57 and 88 μM.     

Activation of the unfolded protein response in Pichia pastoris requires splicing of a HAC1 mRNA intron and retention of the C-terminal tail of Hac1p

We have shown that the unfolded protein response (UPR) in Pichia pastoris requires splicing of a non-conventional intron in the HAC1(u) mRNA in common with other eukaryotes. P. pastoris is a favoured yeast expression host for secreted production of heterologous proteins and the regulation of the UPR in P. pastoris may hold the key to its effective folding and secretion of proteins. We have also shown that the C-terminal region of the Hac1p from P. pastoris is required for functionality. Although the C-terminal regions of Hac1p from both S. cerevisiae and P. pastoris are rich in phenylalanine residues, the P. pastoris Hac1p lacks a C-terminal serine that is known to be important in the efficient functionality of Hac1p from S. cerevisiae.     

From breeding pairs to fox towns: the social organisation of arctic fox populations with stable and fluctuating availability of food

Food availability can impact group formation in Carnivora. Specifically, it has been suggested that temporal variation in food availability may allow a breeding pair to tolerate additional adults in their territory at times when food abundance is high. We investigate group occurrence and intraspecific tolerance during breeding in a socially flexible canid, the arctic fox (Vulpes lagopus). We compare Iceland and Sweden where resource conditions differ considerably. A breeding pair was the most common social unit in both populations, but as predicted, groups were more frequent where food abundance varied substantially between years (Sweden: 6 %) than where food availability was stable (Iceland: ≤2 %). Within Sweden, supplemental feeding increased group occurrence from 6 to 21 %, but there was no effect of natural variation in lemming (Lemmus lemmus) availability since group formation was rare also at lemming highs. Thus, additional factors appeared to influence the trade-off between intraspecific territoriality and tolerance. We report two cases where related females showed enduring social relationships with good-neighbour strategies. Related females also engaged in alloparental behaviour in a ‘fox town’ with 31 foxes (4 adults, 3 litters). In contrast, when unrelated foxes bred close to each other, they moved or split their litters during summer, presumably because of territorial conflict. We suggest that fluctuating food availability is linked to group formation in this Arctic carnivore, but also when food availability increases, additional factors such as relatedness, alloparental benefits, competition and predator defence appear necessary to explain group formation.     

Bacterial microbiome of Coptotermes curvignathus (Isoptera: Rhinotermitidae) reflects the coevolution of species and dietary pattern

Coptotermes curvignathus Holmgren is capable of feeding on living trees. This ability is attributed to their effective digestive system that is furnished by the termite's own cellulolytic enzymes and cooperative enzymes produced by their gut microbes. In this study, the identity of an array of diverse microbes residing in the gut of C. curvignathus was revealed by sequencing the near‐full‐length 16S rRNA genes. A total of 154 bacterial phylotypes were found. The Bacteroidetes was the most abundant phylum and accounted for about 65% of the gut microbial profile. This is followed by Firmicutes, Actinobacteria, Spirochetes, Proteobacteria, TM7, Deferribacteres, Planctomycetes, Verrucomicrobia, and Termite Group 1. Based on the phylogenetic study, this symbiosis can be a result of long coevolution of gut enterotypes with the phylogenic distribution, strong selection pressure in the gut, and other speculative pressures that determine bacterial biome to follow. The phylogenetic distribution of cloned rRNA genes in the bacterial domain that was considerably different from other termite reflects the strong selection pressures in the gut where a proportional composition of gut microbiome of C. curvignathus has established. The selection pressures could be linked to the unique diet preference of C. curvignathus that profoundly feeds on living trees. The delicate gut microbiome composition may provide available nutrients to the host as well as potential protection against opportunistic pathogen.     

Effects of the inclusion of black soldier fly larvae (Hermetia illucens) meal on growth performance and blood plasma constituents in broiler chicken (Gallus gallus domesticus) production

The aim of this study was to identify the effect of inclusion of defatted black soldier fly larvae (Def-BSFL) meal as a protein source on the performance and blood plasma constituents of broiler chickens. A total of 360-day-old chicks were assigned into four dietary groups, which included four different levels of Def-BSFL meal namely control (0% BSFL), T1(4% BSFL), T2 (8% BSFL) and T3 (12% BSFL) for six weeks experimental feeding period. At the end of the experiment, the blood samples of three birds from each treatment were collected to measure plasma constituents. Birds fed control and T1 diets demonstrated higher feed intake during the finisher stage compared with T2 and T3 diets. The heaviest weight for the 6-week feeding trial was recorded at T1 (1043.8 ± 65.9 g). Birds fed T1 (1.1 ± 0.0) and T3 (0.9 ± 0.1) diets displayed lower feed conversion ratio during the finisher stage than those fed control (1.7 ± 0.1) and T2 (1.8 ± 0.3) diets. Birds fed the control diet demonstrated the highest red blood cell with mean and standard deviation of 7.5 ± 0.34, whereas those fed the T2 diet showed the highest haemoglobin levels with mean and standard deviation of 15.8 ± 0.24. Birds fed T1, T2, and T3 diets exhibited a higher number (P < 0.05) of monocytes than those fed a control diet. There were no differences in white blood cell count across all the groups. In addition, birds fed the T2 diet showed higher (P < 0.05) blood urea nitrogen followed by the T3, control, and T1 diets. As a conclusion, the 4% Def-BSFL in the broiler chicken diet could be used to replace fish meal (FM) and soybean meal (SBM) without compromising bird performance and blood traits.     

Hydrothermal liquefaction of Malaysia's algal biomass for high‐quality bio‐oil production

Currently, fossil materials form the majority of our energy and chemical source. Many global concerns force us to rethink about our current dependence on the fossil energy. Limiting the use of these energy sources is a key priority for most countries that pledge to reduce greenhouse gas emissions. The application of biomass, as substitute fossil resources for producing biofuels, plastics and chemicals, is a widely accepted strategy for sustainable development. Aquatic plants including algae possess competitive advantages as biomass resources compared to the terrestrial plants in this current global situation. Bio‐oil production from algal biomass is technically and economically viable, cost competitive, requires no capacious lands and minimal water use and reduces atmospheric carbon dioxide. The aim of this paper is to review the potential of converting algal biomass, as an aquatic plant, into high‐quality crude bio‐oil through applicable processes in Malaysia. In particular, bio‐based materials and fuels from algal biomass are considered as one of the reliable alternatives for clean energy. Currently, pyrolysis and hydrothermal liquefaction (HTL) are two foremost processes for bio‐oil production from biomass. HTL can directly convert high‐moisture algal biomass into bio‐oil, whereas pyrolysis requires feedstock drying to reduce the energy consumption during the process. Microwave‐assisted HTL, which can be conducted in aqueous environment, is suitable for aquatic plants and wet biomass such as algae.