Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0

The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2 .     

1,2,3-Triazole-nimesulide hybrid: Their design,synthesis and evaluation as potential anticancer agents

A new hybrid template has been designed by integrating the structural features of nimesulide and the 1,2,3-triazole moiety in a single molecular entity at the same time eliminating the problematic nitro group of nimesulide. The template has been used for the generation of a library of molecules as potential anticancer agents. A mild and greener CuAAC approach has been used to synthesize these compounds via the reaction of 4-azido derivative of nimesulide and terminal alkynes in water. Three of these compounds showed promising growth inhibition (IC₅₀ ～6–10 μM) of A549, HepG2, HeLa and DU145 cancer cell lines but no significant effects on HEK293 cell line. They also inhibited PDE4B in vitro (60–70% at 10 μM) that was supported by the docking studies (PLP score 87–94) in silico.     

Physical mapping of DNA markers linked to stem rust resistance gene <Emphasis Type="Italic">Sr47</Emphasis> in durum wheat

Key message

Markers linked to stem rust resistance gene Sr47 were physically mapped in three small Aegilops speltoides chromosomal bins. Five markers, including two PCR-based SNP markers, were validated for marker-assisted selection.

Abstract

In durum wheat (Triticum turgidum subsp. durum), the gene Sr47 derived from Aegilops speltoides conditions resistance to race TTKSK (Ug99) of the stem rust pathogen (Puccinia graminis f. sp. tritici). Sr47 is carried on small interstitial translocation chromosomes (Ti2BL-2SL-2BL·2BS) in which the Ae. speltoides chromosome 2S segments are divided into four bins in genetic stocks RWG35, RWG36, and RWG37. Our objective was to physically map molecular markers to bins and to determine if any of the molecular markers would be useful in marker-assisted selection (MAS). Durum cultivar Joppa was used as the recurrent parent to produce three BC₂F₂ populations. Each BC₂F₂ plant was genotyped with markers to detect the segment carrying Sr47, and stem rust testing of BC₂F₃ progeny with race TTKSK confirmed the genotyping. Forty-nine markers from published sources, four new SSR markers, and five new STARP (semi-thermal asymmetric reverse PCR) markers, were evaluated in BC₂F₂ populations for assignment of markers to bins. Sr47 was mapped to bin 3 along with 13 markers. No markers were assigned to bin 1; however, 7 and 13 markers were assigned to bins 2 and 4, respectively. Markers Xrwgs38a, Xmag1729, Xwmc41, Xtnac3119, Xrwgsnp1, and Xrwgsnp4 were found to be useful for MAS of Sr47. However, STARP markers Xrwgsnp1 and Xrwgsnp4 can be used in gel-free systems, and are the preferred markers for high-throughput MAS. The physical mapping data from this study will also be useful for pyramiding Sr47 with other Sr genes on chromosome 2B.

     

Discovery of a Highly Virulent Strain of <Emphasis Type="Italic">Photorhabdus luminescens</Emphasis> ssp<Emphasis Type="Italic">. akhurstii</Emphasis> from Meghalaya,India

Photorhabdus is an insect-pathogenic Gram negative enterobacterium found in the gut of Heterorhabditis nematodes. Photorhabdus is highly virulent to insects, and can kill insects rapidly upon injection at very low concentrations of one to few cells. We characterized the virulence of Photorhabdus symbionts isolated from the Heterorhabditis nematodes collected from various parts of India by injecting different concentrations of bacterial cells into fourth instar larval stage of insect Galleria mellonella. Photorhabdus luminescens ssp. akhurstii strain IARI-SGMG3 from Meghalaya was identified as the most virulent of all the tested strains on the basis of LT₅₀ and LC₅₀ values. This study forms a basis for further investigations on the genetic basis of virulence in Photorhabdus bacteria.     

Exploring the Least Studied Australian Eucalypt Genera: Corymbia and Angophora for Phytochemicals with Anticancer Activity against Pancreatic Malignancies

While the pharmacological and toxicological properties of eucalypts are well known in indigenous Australian medicinal practice, investigations of the bioactivity of eucalypt extracts against high mortality diseases such as pancreatic cancer in Western medicine have to date been limited, particularly amongst the genera Corymbia and Angophora. Four Angophora and Corymbia species were evaluated for their phytochemical profile and efficacy against both primary and secondary pancreatic cancer cell lines. The aqueous leaf extract of Angophora hispida exhibited statistically higher total phenolic content (107.85 ± 1.46 mg of gallic acid equiv. per g) and total flavonoid content (57.96 ± 1.93 mg rutin equiv. per g) and antioxidant capacity compared to the other tested eucalypts (P < 0.05). Both A. hispida and A. floribunda aqueous extracts showed statistically similar saponin contents. Angophora floribunda extract exerted significantly greater cell growth inhibition of 77.91 ± 4.93% followed by A. hispida with 62.04 ± 7.47% (P < 0.05) at 100 μg/ml in MIA PaCa‐2 cells with IC₅₀ values of 75.58 and 87.28 μg/ml, respectively. More studies are required to isolate and identify the bioactive compounds from these two Angophora species and to determine their mode of action against pancreatic malignancies.     

<Emphasis Type="Italic">In silico</Emphasis> analysis of methyltransferase domains involved in biosynthesis of secondary metabolites

Background  

Secondary metabolites biosynthesized by polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) family of enzymes constitute several classes of therapeutically important natural products like erythromycin, rapamycin, cyclosporine etc. In view of their relevance for natural product based drug discovery, identification of novel secondary metabolite natural products by genome mining has been an area of active research. A number of different tailoring enzymes catalyze a variety of chemical modifications to the polyketide or nonribosomal peptide backbone of these secondary metabolites to enhance their structural diversity. Therefore, development of powerful bioinformatics methods for identification of these tailoring enzymes and assignment of their substrate specificity is crucial for deciphering novel secondary metabolites by genome mining.     

Seasonal dynamics of zooplankton in a shallow eutrophic,man-made hyposaline lake in Delhi (India): role of environmental factors

Old Fort Lake, a small (1.6 ha), shallow, and recreational water body in Delhi (India) was studied through monthly surveys in two consecutive years (January, 2000–December, 2001). Precipitation is the major source of water for this closed basin lake. In addition, ground water is used for replenishing the lake regularly. This alkaline, hyposaline hard water lake contains very high ionic concentration, especially of nitrates. Based on overall ionic composition, this lake can be categorized as chloride–sulfate alkaline waters with the anion sequence dominated by SO₄ ²⁻ > Cl⁻ > HCO₃ ⁻, and the cations by Mg⁺⁺ > Ca⁺⁺. The overall seasonal variability in physicochemical profile was largely regulated by the annual cycle of evaporation and precipitation, whereas the ground water largely influences its water quality. The lake exhibited phytoplankton-dominated turbid state due to dominance of the blue green alga, Microcystis aeruginosa. The persistent cyanobacterial blooms and the elevated nutrient levels are indicative of the cultural eutrophication of the lake. This study focuses on the relative importance of eutrophic vis-à-vis hyposaline conditions in determining the structure and seasonal dynamics of zooplankton species assemblages. A total of 52 zooplankton species were recorded and rotifers dominated the community structure qualitatively as well as quantitatively. The genus Brachionus comprised a significant component of zooplankton community with B. plicatilis as the most dominant species. The other common taxa were B. quadridentatus, B. angularis, Lecane grandis, L. thalera, L. punctata, Mesocyclops sp., and Alona rectangula. Multivariate data analysis techniques, Canonical Correspondence Analysis (CCA) along with Monte Carlo Permutation Tests were used to determine the minimum number of environmental factors that could explain statistically significant (P < 0.05) proportions of variation in the species data. The significant variables selected by CCA were NH₃–N followed by percent saturation of DO, COD, SS, BOD, NO₂–N, rainfall, silicates, and PO₄–P. The results indicate that the seasonal succession patterns of the zooplankton species were largely controlled by physicochemical factors related directly or indirectly to the process of eutrophication, whereas hyposaline conditions in the lake determined the characteristic species composition. Guest Editors: J. John & B. Timms Salt Lake Research: Biodiversity and Conservation—Selected papers from the 9th Conference of the International Society for Salt Lake Research     

Design,synthesis, biological evaluation and molecular modelling studies of novel quinoline derivatives against Mycobacterium tuberculosis

We herein describe the synthesis and antimycobacterial activity of a series of 27 different derivatives of 3-benzyl-6-bromo-2-methoxy-quinolines and amides of 2-[(6-bromo-2-methoxy-quinolin-3-yl)-phenyl-methyl]-malonic acid monomethyl ester. The antimycobacterial activity of these compounds was evaluated in vitro against Mycobacterium tuberculosis H37Rv for nine consecutive days upon a fixed concentration (6.25 μg/mL) at day one in Bactec assay and compared to untreated TB cell culture as well as one with isoniazide treated counterpart, under identical experimental conditions. The compounds 3, 8, 17 and 18 have shown 92–100% growth inhibition of mycobacterial activity, with minimum inhibitory concentration (MIC) of 6.25 μg/mL. Based on our molecular modelling and docking studies on well-known diarylquinoline antitubercular drug R207910, the presence of phenyl, naphthyl and halogen moieties seem critical. Comparison of docking studies on different stereoisomers of R207910 as well as compounds from our data set, suggests importance of electrostatic interactions. Further structural analysis of docking studies on our compounds suggests attractive starting point to find new lead compounds with potential improvements.