Structure elucidation and DNA binding specificity of natural compounds from Cassia siamea leaves: A biophysical approach

Nucleic acid binding affinity and antioxidant activity of N-m-Tolyl-4-Chlorophenoxyacetohydroxamicacid

Hydroxamic acids represent a group of weak organic acids, both naturally occurring and synthetically derived, characterized by the general formula RC(= O)N(R'OH). In this study, we investigated the binding behavior of N-m-tolyl-4-chlorophenoxyaceto hydroxamic acid with calf thymus DNA (ct-DNA) and torula yeast RNA (t-RNA) through a combination of techniques including UV-visible spectroscopy, fluorescence emission analysis, viscometry, and computational simulations using AutoDock4 software. Our findings reveal that the mode of binding between the compound and the nucleic acids is consistent with intercalation. Competitive binding experiments demonstrated that the complex competes effectively with ethidium bromide (EB) for binding to ct-DNA/t-RNA, displacing EB from its binding sites. Additionally, the introduction of the compound into the DNA-EB system resulted in a quenching of fluorescence emission peaks. Analysis of absorption spectra indicated a red shift and hypochromic shift when the compound interacted with DNA, further supporting the intercalative binding mode. The calculated binding constant (Kb) value for the compound is 6.62 × 104 M-1 and 5.40 × 103 M-1 indicating a strong interaction with ct-DNA and t-RNA respectively. We determined the Stern-Volmer constants for ct-DNA and t-RNA as 9.96 × 104 M-1 and 8.13 × 105 M-1, respectively. The binding free energy values for ct-DNA/t-RNA were calculated to be - 3.741 × 107 and - 5.425 × 108 kcal/mol, respectively. Viscometric studies corroborated the UV results, showing a continuous increase in relative viscosity of ct-DNA/t-RNA solutions with the addition of the optimal hydroxamic acid concentration. Furthermore, we assessed the antioxidant activity of the compound using DPPH-radical scavenging and β-carotene linoleic acid assays. Gel electrophoresis results demonstrated the compound's remarkable efficacy in preventing DNA damage. Collectively, all experimental evidence supports the conclusion that N-m-tolyl-4-chlorophenoxyaceto hydroxamic acid binds to ct-DNA/t-RNA through an intercalative mechanism, which is consistent with our molecular docking simulations.

Multispectroscopic and computational techniques to study the interaction of anthraquinone appended sensor with calf thymus DNA

An anthraquinone based derivative (AQ) has been designed and synthesized to find its applications for the interactions with calf thymus DNA (ctDNA) involving various spectroscopic techniques, thermodynamic and computational approaches. The UV-vis studies pointed to interaction of AQ with ctDNA via groove binding mode, which has been further supported well by the ionic strength studies, viscosity measurement, circular dichroism and melting temperature (Tm) curves. These findings have been further validated by dye-displacement assay and molecular docking studies. The analysis of thermodynamic parameters supports that the AQ-ctDNA binding is entropy favoured and enthalpy disfavoured and main acting binding interaction is hydrophobic interaction. The outcomes of the molecular modelling suggested that AQ might have entered the A-T abundant area of the ctDNA.Communicated by Ramaswamy H. Sarma.

Inhibition of multiple SARS-CoV-2 proteins by an antiviral biomolecule, seselin from Aegle marmelos deciphered using molecular docking analysis

Our earlier experimental and computational report produced evidence on the antiviral nature of the compound seselin purified from the leaf extracts of Aegle marmelos against Bombyx mori Nuclear Polyhedrosis Virus (BmNPV). In the pandemic situation of COVID-19 caused by the SARS-COV-2 virus, an in silico effort to evaluate the potentiality of the seselin was made to test its efficacy against multiple targets of SARS-COV-2 such as spike protein S2, COVID-19 main protease and free enzyme of the SARS-CoV-2 (2019-nCoV) main protease. The ligand seselin showed the best interaction with receptors, spike protein S2, COVID-19 main protease and free enzyme of the SARS-CoV-2 (2019-nCoV) main protease with a binding energy of -6.3 kcal/mol, -6.9 kcal/mol and -6.7 kcal/mol, respectively. Docking analysis with three different receptors identified that all the computationally predicted lowest energy complexes were stabilized by intermolecular hydrogen bonds and stacking interactions. The amino acid residues involved in interactions were ASP1184, GLU1182, ARG1185 and SER943 for spike protein, SER1003, ALA958 and THR961 for COVID-19 main protease, and for SARS-CoV-2 (2019-nCoV) main protease, it was THR111, GLN110 and THR292. The MD simulation and MM/PBSA analysis showed that the compound seselin could effectively bind with the target receptors. The outcome of pharmacokinetic analysis suggested that the compound had favourable drugability properties. The results suggested that the seselin had inhibitory potential over multiple SARS-COV-2 targets and hold a high potential to work effectively as a novel drug for COVID-19 if evaluated in experimental setups in the foreseeable future. Communicated by Ramaswamy H. Sarma.

Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus robur) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.

Exploring the binding mechanism of β-resorcylic acid with calf thymus DNA: Insights from multi-spectroscopic, thermodynamic and bioinformatics approaches

β-resorcylic acid (BR) is a phytochemical which is widely used in the food industry as a flavouring agent and preservative. It has also been found to exhibit antibacterial action against several types of food-borne bacteria. DNA is the main molecular target for many small molecules of therapeutic importance. Hence, the interest is rapidly growing among the researchers to elucidate the interaction between small molecules and DNA. Thus, paving the way to design novel DNA-specific drugs. In this study, an attempt was made to examine the mechanism of binding of BR with calf thymus DNA (ctDNA) with the help of various experiments based on spectroscopy and in silico studies. The spectroscopic studies like UV absorption and fluorescence affirmed the complex formation between BR and ctDNA. The observed binding constant was in the order of 10³ M^-1 which is indicative of the groove binding mechanism. These findings were further verified by dye-displacement assay, potassium iodide quenching, urea denaturation assay, the study of the effect of ssDNA, circular dichroism and DNA thermal denaturing studies. Different temperature-based fluorescence and isothermal titration calorimetry (ITC) experiments were employed to evaluate thermodynamic parameters. The analysis of thermodynamic parameters supports the enthalpically driven, exothermic and spontaneous nature of the reaction between BR and ctDNA. The forces involved in the binding process were mainly found to be hydrogen bonding, van der Waals and hydrophobic interactions. The results obtained from the molecular docking and molecular dynamics (MD) simulation were consistent with the in vitro experiments, which support the groove binding mode of BR with ctDNA.

Novel indole-thiazole and indole-thiazolidinone derivatives as DNA groove binders

In this study, we report the synthesis of eight novel indole-thiazole and indole-thiazolidinone derivatives, as well as their ability to interact with DNA, analysed through the UV-vis absorption, fluorescence, circular dichroism (CD), viscosity techniques and molecular docking. The ctDNA interaction analysis demonstrated different spectroscopic effects and the affinity constants (Kb) calculated by the UV-vis absorption method were between 2.08 × 10⁵ and 6.99 × 10⁶ M^-1, whereas in the fluorescence suppression constants (Ksv) ranged between 0.38 and 0.77 × 10⁴ M^-1 and 0.60-7.59 × 10⁴ M^-1 using Ethidium Bromide (EB) and 4',6-Diamidino-2-phenylindole (DAPI) as fluorescent probes, respectively. Most derivatives did not alter significantly the secondary structure of the ctDNA according to the CD results. None of the compounds was able to change the relative viscosity of the ctDNA. These results prove that compounds interact with ctDNA via groove binding, which was confirmed by A-T rich oligonucleotide sequence assay with compound JF-252, suggesting the importance of both the phenyl ring coupled to C-4 thiazole ring and the bromo-unsubstituted indole nucleus.

Antiviral activity of seselin from Aegle marmelos against nuclear polyhedrosis virus infection in the larvae of silkworm, Bombyx mori

ETHNOPHARMACOLOGICAL RELEVANCE

Traditional Indian medicine has utilized Aeglemarmelos (L.) Corr. commonly called as bael in several indigenous systems against various diseases. Bioactive components isolated from various plant parts of A. marmelos were used in ethno-medicine. More precisely they are known for its antiviral property against various human and animal viruses.

AIM OF THE STUDY

The study was conducted to investigate the antiviral activity of A.marmelos against Bombyx mori nucleopolyhedrovirus (BmNPV).

MATERIALS AND METHODS

Among the various crude extracts tested, hexane extracts of leaves of A. marmelos with promising anti-BmNPV activity was subjected to bioactivity guided fractionation based on column chromatography. Out of 40 fractions obtained from the fractionation, fractions showing similar TLC profiles were pooled into 14 fractions. A fraction with potential activity was used to purify a molecule with anti-BmNPV activity. This molecule was characterized through structural and functional analyses.

RESULTS

The functionally and structurally characterized molecule in the fraction with prospective anti-BmNPV activity revealed a single crystal compound 'seselin' (8, 8-dimethyl pyrido oxazine-2-one).

CONCLUSION

It is therefore understood that this seselin compound could be used as a natural medicine for the management of NPV infection in the silkworm larvae under commercial conditions after suitable field evaluations.

Synthesis, characterization, anti-proliferative properties and DNA binding of benzochromene derivatives: Increased Bax/Bcl-2 ratio and caspase-dependent apoptosis in colorectal cancer cell line

3-Amino-1-aryl-1H-benzo[f]chromene-2-carbonitrile derivatives were synthesized from three-component reaction of arylaldehyde, malononitrile and 2-naphthol in the presence of 1, 4-bis(4-ferrocenylbutyl)piperazine as a new catalyst. Cytotoxic potencies of the compounds were tested on HT-29 cells. 3-Amino-1-(4-fluorophenyl)-1H-benzo[f]chromene-2-carbonitrile (4c) was more active among these compounds and was selected for further studies. Apoptosis was investigated by acridine orange/ethidium bromide (AO/EtBr) double staining and flow cytometry. The qRT-PCR was used to analyze the expression of pro- and anti-apoptotic genes. The binding attributes of 4c with calf thymus DNA (ctDNA) was examined using multi-spectroscopic measurements. We found that 4c had potent cytotoxic activity against HT-29 cells with an IC₅₀ value of 60 µM through induction of cell cycle arrest in the sub-G1 phase and apoptosis. RT-PCR analysis demonstrated down-regulation of Bcl-2 expression, while the expression of Bax, caspase-3, -8 and -9 genes was up-regulated in HT-29 cells incubated with 4c compared with control cells. These studies revealed that 4c interacts with DNA through groove binding mode with the intrinsic binding constant (K_b) of 3 × 10² M^-1. Thus, 4c is a valuable candidate for further evaluation as a new series of potent chemotherapeutic family in colon cancer treatment.

DNA-binding affinity, cytotoxicity, apoptosis, cell cycle inhibition and molecular docking studies of a new stilbene derivative

Stilbene derivatives have been found to possess promising anticancer activities against human cancer cell lines in vitro. In the present study, we have investigated cytotoxic, apoptosis induction and DNA binding activity of new stilbene derivative, (E)-1-(4-Chlorophenyl)-4,5-diphenyl-2-[4-(4-methoxystryl)phenyl]-1H-imidazol (STIM) on K562 chronic myeloid leukemia cell line. Via MTT assay STIM demonstrated cytotoxic activity against K562 cell line with IC₅₀ value of 150 µM. Apoptosis, as the mechanism of cell death, was evaluated by morphological study and flow cytometric analysis. In vitro DNA binding property of STIM has been studied by vital spectroscopic techniques, which indicated that STIM interact with ctDNA through groove binding mode and binding constant (K_b) was estimated to be 6.9 × 10⁴ M^-1. Docking studies revealed that hydrophobic is the most important interaction in STIM-DNA complex, and that the ligand (STIM) interacts with DNA via groove binding mode and the bindiyspng energy was calculated as -13.37 kcal/mol. Taken together, the present study suggests that STIM exhibits anticancer effect on K562 cell line through the induction of apoptosis as well as cell cycle arrest at Sub-G1 phase and also can bind to double helix DNA in vitro.

Deciphering composition and connectivity of a natural product with the assistance of MS and 2D NMR

A complementary application of three analytical techniques, viz. multidimensional nuclear magnetic resonance spectroscopy (NMR), mass spectrometry (MS), and single-crystal X-ray diffractometry was required to identify and refine two natural products isolated from Millettia versicolor and solvent of crystallization. The two compounds, namely 3-(2H-1,3-benzodioxol-5-yl)-6-methoxy-8,8-dimethyl-4H,8H-pyrano[2,3-h]chromen-4-one, or durmillone, (I), and (2E)-1-(4-{[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-2-hydroxyphenyl)-3-(4-hydroxyphenyl)prop-2-en-1-one, (II), could not be separated by routine column chromatography and cocrystallized in a 2:1 ratio with 0.13 molecules of ethanol solvent. Compound (II) and ethanol could not be initially identified by single-crystal X-ray analysis due to complex disorder in the aliphatic chain region of (II). Mass spectrometry ensured that (II) represented only one species disordered over several positions in the solid state, rather than several species cohabitating on the same crystallographic site. The atomic identification and connectivity in (II) were established by several 2D (two-dimensional) NMR techniques, which in turn relied on a knowledge of its exact mass. The derived connectivity was then used in the single-crystal analysis to model the disorder of the aliphatic chain in (II) over three positions and allowed identification of a partially occupied ethanol solvent molecule that was disordered over an inversion center. The disordered moieties were refined with restraints and constraints.

Structure elucidation, DNA binding specificity and antiproliferative proficiency of isolated compounds from Garcinia nervosa

Garcinia nervosa is an abundant source of bioactive phytochemicals. The present paper deals with the isolation of a novel isoflavone 5,7-dihydroxy-3-(3'-hydroxy-4',5'-dimethoxyphenyl)-6-methoxy-4H-chromen-4-one (1) along with a known compound DL-Allantoin (2) from the ethanolic extract of the leaves of Garcinia nervosa (Family: Guttiferae). Their structures were elucidated on the basis of chemical and physical evidences viz. elemental analysis, UV, FT-IR, ¹H NMR, ¹³C NMR and mass spectral analysis. Single-crystal X-ray analysis was further used for the authentication of structure of both compounds (1 and 2). Interaction studies of compound (1) and (2) with ctDNA were studied by UV-Visible spectroscopy, fluorescence, KI quenching studies, competitive displacement assay and circular dichroism studies, which showed groove binding interaction (non-intercalation) of both the compounds 1 and 2 with ctDNA. However, compound 1 (K=3.9×10⁴M^-1) shows higher binding affinity to the ctDNA than compound 2 (K=1.44×10⁴M^-1). The molecular modeling results also illustrated that compound 1 strongly binds to groove of DNA by relative binding energy of docked structure -6.82kcal/mol. In addition the antiproliferative activity also showed high potential of compound 1 against MCF-7 and MDA-MB 231 cell line with IC₅₀ value 8.44±3.5μM and 6.94±2.6μM, respectively.

Acetylcholinesterase and Cytotoxic Activity of Chemical Constituents of Clutia lanceolata Leaves and its Molecular Docking Study

Phytochemical investigations of the ethanolic extract of leaves of Clutia lanceolata (Family: Euphorbiaceae) resulted in the isolation of four compounds viz. 3,4-dihydroxy-2-methylbenzoic acid (1), 2,2'-dihydroxy-1,1'-binaphthyl (2), 1,3,8-trihydroxy-6-methylanthracene-9,10-dione (3) and 5-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,4,6-trien-3-one (4). Although all the isolated compounds were known but this was the first report from this plant source. Their structures were established on the basis of chemical and physical evidences viz. elemental analysis, FT-IR, ¹H-NMR, ¹³C-NMR and mass spectral analysis. Structure of compound 2 and 4 was further authenticated by single-crystal X-ray analysis and density functional theory calculations. The isolated compounds (1-4) were screened for AChE enzyme inhibition assay in which compound 3 and 4 were found to be more potent AChE inhibitor. Molecular docking study of potent AChE inhibitor was performed to find the probable binding mode of the compounds into the active site of receptor. Moreover, the isolated compounds were also screened for in vivo cytotoxicity by brine shrimp lethality assay.