Xanthoxylin (XAN) is a phenolic compound with well-known bioactivities, including antitumor action, that is exclusively found in the Zanthoxylum genus, commonly known as Szechuan pepper. The interplay between pharmacologically active agents and serum albumin is essential and relevant to pharmacokinetics and pharmacodynamics. This study examines the interaction between XAN and human serum albumin (HSA) using spectroscopic techniques and molecular docking, thereby expanding the scope of previous research, which has primarily focused on bovine serum albumin (BSA). The slight differences in the amino acid sequences of HSA and BSA may influence the binding characteristics of XAN. Absorption and fluorescence spectroscopy affirmed the formation of a complex between XAN and HSA. XAN quenched the intrinsic fluorescence of HSA via static mode, and the binding constant was in the order of 104 M-1, indicating moderate affinity. Thermochemical analyses revealed that the interaction is spontaneous, driven by hydrogen bonds and van der Waals forces. Forster resonance energy transfer demonstrated efficient energy transfer from HSA to XAN, while 3D fluorescence and circular dichroism spectroscopy indicated conformational changes in HSA upon binding to XAN. The thermal denaturation profile suggested that XAN destabilises HSA. Competitive displacement studies and molecular docking projected Site I of HSA as the favoured binding site for XAN . The acting forces computed by docking align with the forces deduced by thermodynamics analysis. The presence of Cu and Zn metal ions influences the binding affinity of XAN for HSA. Additionally, thebilirubin (BR) displacement studies indicate that XAN exhibits minimal displacement of BR.

DNA is one of the primary intracellular targets for various anticancer drugs. Insight into the ligand-DNA interactions is critical for developing novel, promising bioactive molecules for therapeutic use. This is greatly aided by interpreting the interaction mechanism between small molecules and natural polymeric DNAs. The binding of small molecules to the DNA alters the mechanics of the strands, resulting in the inhibition of replication and transcription, providing information on the influence of gene expression. Xanthoxylin (XAN) is a phenolic compound recognised for various therapeutic activities, including anticancer; however, its mode of interaction with DNA has not been elucidated yet. This study investigated the interaction between XAN and calf thymus DNA (Ct-DNA) using docking simulation and spectroscopic techniques. Before DNA-binding studies, XAN was subjected to in silico ADMET analysis using SwissADME and pkCSM web servers. ADMET predictions are crucial to assess the drug-likeness and the safety profile of the bioactive molecules early in the development phase. XAN demonstrated acceptable physicochemical properties, conformance to drug-likeness, and a low risk of toxicity. Docking analysis revealed two distinct binding modes: intercalation and possible minor groove binding. Hyperchromic shifts observed in absorption spectroscopy confirmed the complex formation between XAN and Ct-DNA, with an estimated association constant (Ka) in the order of 104 M−1. The thermodynamic parameters indicated a spontaneous and exothermic binding process, involving van der Waals forces and hydrogen bonding. Dye dislocation studies revealed that XAN binds via the minor groove. Circular dichroism and thermal denaturation profiles further manifested the groove binding mode of XAN. However, molecular docking studies were inconsistent in predicting the precise binding mode, only partially corroborating the in vitro findings. Plasmid nicking assays indicated that XAN does not induce DNA damage and is not a prooxidant. Conversely, it significantly reduced DNA lesions induced by the Fenton reaction, suggesting its role as a reactive oxygen species (ROS)-scavenging agent. These computational and in vitro results evinced that XAN has drug-relevant attributes and can act as a DNA-binding agent and an antioxidant.

Nanoformulations (NFs) can be used as a novel drug delivery system to treat all cancer types. One of the major drawbacks of conventional anticancer drugs is that they have poor specificity and higher toxicity towards normal cells. 5-fluorouracil (5-FU) is a well-studied anticancer drug that has a significant role in various cancers, specifically colorectal cancer therapy. This study was performed to determine the functional groups, particle size, surface charge, heterogeneity, and stability of the NF. The NFs of 5-FU were prepared through the ultrasonication technique by increasing the surfactant (Tween-80) concentrations. Among all three NFs, nanoformulated 5-FU (n5-FU) showed the most effective particle size (10.72 nm) with a zeta potential of (-4.57 mV). The cytotoxicity and apoptosis profiles confirmed that n5-FU enhanced the anticancer effect of the pure drug in HCT-116 cells, as evident from MTT assay, fluorescence microscopy, and FACS analysis. In HCT-116 cells, the IC50 values of pure and n5-FU were obtained as 41.3 μM and 18.8 μM, respectively, indicating that n5-FU was more effective against the cancer cell line. The cellular uptake study was performed to check the intake of NF in cancer cells. However, the microtubule-affinity regulating kinase-4 (MARK-4), a cancer-target protein, was purified to study the inhibition and interaction studies. The inhibition assay confirmed the inhibitory potential of 5-FU against MARK-4 protein. the multi-spectroscopic, molecular docking and MD simulation studies were performed to analyse the conformational changes, binding studies, intermolecular interactions, and stability of MARK-4 protein upon binding 5-FU. This demonstrates that NF can enhance the effectiveness of anticancer drugs.Communicated by Ramaswamy H. Sarma.

The way therapeutic compounds interact with serum protein provides valuable information on their pharmacokinetics, toxicity, effectiveness, and even their structural-related information. Isochroman (IC) is a phytochemical compound obtained from the leaves of Olea europea plant. The derivatives of IC have various pharmacological properties including antidepressants, antihistamines, antiinflammation, anticonvulsants, appetite depressants, etc. The binding of small molecules to bovine serum albumin (BSA) is useful to ensure their efficacy. Thus, in this study, we have found out the binding mode of IC with BSA using several spectroscopic and in silico studies. UV and fluorescence spectroscopy suggested the complex formation between IC and BSA with a binding constant of 10(3) M-1. IC resulted in fluorescence quenching in BSA through static mechanism. The microenvironmental and conformational changes in BSA were confirmed using synchronous and three-dimensional studies. Site marker experiment revealed the IC binding in site-III of BSA. The influence of vitamins, metals and beta-cyclodextrin (beta-CD) on binding constant of IC-BSA complex was also examined. Circular dichroism spectra showed that alpha-helical of BSA decreased upon interaction with IC. Computational and experimental results were complimentary with one another and assisted in determining the binding sites, nature of bonds and amino acids included in the IC-BSA complex formation. Communicated by Ramaswamy H. Sarma

Phenyl isothiocyanate and benzoyl isothiocyanate are the phytochemicals present in the Brassicaceae family. They have antibacterial, antiapoptotic and antifungal properties. Protein-small molecule interaction studies are done to assess the changes in structure, dynamics, and functions of protein and to decipher the binding mechanism. This study is based on the comparative binding of PT and BT with human lysozyme using in vitro and computational techniques. UV, fluorescence emission, and FRET spectra gave insight into the complex formation, quenching mechanism, and binding parameters. Both PT and BT quenched the intrinsic fluorescence of Lyz by a static quenching mechanism. Synchronous, 3D fluorescence and CD spectroscopy substantiated conformational and microenvironmental alterations in the Lyz. The metal ions and β-cyclodextrin had a pronounced effect on the binding strength of Lyz-PT and Lyz-BT complexes. Accessible surface area analysis was determined to characterise the amino acid residue packing. Molecular docking further validated the wet lab experimental results.

Cancer is a multifactorial disease that can cause morbidity and mortality in humans. An altered gene expression in cancer leads to a change in the overall activity of the human cell. Overexpression of cancer protein may give a piece of wide information about the specific type of tumor. Sphingosine kinase-1 (SK-1) is a metabolic enzyme that is mainly overexpressed in several types of cancer and other inflammatory diseases. Similarly, pyruvate kinase-M2 (PK-M2) is an important oncogenic ATP-producing glycolytic enzyme that is upregulated in most cancer cells. The phytocompound of medicinal plants such as Nigella sativa contains a variety of micronutrients that inhibit the proliferation and activity of tumor cells. In this study, the role of phytocompounds in combating cancer was studied against the model kinase proteins, that is, PK-M2 and SK-1. In silico tool like the PASS-Way2Drug server was used to predict the anticancer properties of phytocompounds. Moreover, the CLC-Pred web server provided the cytotoxicity prediction of chemical compounds against several human cancer cell lines. The pharmacokinetics and toxicity profiles were predicted by the SwissADME and pkCSM software. The binding energies were obtained by molecular docking to confirm the intermolecular interaction of selected phytocompounds with proteins. Consequently, molecular dynamics (MD) simulation confirmed the stability, conformational changes, and dynamic behavior of the kinase proteins complexed with the lead phytocompounds, that is, epicatechin, apigenin, and kaempferol.Communicated by Ramaswamy H. Sarma

A wide range of therapeutic molecules uses deoxyribonucleic acid (DNA) as an intracellular target. The interaction of small molecules to DNA is a key feature in pharmacology and plays a vital role in the development of novel and more efficient drugs with increased selective activity and enhanced therapeutic effectiveness. Isochroman (IC) is a constituent of Olea europea plant, which has been shown to exhibit several beneficial pharmacological activities. At present, its interaction studies using calf thymus DNA (ct-DNA) have not been explained. A set of multi-spectroscopic techniques has been performed to determine the interaction mechanism of isochroman with ct-DNA. Absorption spectra and quenching in fluorescence studies show that isochroman and ct-DNA form a complex. The static mode of quenching was determined by the Stern-Volmer plot. The value of binding constant, K-b = 4.0 x 10(3) M-1 revealed moderate type of binding. Effects of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and ionic strength were studied to examine the isochroman binding to ct-DNA. Potassium iodide (KI) quenching effects and competitive binding studies clearly showed that isochroman binds in the minor groove of ct-DNA. Circular dichroic and DNA melting experiments also confirmed these results. The experimental outputs were further corroborated via in silico computational modelling studies. Lipinski's rule of 5 and SwissADME showed drug-likeness and oral bioavailability scores. Protox CYRILLIC CAPITAL LETTER BYELORUSSIAN-UKRAINIAN ICYRILLIC CAPITAL LETTER BYELORUSSIAN-UKRAINIAN I online software predicts oral and organ toxicity. Communicated by Ramaswamy H. Sarma

H2 receptor antagonists are the medication given for treating stomach ulcers, but lately, reports have shown their role in healing several malignant ulcers. The present work entails the interaction of H2 blocker nizatidine with calf thymus (ct)-DNA for determining the binding mode and energetics of the interaction. Multi-spectroscopic, calorimetric, viscometric and bioinformatic analysis revealed that nizatidine interacted with ct-DNA via groove-binding mode and is characterised by exothermic reaction. Moreover, assessment of genotoxic potential of nizatidine in vitro was carried out in peripheral human lymphocytes by alkaline comet assay. DNA damage occurred at high concentrations of nizatidine. Genotoxicity of nizatidine was also evaluated in vivo by assessing cytogenetic biomarkers viz. micronuclei formation and chromosomal aberration test. Nizatidine was able to induce micronuclei formation and chromosomal damage at high dose. Additionally, cytotoxic activity of nizatidine was determined in cancer cell lines, namely HeLa and HCT-116 and compared with the normal human cell line HEK-293 employing MTT assay. It was observed that nizatidine was more toxic towards HeLa and HCT-116 than HEK-293. Cell morphology analysis by compound inverted microscopy further strengthens the finding obtained through MTT assay.

The bovine serum albumin (BSA) is a model carrier protein that transports and deposits the various endogenous and exogenous ligands in the body. β-resorcylic acid (BR) is a phyto-phenolic molecule mainly used in the food industry because of its antibacterial, flavouring and preservative nature. The interactions of small ligand molecules with proteins are of great importance for researchers from the pharmacology perspective. This article explains the mechanism of binding of BR with BSA with the help of multi-spectroscopic approaches and molecular modelling. The UV absorption and fluorescence spectroscopy affirmed the formation of BSA-BR complex. The thermodynamic studies confirmed the nature of the reaction to be spontaneous and exothermic, and the stabilisation of the complex by van der Waals interactions and hydrogen bonding. The energy transfer was found to occur with a high probability. BR induced the microenvironmental and conformational alterations BSA as revealed by synchronous spectra, 3D fluorescence maps, circular dichroism (CD), resonance-enhanced Rayleigh scattering (RRS), red edge excitation shift (REES) and Fourier transform infrared (FT-IR). The β-cyclodextrin (β-cd), metals and vitamins largely influenced the BR-BSA binding strength. Competitive displacement assays further elucidated the BR binds to BSA at subdomain IIIA (site II). Molecular docking and simulations computationally validated the results of the wet lab experiments.

Cancer, as a multifactorial disease, damages healthy cells and organs.

Cancer is a multifactorial disease that can cause morbidity and mortality in humans. An altered gene expression in cancer leads to a change in the overall activity of the human cell. Overexpression of cancer protein may give a piece of wide information about the specific type of tumor. Sphingosine kinase-1 (SK-1) is a metabolic enzyme that is mainly overexpressed in several types of cancer and other inflammatory diseases. Similarly, pyruvate kinase-M2 (PK-M2) is an important oncogenic ATP-producing glycolytic enzyme that is upregulated in most cancer cells. The phytocompound of medicinal plants such as Nigella sativa contains a variety of micronutrients that inhibit the proliferation and activity of tumor cells. In this study, the role of phytocompounds in combating cancer was studied against the model kinase proteins, that is, PK-M2 and SK-1. In silico tool like the PASS-Way2Drug server was used to predict the anticancer properties of phytocompounds. Moreover, the CLC-Pred web server provided the cytotoxicity prediction of chemical compounds against several human cancer cell lines. The pharmacokinetics and toxicity profiles were predicted by the SwissADME and pkCSM software. The binding energies were obtained by molecular docking to confirm the intermolecular interaction of selected phytocompounds with proteins. Consequently, molecular dynamics (MD) simulation confirmed the stability, conformational changes, and dynamic behavior of the kinase proteins complexed with the lead phytocompounds, that is, epicatechin, apigenin, and kaempferol.Communicated by Ramaswamy H. Sarma

4,6-Diacetylresorcinol (1) and 3-O-methylellagic acid dihydrate (2), both biologically significant compounds, were extracted from Bixa orellana and studied using IR, 1H, and 13C NMR, and UV-vis spectroscopic techniques. X-ray crystallographic techniques were also used to establish the molecular structure of the isolated compounds 1 and 2. Geometric parameters, vibrational frequencies, and gauge including atomic orbital (GIAO) 1H and 13C NMR of 1 and 2 in the ground state were computed by the density functional theory (DFT) using B3LYP/6-311G(d,p) basis set backing up experimental studies and established the correct structure of isolated compounds. The parameters obtained from the combined DFT, and X-ray diffraction studies are mutually agreed to establish correct structures of 1 and 2. In addition, an electrostatic potential map and HOMO−LUMO energy gap were made using the DFT calculation to determine the distribution of energy and the chemical reactivity region of the isolated compounds. The current study also provides further insights into the interaction of compound 2 with ct-DNA using numerous biophysical and in silico techniques. Moreover, in silico studies indicate that compound 2 binds to the DNA in the minor groove. Lipinski’s rule of five revealed a higher tendency of compound 2 towards drug-likeness. The bioavailability and synthetic accessibility score for compound 2 was found to be 0.55 and 3.21, suggesting that compound 2 could serve as an effective therapeutic candidate.

The binding mechanism between human lysozyme (Lyz) and beta-resorcylic acid (BR) was systematically examined by various biophysical and computational techniques. The studies like ultraviolet absorbance and steady-state fluorescence confirmed the complex formation with binding constant in the order of 10(3) M-1. The mechanism of fluorescence quenching of Lyz was found to be static. The average binding distance between Lyz and BR was calculated by FRET as per Forster's theory. The changes in conformation and microenvironment in the secondary structure of Lyz in the presence of BR were confirmed by techniques like synchronous, three-dimensional fluorescence spectroscopy, Red edge excitation shift (REES) and circular dichroism (CD). The different temperature-based fluorescence experiments highlighted that the reaction is spontaneous and exothermic in nature. The van der Waals and hydrogen bonding are the main contributing forces in the complex formation as is evident from the negative values of enthalpy (Delta H) and entropy (Delta S). Further, the results obtained from in vitro experiments were also reaffirmed by in silico molecular docking, predicting the active binding site of BR in Lyz. HOMO-LUMO energy gap in BR was estimated by density functional theory (DFT) studies. Moreover, the effects of beta-cyclodextrin, metal ions, and vitamins on the binding of BR with Lyz were also studied. (C) 2021 Elsevier B.V. All rights reserved.

Phytochemical investigations of the ethanolic extract of leaves of Crateva religiosa (Family: Capparaceae) resulted in the isolation of four compounds viz. (E)-ethyl-4-((3-(4-hydroxyphenyl)acryloyl)oxy)-2-methyl-5-oxotetrahydrofuran-2-carboxylate (Cg-1) named as Cratin, Cg-2, Cg-3, and Cg-4. Cg-1 has been reported for the first time from any natural source and has not been synthesized so far. Cg-2, Cg-3, and Cg-4 were also isolated first time from this plant source. Their structures were elucidated based on chemical and physical data viz. (elemental analysis, FT-IR, UV, H-1 NMR, C-13 NMR, and mass). Single crystal X-ray analysis was further used for the authentication of the structure of the isolated compounds in the case of Cg-1, including chemical modification of kaempferol (Cg-2) to Cg-2-Me, to get suitable crystals for X-ray diffraction study. The isolated novel compound Cg-1 and the methyl ether of kaempferol (Cg-2-Me) were screened for DNA binding studies with ct-DNA using UV-visible spectroscopy, fluorescence spectroscopy, and circular dichroism studies. Molecular docking was performed to understand the interaction between DNA and the compounds studied and showed groove binding interaction (non-intercalation). (C) 2021 Elsevier B.V. All rights reserved.

Memantine belongs to the class of cognition enhancers that functions as NMDA receptor antagonist, used to treat Alzheimer's disease. The interaction of memantine with DNA was not investigated. In the present study, the interaction of memantine with ct-DNA, as well as its cytotoxicity on cancer cells, was evaluated. UV-visible spectroscopy, steady-state fluorescence spectroscopic studies revealed the interaction between memantine and ct-DNA. The quenching studies, chemical denaturation, (CD), and DNA melting studies showed the groove binding mode of memantine with ct-DNA. The thermodynamic parameters revealed that the interaction between memantine and ct-DNA is enthalpically driven, and the stabilizing forces involved were hydrogen bonding and van der Waals interaction. The groove-binding was also observed by molecular docking studies, which corroborated the findings of spectroscopic investigations. Density function theory calculations confirmed the existence of electron donor and recipient groups. The stability of memantine and DNA interaction, as well as the critical residues involved in the interaction, was identified by molecular dynamics simulations. Memantine showed cytotoxicity towards the cancer cells as compared to normal cells, as observed by MTT assay. Inverted compound microscopy analysis of memantine treated cancer cell lines further confirmed the results obtained by MTT assay.Communicated by Ramaswamy H. Sarma.

Nanomedicine is a development of nanotechnology in medical research that can be used to discover an advanced treatment for all types of cancer. Conventional drug delivery systems (DDS) of chemotherapeutic drugs placed some critical challenges correlated with the poor specificity, sensitive toxicity, and therapeutic efficacy. Therefore, nanoformulation (NF) of chemotherapeutic drugs pledges to develop advanced DDS with lesser side effects and greater efficacy than the traditional treatments. The nanoscale formulation of chemotherapeutic drugs often referred to as cancer nanomedicines (CNs), assists in delivering and targeting the pharmaceutical, therapeutic, and diagnostic agents to cancer and other targeted cells. Consequently, NF of combined chemotherapeutic drugs improves the DDS by increasing the circulation time and bioavailability. This review summarizes a brief study of CNs, describing their multifunctionality, types of nano-carriers, the status of NFs in clinical trials, and enhanced efficacy of CNs and combined formulations to reduce the off-target toxic effect of chemotherapeutic drugs.

The molecular mechanism behind the anti-cancer potential of dipyridamole, an antiplatelet drug was investigated by examining the interaction of dipyridamole with DNA as well as the genotoxicity and cytotoxicity associated with dipyridamole . Interaction of dipyridamole with calf thymus DNA (Ct-DNA) was determined in order to ascertain the strength and mode of binding as well as the thermodynamic parameters involved. Dipyridamole interacts with Ct-DNA through a groove binding mechanism. Furthermore, a preliminary assessment of the genotoxic effect of dipyridamole was performed in vitro using the plasmid nicking assay and comet assay. Genotoxicity was also confirmed through DAPI nuclear staining of HeLa and HCT-116 cells. Cytotoxicity was assessed in vitro on HeLa, HCT-116 as well as HEK293 cells using the MTT assay as well as through inverted microscopy. Dipyridamole was selectively more toxic towards cancer cells. Dipyridamole demonstrated induction of micronucleus and chromosomal aberrations only at high concentrations in bone marrow cells of male Wistar rats, suggesting its safe usage at clinically relevant concentrations. These results indicated the existence of an intrinsic genotoxic potential of dipyridamole which may be contributing to its anti-cancer properties . (c) 2021 Elsevier B.V. All rights reserved.

beta-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 10(3) 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. (C) 2021 Elsevier B.V. All rights reserved.

Scopolamine is used to treat various CNS disorder like urinary incontinence, motion sickness, spasmic movements. Despite its pharmaceutical properties, its interaction with DNA is not yet reported. In this article, the interaction between scopolamine and ct-DNA is reported using a combination of biophysical techniques. UV–visible and steady-state fluorescence spectroscopy were used to study interaction and complex formation. Competitive displacement assays and potassium iodide quenching confirmed the mode of binding between scopolamine and DNA. Structural changes induced in the ct-DNA in the presence of scopolamine were evaluated by CD spectroscopy. The plasmid nicking and NBT assay confirmed the genotoxic effect of scopolamine. In-silico study by molecular docking and molecular dynamics simulation revealed the mode of interaction, major stabilizing forces as well as the nucleotide sequences to which the scopolamine binds.

The interaction between proteins and drugs/ligands has been explored thoroughly over the past years. Numerous spectroscopic and in silico tools are employed to decipher the binding mechanism of drugs/ligands with serum albumin. Serum albumin is the principal component present in the blood plasma and is responsible for carrying both exogenous and endogenous substances to its target site. The binding affinity between drugs/ligands and serum albumin plays a significant role in designing novel drugs/ligands and altering the doses of pre-existing drugs/ligands to achieve the desired therapeutic efficacy. This review mainly focuses on various techniques used to study the binding mechanism involved between drugs/ligands and serum albumin. Moreover, several techniques that can be implemented to explore the conformational changes induced in serum albumin during the transport process are also discussed. These techniques come up with data that are simple to interpret and give reliable information regarding the interaction between therapeutic molecules and proteins.