Molecular recognition pattern of cytotoxic alkaloid vinblastine with multiple targets

Molecular interaction of antiviral drug penciclovir with DNA and HSA insights from experimental and docking studies

One approach to accelerate the availability of new cancer drugs is to test drugs approved for other conditions as anticancer agents. During recent decades, penciclovir (PNV) has been frequently utilized as a potent antiviral drug, in particular against infections caused by herpes viruses. Many antivirals interact with DNA and change their expression level, so determining the binding mode is of great importance. In our laboratory, we have focused our attention to design improved drugs that target cellular DNA, to understand the mechanism of action at the molecular level, and also to investigate the effect of antiviral drugs as anticancer agents. The results of ct-DNA-PNV interactions at physiological pH using fluorescence spectroscopy, UV-visible absorption spectroscopy, and molecular modeling reveal this drug binds well to ct-DNA through groove binding. The circular dichroism measurements displayed that PNV caused a slight change in the DNA structure which affirmed that the binding of PNV with the DNA occurs through the groove mode. Besides, multi-spectroscopic and molecular docking were used to evaluate how PNV interacts with human serum albumin under physiological conditions. The findings of fluorescence quenching suggested that static quenching was involved in the spontaneous development of HSA-PNV complex through hydrophobic force. The docking simulation results validated the findings of spectroscopic techniques.Communicated by Ramaswamy H. Sarma.

Binding studies of sertraline hydrochloride with CT-DNA using experimental and computational techniques

Sertraline Hydrochloride (STH) is an antidepressant drug that belongs to the selective serotonin reuptake inhibitor family (SSRIs), which inhibits serotonin uptake in presynaptic nerve fibers. The use of these medications without a legitimate prescription might result in adverse effects, and in rare circumstances, death. The interaction mechanism and binding mode of STH with duplex DNA were extensively investigated using spectroscopic and modeling techniques at different temperatures. The hypochromic shift of the absorption spectra of STH on binding with CT-DNA indicated groove binding. Fluorescence spectroscopic studies showed that CT-DNA quenches the fluorescence intensity of STH through a static quenching mechanism. The thermodynamic parameters indicated that the complex formation was spontaneous, and enthalpy driven. The competitive displacement binding study revealed that STH displaced DAPI from the minor groove of DNA. Molecular docking and molecular dynamics simulations also revealed that the complex was stable over 150 ns and that STH preferred the minor groove of DNA. The binding energy of the stable conformations were evaluated through MM/PBSA methods. A comparison of the bound poses at different timescales showed minor changes in STH structure upon DNA binding. Furthermore, a structural analysis of CT-DNA indicated that STH induced changes in the sugar-phosphate backbone had an impact on the minor groove's width which are in agreement with the CD spectroscopic results. This study provides a better understanding of STH binding with duplex DNA.

A comparison on the biochemical activities of Fluorescein disodium, Rose Bengal and Rhodamine 101 in the light of DNA binding, antimicrobial and cytotoxic study

Biochemical activities of Fluorescein, Rose Bengal and Rhodamine 101 were studied by DNA binding, antibacterial and cytotoxic studies. DNA binding studies were done using spectroscopic, thermodynamic and molecular modeling techniques. Antibacterial activities were investigated against a gram-negative bacteria Escherichia coli and a gram-positive bacteria Staphylococcus aureus. Cytotoxic activities were studied against Wi-38 cell line. We observed these dyes bound to minor groove of DNA and structural diversity of dyes affect the phenomenon. No significant antibacterial and cytotoxic activities of these dyes were found in our observations.

Thermodynamic and structural profiles of multi-target binding of vinblastine in solution

Structural information about drug-receptor interactions is paramount in drug discovery and subsequent optimization processes. Drugs can bind to multiple potential targets as they contain common chemical entities in their structures. Understanding the details of such interactions offer possibilities for repurposing and developing potent inhibitors of disease pathways. Vinblastine (VLB) is a potent anticancer molecule showing multiple receptor interactions with different affinities and degrees of structural perturbations. We have investigated the multi-target binding profile of VLB with DNA and human serum albumin (HSA) in a dynamic physiological environment using spectroscopic, molecular dynamics simulations, and quantum mechanical calculations to evaluate the structural features, mode, ligand and receptor flexibility, and energetics of complexation. These results confirm that VLB prefers to bind in the major groove of DNA with some inclination toward Thymidine residue and the TR-5 binding site in HSA with its catharanthine half making important contacts with both the receptors. Spectroscopic investigation at multiple temperatures has also proved that VLB binding is entropy driven indicating the major groove and TR-5 binding site of interaction. Finally, the overall binding is facilitated by van der Waals contacts and a few conventional H-bonds. VLB portrays reasonable conformational diversity on binding with multiple receptors.

Structural aspects of formetanate hydrochloride binding with human serum albumin using spectroscopic and molecular modeling techniques

Formetanate Hydrochloride (FMT), a highly potent chemical, acts as an insecticide, acaricide, and miticide to protect various fruits and vegetables. The widespread use elevates concern about its presence in the ecosystem, impact upon human health via interaction with biological receptors. Spectroscopic and molecular modeling techniques at different temperatures were used to investigate the binding of FMT with Human serum albumin (HSA) at the molecular level. The experimental and computational results have provided the binding affinity, binding mode, conformational flexibility, and thermodynamic profile of FMT-HSA complex. The FMT binding appears to be spontaneous, and entropy driven. Overall binding affinity of FMT falls within -7.29 to -4.67 Kcal M-1. FMT binds in domain I, subdomain IA of HSA and is stabilized by hydrophobic interactions. Molecular dynamics simulations of the FMT-HSA complex over 100 ns at 288 K, 298 K and 308 K indicated that FMT showed minor adjustments in conformation and placement within the binding site. While, MM/PBSA analysis of the complex provided individual contributions of energy terms. Quantum mechanical (QM) calculations were used to calculate absolute energy values of different poses of FMT which in turn showed minor variations in energy suggesting slight conformational variation in the bound form. The computational results are in agreement with experimental findings.

Depicting the DNA Binding and Cytotoxicity Studies against Human Colorectal Cancer of Aquabis (1-Formyl-2-Naphtholato-k2O,O′) Copper(II): A Biophysical and Molecular Docking Perspective

In this study, we attempted to examine the biological activity of the copper(II)–based small molecule aquabis (1-formyl-2-naphtholato-k2O,O′)copper(II) (1) against colon cancer. The characterization of complex 1 was established by analytical and spectral methods in accordance with the single-crystal X-ray results. A monomeric unit of complex 1 exists in an O4 (H2O) coordination environment with slightly distorted square pyramidal geometry (τ = ~0.1). The interaction of complex 1 with calf thymus DNA (ctDNA) was determined by employing various biophysical techniques, which revealed that complex 1 binds to ctDNA at the minor groove with a binding constant of 2.38 × 105 M–1. The cytotoxicity of complex 1 towards human colorectal cell line (HCT116) was evaluated by the MTT assay, which showed an IC50 value of 11.6 μM after treatment with complex 1 for 24 h. Furthermore, the apoptotic effect induced by complex 1 was validated by DNA fragmentation pattern, which clarified that apoptosis might be regulated through the mitochondrial-mediated production of reactive oxygen species (ROS) causing DNA damage pathway. Additionally, molecular docking was also carried out to confirm the recognition of complex 1 at the minor groove.

A comparative study based on activity, conformation and computational analysis on the inhibition of human salivary aldehyde dehydrogenase by phthalate plasticizers: Implications in assessing the safety of packaged food items

Phthalate plasticizers are commonly used in various consumer-end products. Human salivary aldehyde dehydrogenase (hsALDH) is a detoxifying enzyme which defends us from the toxic aldehydes. Here, the effect of phthalates [Di-2-ethylhexyl phthalate (DEHP), Diethyl phthalate (DEP) and Dibutyl phthalate (DBP)] on hsALDH has been investigated. These plasticizers inhibited hsALDH, and the IC₅₀ values were 0.48 ± 0.04, 283.20 ± 0.09 and 285.00 ± 0.14 μM for DEHP, DEP and DBP, respectively. DEHP was the most potent inhibitor among the three plasticizers. They exhibited mixed-type linear inhibition with inclination towards competitive-non-competitive inhibition. They induced both tertiary and secondary structural changes in the enzyme. Quenching of intrinsic hsALDH fluorescence in a constant manner was observed with a binding constant (K_b) of 8.91 × 10⁶, 2.80 × 10⁴, and 1.31 × 10⁵ M^-1, for DEHP, DEP and DBP, respectively. Computational analysis showed that these plasticizers bind stably in the proximity of hsALDH catalytic site, reciprocating via non-covalent interactions with some of the amino acids which are evolutionary conserved. Therefore, exposure to these plasticizers inhibits hsALDH which increases the risk of aldehyde induced toxicity, adversely affecting oral health. The study has implications in assessing the safety of packaged food items which utilize phthalates.

Antileishmanial Potential of Berberine Alkaloids From Berberis glaucocarpa Roots: Molecular Docking Suggests Relevant Leishmania Protein Targets

Leishmaniases are a spectrum of poverty-linked neglected parasitic diseases that are endemic in 88 countries around the globe and affect millions of people every year. Currently available chemotherapeutic options are inadequate due to side effects, high cost, prolonged treatment, and parasite resistance. Thus, there is an existing need to develop new potent and safer leishmanicidal drugs. Considering the folkloric antiulcer and leishmanicidal use of the genus Berberis and its alkaloids, 5 reported alkaloids, namely berberine (1), palmatine (2), columbamine (3), 8-trichloromethyldihydroberberine (4), and jatrorrhizine (5), were isolated from the roots of Berberis glaucocarpa using classical (column and preparative chromatography) and modern isolation techniques (Sephadex LH-20). Their structures were elucidated and established from 1D and 2D spectroscopic data. The isolated alkaloids displayed excellent antileishmanial potential with IC50 values ranging from 1.50 to 2.56 µM: 1 (1.50 ± 0.53 µM), 2 (2.31 ± 0.37 µM), 3 (2.56 ± 0.48 µM), 4 (1.40 ± 0.90 µM), 5 (2.44 ± 1.34 µM). While the IC50 value for the standard drug (Amphotericin-B) was found to be 1.08 ± 0.95 µM. All of the isolated alkaloids displayed excellent antileishmanial potential as well as minimal cytotoxicity against THP-1 monocytic cells. Molecular docking analysis has revealed Leishmania N-myristoyl transferase, methionyl-tRNA synthetase, pteridine reductase 1, oligopeptidase B, tyrosyl-tRNA synthetase, and/or glycerol-3-phosphate dehydrogenase to be potential protein targets for the alkaloids.

Computer-Aided Drug Design Applied to Secondary Metabolites as Anticancer Agents

Computer-Aided Drug Design (CADD) techniques have garnered a great deal of attention in academia and industry because of their great versatility, low costs, possibilities of cost reduction in in vitro screening and in the development of synthetic steps; these techniques are compared with highthroughput screening, in particular for candidate drugs. The secondary metabolism of plants and other organisms provide substantial amounts of new chemical structures, many of which have numerous biological and pharmacological properties for virtually every existing disease, including cancer. In oncology, compounds such as vimblastine, vincristine, taxol, podophyllotoxin, captothecin and cytarabine are examples of how important natural products enhance the cancer-fighting therapeutic arsenal. In this context, this review presents an update of Ligand-Based Drug Design and Structure-Based Drug Design techniques applied to flavonoids, alkaloids and coumarins in the search of new compounds or fragments that can be used in oncology. A systematical search using various databases was performed. The search was limited to articles published in the last 10 years. The great diversity of chemical structures (coumarin, flavonoids and alkaloids) with cancer properties, associated with infinite synthetic possibilities for obtaining analogous compounds, creates a huge chemical environment with potential to be explored, and creates a major difficulty, for screening studies to select compounds with more promising activity for a selected target. CADD techniques appear to be the least expensive and most efficient alternatives to perform virtual screening studies, aiming to selected compounds with better activity profiles and better "drugability".

Insight into the In Vitro Antiglycation and In Vivo Antidiabetic Effects of Thiamine: Implications of Vitamin B1 in Controlling Diabetes

Hyperglycemia is considered to be a driving factor for advanced glycated end products (AGEs) formation. Inhibition of this process plays a vital role in reducing the problems of diabetes. This study aimed to explore the in vitro antiglycation and in vivo antidiabetic effect of thiamine. Human serum albumin (HSA) was used as a model protein to delineate the antiglycation potential of thiamine. Fructosamine levels were low in the presence of thiamine, implying the inhibition of early stages of glycation by thiamine. Furthermore, HSA-glucose assays depict the inhibition of post-Amadori products by thiamine. CD spectroscopy suggested fewer alterations in the secondary structure in the presence of thiamine. It was found that the administration of thiamine to diabetic rats leads to an increase in hexokinase activity and increased insulin secretion coupled with glycolysis utilization of glucose. Moreover, the activity of glucose-6-phosphatase and fructose- 1-6-phosphatase (increased in the liver and kidney of diabetic rats) is restored to near-normal levels upon thiamine administration. Histopathological studies also advocated that thiamine supplementation decreases the pathological abnormalities associated with diabetes in the liver and kidney. This study provides a rationale that vitamins can be implicated in controlling diabetes.

Mechanistic insight into glycation inhibition of human serum albumin by vitamin B9: Multispectroscopic and molecular docking approach

Advanced glycation end products (AGEs) formation produces free radicals that play a role in diabetes mellitus; hence inhibition of glycation plays a part in minimizing diabetes-related complications. This study was intended to examine the AGEs formation of HSA upon prolonged incubation of 28 days at 37 °C and further investigate the antiglycation potential of folic acid (FA). FA shows a significant binding affinity to the HSA with a binding constant (K) of 10⁴ M^-1. The evaluation of enthalpy change (∆H⁰) and entropy change (∆S^o) implied that the HSA-FA complex is stabilized primarily by hydrophobic interaction and hydrogen bonding. Molecular docking analysis depicted that FA binds with HSA in subdomain IIA (Sudlow's site I) with a binding energy of -7.0 kcal mol^-1. AGEs were characterized by free lysine and thiol groups, carbonyl content, and AGEs specific fluorescence. The presence of FA significantly decreased glycation from free lysine and carbonyl content estimation and AGEs specific fluorescence. Multispectroscopic observations and molecular docking and examination of various biomarkers demonstrate the antiglycation activity of FA and its capacity to prevent disease progression in diabetes.

Naringin inhibits the biofilms of metallo-β-lactamases (MβLs) producing Pseudomonas species isolated from camel meat

Food producing animals harbouring bacteria carrying drug resistance genes especially the metallo-beta-lactamase (MBL) pose high risk for the human population. In addition, formation of biofilm by these drug resistant pathogens represents major threat to food safety and public health. In this study, metallo-β-lactamases (MβLs) producing Pseudomonas spp. from camel meat were isolated and assessed for their biofilm formation. Further, in vitro and in silico studies were performed to study the effect of flavone naringin on biofilm formation against isolated Pseudomonas spp. A total of 55% isolates were found to produce metallo-β-lactamase enzyme. Naringin mitigated biofilm formation of Pseudomonas isolates up to 57%. Disturbed biofilm architecture and reduced the colonization of bacteria on glass was observed under scanning electron microscope (SEM) and confocal laser scanning microscope (CLSM). The biofilm related traits such as exopolysaccharides (EPS) and alginate production was also reduced remarkably in the presence of naringin. Eradication of preformed biofilms (32–60%) was also observed at the respective 0.50 × MICs. Molecular docking revealed that naringin showed strong affinity towards docked proteins with binding energy ranging from −8.6 to −8.8 kcal mol⁻¹. Presence of metallo-β-lactamase producers indicates that camel meat could be possible reservoir of drug-resistant Pseudomonas species of clinical importance. Naringin was successful in inhibiting biofilm formation as well as eradicating the preformed biofilms and demonstrated strong binding affinity towards biofilm associated protein. Thus, it is envisaged that naringin could be exploited as food preservative especially against the biofilm forming food-borne Pseudomonas species and is a promising prospect for the treatment of biofilm based infections.

Glyburide inhibits non-enzymatic glycation of HSA: An approach for the management of AGEs associated diabetic complications

Advanced glycation endproducts (AGEs) are the final product of glycation, highly reactive in nature and contribute directly or indirectly to numerous complications related to diabetes. In this study, the antiglycation activity of glyburide was investigated using HSA as model protein, both against glucose and methylglyoxal mediated glycation. The possible mechanism of action was also deciphered using biophysical and computational tools. Approximately 70% inhibition of both early and advanced glycation end products were recorded in the presence of glyburide. Free lysine modification was reduced by glyburide treatment and improvement in biochemical markers such as free thiol groups and carbonyl content was observed. Interaction studies revealed that glyburide showed moderate to strong binding affinity towards HSA with binding constant in the order of 10⁶ M^-1. The interaction of glyburide with HSA was entropically favourable and spontaneous in nature. Molecular dynamics simulation deciphered that glyburide-HSA complex was quite stable where RMSD, RMSF, R_g, SASA, and secondary structure of HSA remained approximately same over the entire simulation period. The average binding energy of the MD simulation for glyburide-HSA complex was found to be -15.386 kJ mol^-1. The findings demonstrate the antiglycation potential of glyburide and its possible mechanism of action.

Carbamylation of human serum albumin generates high-molecular weight aggregates: fine characterization by multi-spectroscopic methods and electron microscopy

Carbamylation is the non-enzymatic reaction between isocyanic acid and macromolecules (mainly proteins) which results in carbamylation-derived products (CDPs) generation, wherein the macromolecules show altered structure and function. In this study, we examined the modifications caused in human serum albumin (HSA) upon interaction with potassium cyanate (KCNO). HSA was incubated with varying concentrations of KCNO for 6 h at 37 °C. The resultant product was characterized by biochemical and biophysical techniques. Among other changes, the carbamylated-HSA showed homocitrulline generation (LC-MS), increase in mass (DLS), and amyloidogenic aggregate formation (Congo red, SEM, TEM). The Gibb's free energy was calculated to be -2.91 to -3.95 kcal mol^-1, suggesting that the binding was spontaneous and energetically favourable. The results indicate that in chronic kidney disease patients, elevated levels of isocyanic acid (formed from urea) may modify the albumin structure and lead to its conversion into amyloidogenic aggregates, thus accelerating kidney damage.

Targeting stress granules: A novel therapeutic strategy for human diseases

Stress granules (SGs) are assemblies of mRNA and proteins that form from mRNAs stalled in translation initiation in response to stress. Chronic stress might even induce formation of cytotoxic pathological SGs. SGs participate in various biological functions including response to apoptosis, inflammation, immune modulation, and signalling pathways; moreover, SGs are involved in pathogenesis of neurodegenerative diseases, viral infection, aging, cancers and many other diseases. Emerging evidence has shown that small molecules can affect SG dynamics, including assembly, disassembly, maintenance and clearance. Thus, targeting SGs is a potential therapeutic strategy for the treatment of human diseases and the promotion of health. The established methods for detecting SGs provided ready tools for large-scale screening of agents that alter the dynamics of SGs. Here, we describe the effects of small molecules on SG assembly, disassembly, and their roles in the disease. Moreover, we provide perspective for the possible application of small molecules targeting SGs in the treatment of human diseases.

Glyoxal Induced Transition of Transferrin to Aggregates: Spectroscopic, Microscopic and Molecular Docking Insight

BACKGROUND & OBJECTIVE

The present study was aimed at characterizing the conformational alterations induced in human transferrin, the iron regulatory protein by glyoxal. Since protein aggregation is at the core of many disorders, thus interest in this domain has increased significantly during the past years.

METHODS

In our present study, the effect of glyoxal was monitored on human transferrin using multispectroscopic and multi-microscopic studies.

RESULTS

Intrinsic fluorescence spectroscopy suggested changes in native conformation of human transferrin evident by decreased fluorescence and blue shift in the presence of glyoxal. Further, extrinsic fluorescence was retorted and the results showed the formation of aggregates; apparent by increased Congo red (CR) absorbance, Thioflavin T (ThT) and ANS fluorescence and TEM of human transferrin in the presence of glyoxal. Molecular docking was also employed to see which residues are at core of human transferrin and glyoxal interaction. Reactive oxygen species (ROS) generation assays revealed enhanced ROS levels by human transferrin after treatment with glyoxal.

CONCLUSION

Thus, our study proposes that glyoxal induces the formation of aggregates in human transferrin. These aggregates further generate ROS which are key players in the complications associated with diabetes mellitus, giving our study clinical perspective.

Unravelling the interaction of glipizide with human serum albumin using various spectroscopic techniques and molecular dynamics studies

Glipizide is known to stimulate insulin secretion by β-cells of the pancreas. It is a second-generation sulfonylurea drug used in the management of type 2 diabetes. The shorter biological half-life makes it a suitable candidate to be designed as a controlled release formulation. Human serum albumin (HSA), a major plasma protein plays a crucial role in the transportation of drugs, hormones, fatty acids, and many other molecules and determines their physiological fate and biodistribution. In this study, the interaction of glipizide with HSA was investigated under physiological conditions using multi-spectroscopic techniques corroborated with molecular docking and dynamics approach. It was found that glipizide integrates to HSA with a binding constant in the order of 10⁵ M^-1. The mode of fluorescence quenching by glipizide is static in nature with one binding site. Glipizide preferentially interacts with sub-domain IIA of HSA and their complexion is thermodynamically favorable. This interaction results in the loss of α-helical content of HSA. The energy transfer efficiency from HSA to glipizide was found to be 26.72%. In silico molecular docking and simulation studies ratified in vitro findings and revealed that hydrogen bonds and hydrophobic interactions are accountable for glipizide-HSA complex formation.Communicated by Ramaswamy H. Sarma.

Metabolites of Vinca Alkaloid Vinblastine: Tubulin Binding and Activation of Nausea-Associated Receptors

Vinblastine (VLB) is an antimitotic drug that binds to the vinca site of tubulin. The molecule possesses a high molecular weight and a complex chemical structure with many possibilities of metabolization. Despite advances in drug discovery research in reducing drug toxicity, the cause and mechanism of VLB-induced adverse drug reactions (ADRs) remains poorly understood. VLB is metabolized to at least 35 known metabolites, which have been identified and collected in this present work. This study also explores how VLB metabolites affect nausea-associated receptors such as muscarinic, dopaminergic, and histaminic. The metabolites have stronger binding interactions than acetylcholine (ACh) for muscarinic M₁, M₄, and M₅ receptors and demonstrate similar binding profiles to that of the natural substrate, ACh. The affinities of VLB metabolites to dopaminergic and histaminic receptors, their absorption, distribution, metabolism, excretion, toxicity properties, and the superiority of VLB to ACh for binding to M₅R, indicate their potential to trigger activation of nausea-associated receptors during chemotherapy with VLB. It has been shown that metabolite 20-hydroxy-VLB (metabolite 10) demonstrates a stronger binding affinity to the vinca site of tubulin than VLB; however, they have similar modes of action. VLB and metabolite 10 have similar gastric solubility (FaSSGF), intestinal solubility (FeSSIF), and log P values. Metabolite 10 has a more acceptable pharmacokinetic profile than VLB, a better gastric and intestinal solubility. Furthermore, metabolite 10 was found to be less bound to plasma proteins than VLB. These are desired and essential features for effective drug bioavailability. Metabolite 10 is not a substrate of CYP2D6 and thus is less likely to cause drug-drug interactions and ADRs compared to its parent drug. The hydroxyl group added upon metabolism of VLB suggests that it can also be a reasonable starting compound for designing the next generation of antimitotic drugs to overcome P-glycoprotein-mediated multidrug resistance, which is often observed with vinca alkaloids.

In vitro relationship between serum protein binding to beta-carboline alkaloids: a comparative cytotoxic, spectroscopic and calorimetric assays

The work highlighted interaction of harmalol, harmaline and harmine with human serum albumin by biophysical and biochemical assays. Presence of serum protein in the media negatively affects the cytotoxicity of the alkaloids. MTT assay indicates concentration-dependent growth inhibitory effect of the alkaloids on A375, MDA-MB-231, HeLa, A549, ACHN and HepG₂ cell, having maximum cytotoxicity with GI₅₀ value of 6.5 μM on ACHN by harmine in 1% of fetal bovine serum. Detail cytotoxic studies on ACHN cell by harmine, the most cytotoxic among the three, reveal nucleosomal fragmentation, formation of comet tail, generation of reactive oxygen species, decreased mitochondrial membrane potential, up regulation of p53, caspase 3 and significant increase in G₂/M population that made the cancer cells prone to apoptosis. Furthermore, the findings unequivocally pointed out that harmine binds strongly to the protein with a binding constant of 5.53 × 10⁴ M^-1 followed by harmaline and least with harmalol. Thermodynamic results revealed enthalpy dominated, entropy favored, 1:1 binding. Molecular docking and circular dichroism suggested changed conformation of protein by partial unfolding on complexation. Further supported by infrared analysis where protein secondary structure was altered with a major decrease of α-helix from 53.68% (free protein) to 8-11% and change in β-sheet from 25.31% (free protein) to 1-6% upon binding, inducing partial protein destabilization. Site markers demonstrated site I (subdomain IIA) binding of the alkaloids to the protein. The results serve as data for the future development of serum protein-based targeted drugs. AbbreviationsCD: circular dichroism; FBS: fetal bovine serumFRETForster resonance energy transferFTIRFourier transform infraredHSAhuman serum albumin; ROS: reactive oxygen speciesCommunicated by Ramaswamy H. Sarma.

Mechanism of non-enzymatic antiglycation action by coumarin: a biophysical study

Coumarin inhibited non-enzymatic glycation by masking the free amino groups and scavenging carbonyl groups of protein.

Antioxidant properties and anti-mutagenic potential of Piper Cubeba fruit extract and molecular docking of certain bioactive compounds

Spices and herbs are recognized as sources of natural antioxidants and thus play an important role in the chemoprevention of diseases and aging. Piper cubeba is one among them and known for its medicinal properties for decades. Various biological activities are associated with its extract and phytocompounds. However, the anti-mutagenic activity of antioxidant rich extract is less explored. In this study, we performed the fraction-based antioxidant activity of P. cubeba using four different assays and evaluated the anti-mutagenic activity of most potent antioxidant fraction using Salmonella typhimurium tester strains against four mutagens (methyl methanesulfonate [MMS], sodium azide [SA], benzo(a)pyrene, and 2-aminoflourene) respectively. Among all tested fractions at 25-200 µg/ml, ethanolic extract revealed highest antioxidant activity and significant anti-mutagenicity against both direct and indirect acting mutagens at least one tester strain. Phytochemical analysis by gas chromatography-mass spectrometry (GC/MS) revealed the presence of various phytocompounds including copaene, isocaryophyllene, α-cubebene, etc. Molecular docking studies on DNA binding interactions of GC/MS detected phytocompounds highlight the possible mode of binding. In summary, these in vitro studies have provided the scientific basis for validation of using this plant in the traditional system of medicine and highlighted the need for exploring the role of various compounds for therapeutic efficacy. On the other hand, synergistic interaction among phytocompounds is to be explored to optimize or standardize the extracts for the exploitation in modern phytomedicine.

Multi-spectroscopic and molecular modelling approach to investigate the interaction of riboflavin with human serum albumin

Riboflavin (RF) plays an important role in various metabolic redox reactions in the form of flavin adenine dinucleotide and flavin mononucleotide. Human serum albumin (HSA) is an important protein involved in the transportation of drugs, hormones, fatty acid and other molecules which determine the biodistribution and physiological fate of these molecules. In this study, we have investigated the interaction of riboflavin RF with HSA under simulative physiological conditions using various biophysical, calorimetric and molecular docking techniques. Results demonstrate the formation of riboflavin-HSA complex with binding constant in the order of 10⁴ M^-1. Fluorescence spectroscopy confirms intermediate strength having a static mode of quenching with stoichiometry of 1:1. Experimental results suggest that the binding site of riboflavin mainly resides in sub-domain IIA of HSA and that ligand interaction increases the α-helical content of HSA. These parameters were further verified by isothermal titration calorimetry ITC which confirms the thermodynamic parameters obtained by fluorescence spectroscopy. Molecular docking was employed to suggest a binding model. Based on thermodynamic, spectroscopic and computational observations it can be concluded that HSA-riboflavin complex is mainly stabilized by various non-covalent forces with binding energy of -7.2 kcal mol^-1.

Interaction of capsaicin with calf thymus DNA: A multi-spectroscopic and molecular modelling study

Studying the mode of interaction between small molecules and DNA has received much attention in recent years, as many drugs have been reported to directly interact with DNA thereby regulating the expression of many genes. Capsaicin is a capsaiciniods family phytocompound having many therapeutic applications including diabetic neuropathy, rheumatoid arthritis, prevention of DNA strand breaks and chromosomal aberrations. In this study, we have investigated the interaction of capsaicin with calf thymus DNA using a number of biophysical techniques to get an insight and better understanding of the interaction mechanism. Analysis of UV-vis absorbance spectra and fluorescence spectra indicates the formation of complex between capsaicin and Ct-DNA. Thermodynamic parameters ΔG, ΔH, and ΔS measurements were taken at different temperatures indicated that hydrogen bonding and van der Waal's forces played major role in the binding process. Additional experiments such as iodide quenching, CD spectroscopy suggested that capsaicin possibly binds to the minor groove of the Ct-DNA. These observations were further confirmed by DNA melting studies, viscosity measurements. Molecular docking provided detailed computational interaction of capsaicin with Ct-DNA which proved that capsaicin binds to Ct-DNA at minor groove. Computational molecular docking also revealed the exact sites and groups to which capsaicin interacted.

Understanding the mechanism of non-enzymatic glycation inhibition by cinnamic acid: an in vitro interaction and molecular modelling study

Under hyperglycaemic conditions non-enzymatic glycation of proteins gives rise to advanced glycation end products (AGEs).