Investigating the preferential interaction between imatinib mesylate and VEGF G-quadruplex DNA as therapeutic strategies for cancer treatment: Biophysical and molecular modelling approaches

G-Quadruplex DNA (GQ-DNA) is one of the most important non-canonical nucleic acid structures. GQ-DNA forming sequences are present in different crucial genomic regions and are abundant in promoter regions of several oncogenes. Therefore, GQ-DNA is an important target for anticancer drugs and hence binding interactions between GQ-DNA and small molecule ligands are of great importance. Since GQ-DNA is a highly polymorphic structure, it is important to identify ligand molecules which preferentially target a particular quadruplex sequence. In this present study, we have used a FDA approved drug called imatinib mesylate (ligand) which is a selective tyrosine kinase inhibitor, successfully used for the treatment of chronic myelogenous leukaemia, gastrointestinal stromal tumours. Different spectroscopic techniques as well as molecular docking investigations and molecular simulations have been used to explore the interaction between imatinib mesylate with VEGF GQ DNA structures along with duplex DNA, C-Myc, H-Telo GQ DNA. We found that imatinib mesylate shows preferential interaction towards VEGF GQ DNA compared to C-Myc, H-Telo GQ and duplex DNA. Imatinib mesylate seems to be an efficient ligand for VEGF GQ DNA, suggesting that it might be used to regulate the expression of genes in cancerous cells.

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.

Bimetallic bis-Aroyldihydrazone-Isatin Complexes of High O=V(IV) and Low Cu(II) Valent Ions as Effective Biological Reagents for Antimicrobial and Anticancer Assays

Due to the versatile bioreactivity of aroyldihydrazone complexes as cost-effective alternatives with different transition metals, two novel bimetallic homo-complexes (VOLph and CuLph) were prepared via the coordination of a terephthalic dihydrazone diisatin ligand (H2Lph) with VO2+ and Cu2+ ions, respectively. The structure elucidation was confirmed by alternative spectral methods. Biologically, the H2Lph ligand and its MLph complexes (M2+ = VO2+ or Cu2+) were investigated as antimicrobial and anticancer agents. Their biochemical activities towards ctDNA (calf thymus DNA) were estimated using measurable titration viscometrically and spectrophotometrically, as well as the gel electrophoresis technique. The growth inhibition of both VOLph and CuLph complexes against microbial and cancer cells was measured, and the inhibition action, MIC, and IC50 were compared to the inhibition action of the free H2Lph ligand. Both VOLph and CuLph showed remarkable interactive binding with ctDNA compared to the free ligand H2Lph, based on Kb = 16.31, 16.04 and 12.41 × 107 mol-1 dm3 and ΔGb≠ = 47.11, -46.89, and -44.05 kJ mol-1 for VOLph, CuLph, and H2Lph, respectively, due to the central metal ion (VIVO and CuII ions). VOLph (with a higher oxidation state of the V4+ ion and oxo-ligand) exhibited enhanced interaction with the ctDNA molecule compared to CuLph, demonstrating the role and type of the central metal ion within the performed electronegative and electrophilic characters.

Bioreactivity of divalent bimetallic vanadyl and zinc complexes bis-oxalyldihydrazone ligand against microbial and human cancer series. ctDNA interaction mode

Two novel divalent bimetallic complexes were constructed from the complexation of O=V4+ and Zn2+ ions (VOL and ZnL), respectively, with diisatin oxalyldihydrazone ligand (H2L). Various spectroscopic tools were used to confirm their chemical structures (FT-IR, NMR, EI-Mass, and electronic spectra), besides, elemental analyses and conductivity features. To estimate the role of divalent metal ions in their coordination compound for developing their bio-reactivity, the free ligand H2Lox, and its complexes (VOL and ZnL) were employed spectroscopic investigations against the growth of some microbial series (fungi and bacteria) and also against three human cancer/normal cells. Furthermore, their interaction behavior against calf thymus DNA (ctDNA) was studied through viscometric and spectrophotometric studies to discover the role of O=V4+ and Zn2+ ions to determine the mode of binding with ctDNA. The inhibiting effect of H2L, VOL, and ZnL versus the titled microbial (bacterial and fungal) was built upon their inhibited zone areas in mm and the MIC concentrations in μM. Their action against the three human cancer cells' growth was evaluated by IC50 values in μM and the selectivity index in percentage. Both VOL and ZnL complexes exhibited an amazing series with three human cancer cell growth (according to the zone values in mm of inhibition, MIC in μM, and IC50 values in μM) compared to those of their uncoordinated H2L ligand. VOL demonstrated a distinguished interacting behavior with ctDNA more than that interaction of ZnL depending on the variation of the central metal ion chemical features. Within the covalent and non-covalent interaction modes, the interaction binding between H2L, VOL, and ZnL with ctDNA was discussed based on the electronic spectroscopic observation.

Mechanistic investigation into the binding property of Yohimbe towards natural polymeric DNAs

DNA interactions with multivalent ligand(s) have increasingly become the subject of substantial research. For several small molecules with therapeutic potential, nucleic acids serve as their primary molecular target. Such interaction has been shown to affect transcription or replication, ultimately leading to apoptotic cell death. As a result, researchers are becoming increasingly interested in understanding how small molecules interact with DNA making it possible to develop new, DNA-specific drugs. The bioactive indole alkaloid, Yohimbe (Yohimbine; Yh) has been broadly studied in pharmacological properties while its binding mode to DNA has not been explicated so far. This study adopted molecular modelling and multi-spectroscopic methods to investigate the interaction between Yohimbine and herring testes (HT DNA) in physiological conditions. Minor hypochromic and bathochromic shifts of fluorescence intensity were observed, suggesting the binding of Yh to HT DNA. The Scatchard plot analyses using the McGhee-von Hipple method revealed non-cooperative binding and affinities in the range of 105 M-1. The thermodynamic parameters suggested exothermic binding, which was favoured by negative enthalpy and positive entropy changes from temperature-dependent fluorescence experiments. Salt-dependent fluorescence suggested that the interaction between the ligand and DNA was governed by non-polyelectrolytic forces. The results of iodide quenching, urea denaturation assay, dye displacement, and in silico molecular docking, suggested groove binding of Yh to HT DNA. Thus, the groove binding mechanism of interaction was validated by both biophysical and computational techniques. The structural elucidation and energetic profiling of Yh's interaction with naturally occurring polymeric DNA can be useful to the development of DNA-targeted therapeutics.

Uncovering the Contrasting Binding Behavior of Plant Flavonoids Fisetin and Morin Having Subsidiary Hydroxyl Groups (-OH) with HRAS1 and HRAS2 i-Motif DNA Structures: Decoding the Structural Alterations and Positional Influences

Research on the interactions of naturally existing flavonoids with various noncanonical DNA such as i-motif (IM) DNA structures is helpful in comprehending the molecular basis of binding mode as well as providing future direction for the application and invention of novel effective therapeutic drugs. IM DNA structures have been identified as prospective anticancer therapeutic targets, and flavonoids are smaller molecules with a variety of health-promoting attributes, including anticancer activities. The extensive investigation comprising a series of techniques reveals the contrasting mode of the binding behavior of fisetin and morin with various IM DNA structures. We have discovered that structural alterations of hydroxyl groups located at different places of aromatic rings influence flavonoid's reactivity. This minor structural alteration appears to be critical for fisetin and morin's capacity to interact differentially with HRAS1 and HRAS2 IM DNA. Hence, fisetin appears to be an efficient ligand for HRAS1 and morin is considered to be an efficient ligand for HRAS2 IM DNA. This novel exploration opens up the possibility of employing the strategy for regulation of gene expression in cancerous cells. Our finding also reveals the flavonoid-mediated specific interaction with IM DNA while pointing toward tangible strategies for drug discovery and other essential cellular functions.

Insight into the binding interactions of fluorenone-pendent Schiff base with calf thymus DNA

A novel fluorenone appended Schiff base (L) has been synthesized and utilized for studying the binding interactions with Calf Thymus DNA (ct-DNA). The mechanism of binding with ct-DNA was explored by employing various spectroscopic techniques viz. UV-Vis absorption spectroscopy, fluorescence emission spectroscopy, gel-electrophoresis, circular dichroism (CD), melting studies, viscosity arrays and molecular modelling methodology. The interpretation of UV-vis absorbance spectra pointed to binding of L within minor groove of ct-DNA with the binding constant of K_b = 0.15 × 10⁴ M^-1. Dye-displacement studies with Rhodamine-B (RhB) and Ethylene Bromide (EB) in fluorescence spectroscopy verified the groove binding mode of interaction between L and ct-DNA. Melting studies, circular dichroism, and viscosity studies further elucidated the binding modes of L with ct-DNA. Thermodynamic variable measurements taken at various temperatures such as ΔG^⁰, ΔH^⁰, and ΔS^⁰ revealed that hydrophobic forces played a significant role in the binding process. The meticulous computational interaction demonstrated by molecular docking confirmed the minor groove binding of L with ct-DNA.

Mode of interaction of altretamine with calf thymus DNA: biophysical insights

Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 10³ M^-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol^-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol^-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK^-1 mol^-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.

Studying the interaction of scopolamine with calf-thymus DNA: An in-vitro and in-silico approach and genotoxicity

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.

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.

DNA-binding activities of compounds acting as enzyme inhibitors, ion channel blockers and receptor binders

The DNA-binding activities of compounds used as remedies can display DNA-protection, but also damaging effects in biological systems. The current review compiles literature data on DNA-binding activities of drugs widely used as remedies with different therapeutic indications. The compounds are classified according their mechanism of action: enzyme inhibitors, ion channel inhibitors, inhibitors of viral RNA replication and HIV protease and receptor agonists. DNA binding was reported for such widely used drugs as paracetamol, aspirin, metformin, statins and many others. The capability of the drug to bind DNA is sometimes coupled to genotoxic effects, but in some cases - to genome protection. Data on atoms and chemical groups involved in the drug-DNA interactions are also presented. In many cases the same atoms are involved in both interactions of the compounds with proteins and DNA.

Revealing the binding properties between resorcinol and DNA

Resorcinol (1,3-dihydroxybenzene) is a common coupling agent in permanent hair dyes, and has arrested people's attention for its potential hazard to human health. However, the action mechanism of resorcinol and human DNA has not been elucidated. In this research, the binding properties between resorcinol and calf thymus DNA (ct-DNA) were studied for the first time through various spectral and molecular docking techniques. Spectral studies showed that the initial fluorescence quenching of resorcinol against DNA was a static one. The result of ΔH < 0 and ΔS > 0 was produced from thermodynamic experimental data, therefore it could be concluded that electrostatic force was the major driving force, while binding constant K_b was 1.56 × 10⁴  M^-1 at 298 K. The electrostatic binding network between resorcinol and ct-DNA was established explicitly through competitive substitution analysis and other spectral approaches. The results of FT-IR absorption spectra indicated that resorcinol had bound to the DNA phosphate skeleton. Molecular docking clearly revealed that binding occurred between hydroxyl groups of resorcinol and phosphorus oxygen bonds (P-O) of the DNA skeleton. These findings may deepen our understanding of the action mechanism between resorcinol and ct-DNA and provide some useful data on the effect of resorcinol on human diseases.

The Influence of UV Light on Photodegradation of Acetylsalicylic Acid

Photodegradation of the aqueous solutions of acetylsalicylic acid, in the absence (ASA) and the presence of excipients (ASE), is demonstrated by the photoluminescence (PL). A shift of the PL bands from 342 and 338 nm to 358 and 361-397 nm for ASA and ASE in solid state and as aqueous solutions was reported. By exposure of the solution of ASA 0.3 M to UV light, a decrease in the PL band intensity was highlighted. This behavior was revealed for ASA in the presence of phosphate buffer (PB) having the pH equal to 6.4, 7, and 8 or by the interaction with NaOH 0.3 M. A different behavior was reported in the case of ASE. In the presence of PB, an increase in the intensity of the PL band of ASE simultaneously with a change of the ratio between the intensities of the bands at 361-364 and 394-397 nm was highlighted. The differences between PL spectra of ASA and ASE have their origin in the presence of salicylic acid (SAL). The interaction of ASE with NaOH induces a shift of the PL band at 405-407 nm. Arguments for the reaction of ASA with NaOH are shown by Raman scattering and FTIR spectroscopy.

Designing a two-stage colorimetric sensing strategy based on citrate reduced gold nanoparticles: Sequential detection of Sanguinarine (anticancer drug) and visual sensing of DNA

Distance dependent optical properties of colloidal gold nanoparticles offer designing of colorimetric sensing modalities for detection of a variety of analytes. Herein, we report a simple and facile colorimetric detection assay for an anti-cancer drug, Sanguinarine (SNG) and Calf Thymus DNA (Ct-DNA) based on citrate reduced gold nanoparticles (CI-Au NPs). The electrostatic interaction between SNG and CI-Au NPs induce aggregation of Au NPs accompanied with visible colour change of colloidal solution. The assay conditions like salt concentration, pH and reaction time had been adjusted to achieve highly sensitive and fast colorimetric response. Furthermore, the optimized CI-Au NPs/SNG sensing system is used for the detection of Ct-DNA based on the mechanism of anti-aggregation of CI-Au NPs. The simultaneous presence of SNG and Ct-DNA prevent aggregation of Au NPs owing to preferential formation of Ct-DNA-SNG intercalation complex and colour of the Au NPs solution tends to remain red, depending on the concentration of Ct-DNA in solution. The degree of aggregation and anti-aggregation of CI-Au NPs was monitored using Transmission electron microscopic (TEM) measurements and UV-Visible spectrophotometry by analysing the ratio of absorptions for aggregated and dispersed Au NPs. The intercalation mode of binding between SNG and Ct-DNA in CI-Au NPs/SNG sensing system was determined by Fluorescence spectral studies and UV-thermal melting studies. The absorption ratio (A₆₂₇/A₅₂₅) of Au NPs exhibited a linear correlation with SNG concentrations in the range from 0 to 0.9 μM with detection limit as 0.046 μM. This optical method can determine Ct-DNA as low as 0.36 μM and the calibration is linear for concentration range 0 to 5 μM. The proposed sensing strategy enables detection as well as quantification of SNG & Ct-DNA in real samples with satisfactory results and finds application in drug or DNA monitoring.

Synthesis, Antiproliferative and Cytotoxic Activities, DNA Binding Features and Molecular Docking Study of Novel Enamine Derivatives

Novel enamine derivatives were synthesized from the reaction of lactone and chalcones and their antiproliferative and cytotoxic activities against six cancer cell lines (e. g., HeLa, HT29, A549, MCF7, PC3 and Hep3B) and one normal cell lines (e. g., FL) were investigated along with their mode of interactions with CT-DNA. Most of the enamine derivatives with IC₅₀ values of 86-168 μM demonstrated much stronger antiproliferative activity than the starting molecules against the cancer cells. While, among the enamine derivatives, four compounds displayed higher cytotoxic potency than the control drugs (5-fluorouracil and cisplatin) against the Hep3B cell lines, these compounds did not exhibit any significant toxicity against normal cells, FL. The UV/VIS spectral data suggest that eight compounds cause hypochromism with a slight bathochromic shift (∼6 nm), indicating that they bind to the DNA by way of an intercalative or minor groove binding mode. The binding constants of the compounds are in the range of 0.1×103 M^-1 -2.3×104 M^-1 . The antiproliferative activity of studied enamine derivatives could possibly be due to their DNA binding as well as their cytotoxic properties. In addition to these assays, the chalcones and enamine derivatives were investigated by molecular docking to calculate the synergistic effect of antiproliferative activities against six human cancer cell lines.

Solid phase drug-drug pharmaceutical co-crystal formed between pyrazinamide and diflunisal: Structural characterization based on terahertz/Raman spectroscopy combining with DFT calculation

Both pretty low solubility and high membrane permeability of diflunisal (DIF) would affect significantly its oral bioavailability as a typical non-steroidal anti-inflammatory substance. Meanwhile, pyrazinamide (PZA), known as one kind of important anti-tuberculosis drugs, has also several certain side effects. These deficiencies affect the large-scale clinical use of such drugs. Solid-state pharmaceutical co-crystallization is of contemporary interest since it offers an easy and efficient way to produce prospective materials with tunable improved properties. In the current work, a novel solid phase drug-drug co-crystal involving DIF and PZA with molar ratio 1:1 was prepared through the mechanical grinding approach, and vibrational spectroscopic techniques including terahertz time-domain spectroscopy (THz-TDS) and Raman spectroscopy were performed to identify DIF, PZA and their pharmaceutical drug-drug co-crystal. The absorption peaks observed in the THz spectra of the co-crystal were at 0.35, 0.65, 1.17, 1.31 and 1.42 THz respectively, which are obviously different from parent materials. Similarly, Raman spectra could also be used to characterize the difference shown between the co-crystal and parent compounds. Structures and vibrational patterns of three kinds of possible co-crystal theoretical forms (form I, II and III) between DIF and PZA have been simulated by performing density functional theory (DFT) calculations. Theoretical results and THz/Raman vibrational spectra of DIF-PZA co-crystal show that the DIF links to PZA via the carboxylic acid-pyridine hetero-synthon association establishing the theoretical form I, which is a much-higher degree of agreement with experimental results than those of other two co-crystal forms. These results provide us a unique method for characterizing the composition of co-crystal structures, and also provide a wealth of drug-drug co-crystal structural information for improving physicochemical properties and pharmacological activities of specific drugs at the molecular-level.

Structural modification of aspirin to design a new potential cyclooxygenase (COX-2) inhibitors

Aspirin (Asp) is one of the most important and ancient member of nonsteroidal anti-inflammatory drugs (NSAID), commonly used in medication of fever, pain and inflammation. It can inhibit the synthesis of prostaglandin by blocking the cyclooxygenase (COX). Attempts have been taken to analyze aspirin together with some of its modified derivatives applying quantum mechanical calculations in order to compare their physicochemical and biochemical properties. Density functional theory (DFT) with B3LYP/6-31G (d, p) basis set has been employed to elucidate their thermal, molecular orbital, equilibrium geometrical properties in gas phase. Molecular docking and nonbonding interactions have been performed against human cyclooxygenase-2 protein 5F1A to investigate the binding affinity and mode(s) of newly designed aspirin derivatives. ADMET prediction has been utilized to compare the absorption, metabolism, and carcinogenic properties of new derivatives with parent drug (Asp). Thermal and geometrical results support the thermochemical stability and equilibrium geometry of all the structures. From the molecular docking simulation, most of the derivatives exhibited better binding affinity than parent drug (Asp) with the receptor protein (5F1A). ADMET prediction disclosed the improved pharmacokinetic properties with lower acute oral toxicity of some derivatives. Based on quantum chemical, molecular docking and ADMET analysis, this investigation can be useful to understand the physicochemical and biochemical/biological activities of Asp and its modified derivatives to search a new antipyretic analgesic drug.

Structural investigation of a 2:1 co-crystal between diflunisal and isonicotinamide based on terahertz and Raman spectroscopy

In order to characterize molecular structure changes of drugs upon co-crystallization by means of spectroscopic techniques, vibrational spectra of solid-state diflunisal (DIF), isonicotinamide (ISO) and their 2:1 co-crystal have been investigated by using terahertz time-domain spectroscopy (THz-TDS) and Raman spectroscopy. A 2:1 DIF-ISO co-crystal between DIF and ISO has been synthesized by slow solution crystallization from ethanol. The experimental THz spectroscopy shows that the co-crystal has a few significantly different absorption peaks compared with raw parent materials within the frequency region from 0.2 to 1.6 THz. Likewise, some differences of vibrational spectra between the co-crystal and starting compounds could also be characterized by Raman spectral results. Density functional theory (DFT) was used to simulate optimized structures and vibrational modes of two kind of possible co-crystal theoretical forms (form I and II) between DIF and ISO. Theoretical co-crystal form I is shown with 2:1 theoretical binary-adduct formed by carboxylic acid-amide and carboxylic acid-pyridine under inter-molecular hydrogen bonding. Theoretical co-crystal form II has a similar structure as form I, meanwhile the only difference is that O63 atom simultaneously forms hydrogen bond with H33 and H64. Also the hydroxyl -OH and carboxyl group -COOH establish molecular heterocycle under intra-molecular hydrogen bonds in both forms. The theoretical results show that both THz and Raman spectra of co-crystal form II between DIF and ISO is more consistent with the experimental observations than those of co-crystal form I. These results provide us with a wealth of information and unique method for characterizing the composition of co-crystal structures and also inter-molecular hydrogen bonding interactions shown within pharmaceutical co-crystallization at the molecular level.

DNA minor groove binding of a well known anti-mycobacterial drug dapsone: A spectroscopic, viscometric and molecular docking study

Dapsone is a sulfone drug mainly used as anti-microbial and anti-inflammatory agent for the treatment of various diseases including leprosy. Recently, its interaction with protein (bovine serum albumin) is evidenced. But, the binding propensity of this anti-mycobacterial drug towards DNA is still unknown. Also, the mode of dapsone-DNA interaction (if any) is still an unknown quantity. In this study, we have taken a thorough attempt to understand these two unknown aspects using various biophysical and in silico molecular docking techniques. Both UV-visible and fluorescence titrimetric studies indicated that dapsone binds to CT-DNA with a binding constant in order of 10⁴ M^-1. Circular dichroism, thermal denaturation and viscosity experiments revealed that dapsone binds to the grooves of CT-DNA. Competitive DNA binding studies clearly indicated the minor groove binding property of this anti-mycobacterial drug. Molecular docking provided detailed information about the formation of hydrogen bonding in the dapsone-DNA complex. This in silico study further revealed that dapsone binds to the AT-rich region of the minor groove of DNA having a relative binding energy of -6.22 kcal mol^-1. Overall, all these findings evolved from this study can be used for better understanding the medicinal importance of dapsone.

Photophysical and thermodynamic evaluation on the in vitro and in silico binding profile of Camptothecin with DNA

Camptothecin (CMT) is an anti-tumour alkaloid drug exhibiting selective topoisomerase-I inhibitory activity by eventually hindering dynamic functions of DNA duplex via initiating apoptosis. Unravelling the binding mechanism of CMT with bio macromolecular systems can offer fundamental information regarding the mechanism of actions which can lead to the design of rational proactive drugs. This study endeavoured the binding interactions of CMT with calf thymus DNA (ct-DNA) along with the structural alterations attained by the DNA duplex owing to CMT interactions through multi-spectroscopic, calorimetric and molecular docking studies. The UV-visible absorbance and fluorescence quenching studies revealed the binding strength of CMT with ct-DNA, evident from the binding constants K₁ = 3.79 × 10³ M^-1 and Kq = 2 × 10³ M^-1. The time-resolved lifetime measurements inferred that the quenching was static due to the non-fluorescent ground state complex formation. The dye displacement study, temperature melting and viscosity measurements established a typical non-intercalative binding mode of CMT with ct-DNA. The binding isotherm deduced from ITC was found to be spontaneous and exothermic exerting a promising ΔG value of -6.2 kcal mol^-1. The thermal kinetic parameters implied that the forces primarily involved in the CMT-ct-DNA complexation are hydrogen bonding and van der Waals interactions. Moreover, the structural alterations of DNA duplex reflected in the CD and FTIR spectra could undeniably confirm the groove binding manner of CMT. The in silico extra precision docking study explored more accurate molecular illustrations of sequence specific minor groove binding mechanism evolved between CMT and DNA corroborating well with the experimental results. These innovative findings may shorten the path towards the development of novel and more effective CMT drug derivatives.

A saccharinate-bridged palladacyclic dimer with a Pd–Pd bond: experimental and molecular docking studies of the interaction with DNA and BSA and in vitro cytotoxicity against human cancer cell lines

The synthesis, characterization and biological activities of a saccharinate-bridged palladacyclic dimer are reported in this work.

Molecular spectroscopic and thermodynamic studies on the interaction of anti-platelet drug ticlopidine with calf thymus DNA

Ticlopidine is an anti-platelet drug which belongs to the thienopyridine structural family and exerts its effect by functioning as an ADP receptor inhibitor. Ticlopidine inhibits the expression of TarO gene in S. aureus and may provide protection against MRSA. Groove binding agents are known to disrupt the transcription factor DNA complex and consequently inhibit gene expression. Understanding the mechanism of interaction of ticlopidine with DNA can prove useful in the development of a rational drug designing system. At present, there is no such study on the interaction of anti-platelet drugs with nucleic acids. A series of biophysical experiments were performed to ascertain the binding mode between ticlopidine and calf thymus DNA. UV-visible and fluorescence spectroscopic experiments confirmed the formation of a complex between ticlopidine and calf thymus DNA. Moreover, the values of binding constant were found to be in the range of 10³M^-1, which is indicative of groove binding between ticlopidine and calf thymus DNA. These results were further confirmed by studying the effect of denaturation on double stranded DNA, iodide quenching, viscometric studies, thermal melting profile as well as CD spectral analysis. The thermodynamic profile of the interaction was also determined using isothermal titration calorimetric studies. The reaction was found to be endothermic and the parameters obtained were found to be consistent with those of known groove binders. In silico molecular docking studies further corroborated well with the experimental results.

Interaction of indomethacin with calf thymus DNA: a multi-spectroscopic, thermodynamic and molecular modelling approach

Indomethacin belongs to the acetic acid derivative class of non-steroidal anti-inflammatory drugs with diverse pharmacological and biological activities. Understanding the mechanism of interaction of drugs with possible target and off-target biomolecules can prove useful in the development of a rational drug designing system. In this paper, we have attempted to ascertain the mode of binding of indomethacin with calf thymus DNA (Ct-DNA) through various biophysical techniques and in silico molecular docking. Analysis of the UV-visible absorbance spectra and fluorescence emission profile of indomethacin upon addition of Ct-DNA indicates the formation of a drug-DNA complex. UV-visible absorbance and steady state fluorescence experiments revealed a binding constant on the order of 103 L mol-1, which is consistent with those of well-known groove binders. Competitive displacement studies with ethidium bromide, acridine orange and Hoechst 33258 further suggested that indomethacin binds to the minor groove of the Ct-DNA. The above observations were further confirmed by KI induced quenching experiments, DNA melting studies, CD spectral analysis and viscosity measurements. The thermodynamic parameters like spontaneous free energy (ΔG < 0) and large favourable enthalpy (ΔH < 0) obtained from isothermal calorimetry indicated the involvement of hydrogen bonding and van der Waals forces in the binding process. Molecular docking further corroborated the experimental results.

Elucidating the interaction of sulindac with calf thymus DNA: biophysical and in silico molecular modelling approach

Sulindac is one of the most effective NSAIDs and belongs to the arylalkanoic acid class.

Exploring the preferential interaction of quercetin with VEGF promoter G-quadruplex DNA and construction of a pH-dependent DNA-based logic gate

The plant flavonoid quercetin (Que) binds more efficiently to VEGF G-quadruplex DNA (G4–DNA) compared to double stranded DNA as well as other G4–DNAs.

Chitosan promotes ROS-mediated apoptosis and S phase cell cycle arrest in triple-negative breast cancer cells: evidence for intercalative interaction with genomic DNA

Chitosan (CS) is a semi-synthetic bio-based polysaccharide with promising biological and antitumor properties.

Intercalation of the daphnetin–Cu(ii) complex with calf thymus DNA

The daphnetin–Cu(ii) complex binds to the A–T bases region of ctDNA and causes cleavage of plasmid DNA.

Synthesis and characterization of steroidal heterocyclic compounds, DNA condensation and molecular docking studies and their in vitro anticancer and acetylcholinesterase inhibition activities

A facile and efficient approach for the synthesis of steroidal heterocyclic compounds (4–12) has been performed. Furthermore, these newly synthesized compounds were evaluated for their various biological activities.

Partial intercalative binding of the food colorant erythrosine to herring sperm DNA

Erythrosine partially inserts into the G–C rich region of hsDNA and induces moderate conformational perturbation of the DNA.