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Photo Physical Behaviour of

Naproxen

DNA, RNA, BSA,

Dendrimer and Silver Nanoparticles: Spectral and Molecular

Docking Studies

Narayanasamy Rajendiran1*, Ayyadurai Mani1, Poomalai Senthilraja2, S. Senthilmurugan3

1 Department of Chemistry, Annamalai University, Annamalai Nagar, Tamilnadu, India

2 Department of Bioinformatics, Bharathidasan University, Tiruchy, Tamilnadu, India

3 Department of Zoology, Annamalai University, Annamalai Nagar, Tamilnadu, India

*Corresponding Author

DOI: https://doi.org/10.51583/IJLTEMAS.2026.150300117

Received: 31 March 2026; 06 April 2026; Published: 23 April 2026

ABSTRACT

Absorption, emission and molecular docking characteristics of the naproxen drug with (

DNA, RNA, BSA,

Dendrimer)

biomolecules and silver nanoparticles were analysed. With the addition of NP, the absorption and

emission maxima of the biomolecules completely disappeared, and no significant spectral shift was noticed in

the NP drug. When biomolecule concentrations increased, the absorption and emission intensities of the drug

were gradually changed. The negative free energy values indicate the spontaneity of the binding between the

drugs and biomolecules. van der Waals force and hydrogen bonding play major roles in the sensing of the drugs

and biomolecules. Due to Ag nanoparticles interaction with NP/biomolecules, a blue or red shift was noticed

in the absorption and emission spectra. Molecular docking results indicated that the biomolecules interacted

with the O and H groups of the NP drug. The sensing behaviour of NP with DNA is higher than other

biomolecules. NP drug demonstrates promising anticancer activity through interactions with both the 1r51 and

2oh4 EGFR protein targets.

Keywords: DNA, RNA, BSA, Dendrimer, naproxen, Silver nanoparticles, Anticancer activity

INTRODUCTION

DNA, RNA and BSA-proteins interactions play important roles in a variety of biomolecular functions. Gene

expression, transcription, replication, recombination, packaging and repairs all are controlled by DNA-protein

interactions. Although the physical basis for these recognition processes is not fully understood, x-ray

crystallography, NMR spectroscopy and molecular modelling provide us with a wealth of information on DNA

recognitions [1-5]. The quantitative assessment of DNA-protein interaction is essential to understanding

transcription, the beginning of biological processes including normal cellular function, development and many

diseases [6]. RNA plays a major role in diverse functions within the cell. Protein-RNA complexation is essential

in many of these biological functions. Transfer RNAs bind to aminoacyl-tRNA synthetases for the translation

of the genetic code during protein synthesis [7,8], while ribonucleoproteins bind RNA in post-transcriptional

regulation of gene expression [9]. Although the biological significance of protein complexation with RNA has

been well recognized, the specific mechanism of protein-RNA interaction is not fully understood [10].

Measurement of sequence-specific DNA, RNA and BSA-protein interactions is a key experimental procedure

in molecular biology of gene regulation.

Numerous studies have experimentally examined the interaction of drugs with deoxyribonucleic acid (DNA),

ribonucleic acid (RNA), bovine serum albumin (BSA) and PAMAM-OH (dendrimer). Naproxen [(+)-6-

methoxy-et-methyl-2-naphthalene acetic acid, Fig.1] is a non-steroidal anti-inflammatory (NSAID) drug which

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is recommended for the treatment of rheumatoid arthritis, inflammatory rheumatic disorders, degenerative joint

disease, and ankylosing spondylitis. Further, it is useful in lowering the development of granuloma tissue in

rats after subcutaneous implantation of cotton pellets laced with carrageenan.

The spec

proper

es of NP with DNA, RNA, BSA, PAMAM-OH (Dendrimer) have been investigated

by using UV-v

e, f

uorescence and molecular docking methods. Further, we synthesis

Ag/NP/biomolecules nanomaterials and characterized by UV-v

e and f

uorescence methods.

Fig. 1. Chemical structure of Naproxen

Experimental

Preparation of Drug: Biomolecule solution

Solutions comprising biomolecules such DNA, RNA, BSA, or PAMAM-OH dendrimer (1.0 × 10⁻⁴ M) were

produced in a 10 mL standard volumetric flask at different quantities ranging from 0.1 to 1.0 mL. 0.2 mL of an

NP solution (2 × 10⁻² M) was added to each flask. After carefully mixing the solutions, triple-distilled water

was used to dilute them to a final volume of 10 mL. Each flask's ultimate NP concentration as a result of this

process was 4 × 10⁻⁴ M.

Preparation of Silver and Ag/NP/Biomolecule Nanoparticles

To prepare silver nanoparticles, 0.01 M silver nitrate was dissolved in 200 mL of deionized water and the

solution was heated to 50–60 °C for 30 minutes. While stirring vigorously, 1–2 mL of 1% trisodium citrate

solution (prepared by dissolving 1 g of trisodium citrate in 100 mL of deionized water) was added. The

formation of silver nanoparticles was confirmed by the appearance of a pale-yellow color [11-14].

To prepare the Ag/NP/biomolecule complex, NP (2 × 10⁻³ M, dissolved in 20 mL of ethanol) was gradually

added to the biomolecule solution (2 × 10⁻⁴ M in 80 mL of deionized water). This mixture was heated to 50 °C

and stirred continuously on a hot plate with a magnetic stirrer for two hours. Subsequently, 50 mL of the silver

nanoparticle solution (0.01 M) was added to 50 mL of the NP/biomolecule solution, and the mixture was stirred

for an additional two hours [11-14].

Molecular docking method

AutoDock is a widely utilized software suite for automated molecular docking that employs various techniques

such as simulated annealing, local gradient search, and genetic algorithms [15–20]. Version 4.2.6 of AutoDock

is freely available under the GNU General Public License (GPL) and can be downloaded from

http://autodock.scripps.edu for Linux, macOS, and Windows platforms. Both AutoDock 4.2.6 and AutoDock

Vina are commonly used in docking studies. In the present work, docking simulations were carried out using

the Lamarckian Genetic Algorithm (LGA) in combination with the Solis & Wets local search method. The

initial placement, orientation, and torsional angles of the drug molecules were assigned randomly. Each docking

experiment included 10 independent runs, with each run allowing a maximum of 2.5 × 10⁵ energy evaluations.

A population size of 150 was maintained. The docking procedure employed a translational step size of 0.2 Å,

while the rotational and torsional step sizes were set to 5° [18-20].

Anticancer Potential of naproxen

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A computational method for examining the intermolecular interactions and binding mechanisms between a

pharmacological molecule and a biomolecule is called molecular docking. The micro molecule functions as the

ligand in this process, and the macromolecule as the protein receptor. The licensed program Dassault Systèmes

BIOVIA Discovery Studio version 22.1.100 was used to perform the docking analysis. Through

https://www.rcsb.org/, the target protein's three-dimensional (3D) structure the Epidermal Growth Factor

Receptor (EGFR) complexed with epiregulin (EREG) was acquired from the Protein Data Bank (PDB ID:

5WB7). Proteins were prepared by removing ions and water molecules, adding hydrogen atoms, and setting up

a grid to find the best binding sites. The interaction between the ligand and the receptor was then examined

using docking simulations.

RESULTS AND DISCUSSION

Absorption and emission spectral studies of Naproxen with Biomolecules

Absorption and emission spectral maxima of the naproxen (NP) drug were measured with different

concentrations of biomolecules [DNA, RNA, BSA, PAMAM-OH (Dendrimer)] and the relevant data is given

in Table 1, Fig. 2. In water, the absorption maxima of NP were appearing at 329, 316, 270, 261, 233 nm and

the emission maximum appeared at 352 nm. In the aqueous solution of the isolated DNA, single absorption

maximum was appearing at 260 nm while three emission maxima were noticed at 467, 357 and 320 nm. With

increasing the DNA concentrations in NP: a) no significant change was observed in the absorption maxima at

329, 316, 282, 230 nm and the absorbance decreased, b) the triple emission maxima of the DNA were lost,

while single was emission noticed at 353 nm and the emission intensities decreased.

In the aqueous solution of the isolated RNA, a single absorption maximum was appearing at 258 nm while dual

emission was noticed at 362 and 463 nm. With increasing the RNA concentrations with NP: a) no significant

shift was noticed in the absorption spectrum at 329, 316, 282 and 230 nm and the absorbance decreased, b)

both the shorter and the longer wavelength emissions of the RNA were lost whereas the NP emission noticed

at 353 nm, c) the emission intensities decreased at the same wavelength.

Isolated BSA exhibits a single absorption and emission maxima at 278 nm and 336 nm, respectively in the

aqueous solution. With increasing the BSA concentration in NP: a) no significant shift was noticed in the

absorption spectrum at 329, 316, 270, 262, and 239 nm and the absorbance decreased, b) a single emission was

noticed at 353 nm and the emission intensity decreased at the same wavelength.

In aqueous solution the PAMAM-OH which was isolated gives a single absorption maximum appearing at 282

nm, while three emission maxima were noticed at 300, 355 and 440 nm. With increasing the PAMAM-OH

concentrations in NP: a) no significant shift was noticed in the absorption spectrum at 329, 316, 270, 262, 235

and the absorbance decreased, b) the triple emission maxima of the PAMAM-OH were lost, while a single

emission maximum was noticed at 353 nm, c) the emission intensities decreased at the same wavelength. The

absorption and emission results indicate that NP interacted with all the biomolecules. The skeleton structure of

the biomolecules restricts the free rotation of the drug molecule; hence, the absorption and emission intensities

of the drug were changed in the biomolecule solution.

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Table 1. Absorption and fluorescence maxima of naproxen [0.2 x 10-4 M] with different DNA,

RNA, BSA and PAMAM-OH-Dendrimer concentrations [x10-6 M].

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Fig.2. Absorption and fluorescence spectra of naproxen [0.2 x10-4 M) with different concentrations of

biomolecules (DNA, RNA, BSA, Dendrimer) (M x 10-6): 1) 0, 2) 2, 3) 4, 4) 6, 5) 8, 6) 10, dotted line indicates

pure biomolecules spectra.

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The binding strength of the drugs with biomolecules is mirrored in the intrinsic binding constant K, which

represents the binding constant per DNA and RNA base pair and per BSA amino acid. It can be obtained by

monitoring the changes in the corresponding absorption wavelength with increasing the concentrations of the

biomolecules. From the slope and intercept of the Benesi-Hildebrand plot the binding constant (K) and

stoichiometry ratio of the biomolecule interactions were calculated. The presence of an isosbestic point and

the plot in the absorption spectrum confirm the formation of a 1:1 complex. Further, the plot of 1/(A-A0) versus

1/[Biomolecules]2 and 1/(I-I0) vs. 1/[Biomolecules]2 gives the concave line suggesting the 1:2 complex is not

formed [21-30]. The negative free energy change (ΔG) values (Table 1), reveal that the binding process was

spontaneous and thermodynamically stable at the experimental temperature. The negative ΔG value indicated

the spontaneity of the sensing between drug and biomolecules. ΔG for NP-DNA is more negative than other

biomolecules indicated that its sensing behavior is more spontaneous. The change in free energy of NP-DNA

is -62.8 kcal mol-1. This also confirms the sensing is higher than that of other drug-biomolecule interactions.

In the ground state, the drug sensing behaviour of DNA is higher than other biomolecules, whereas in the

excited state, dendrimer is higher than that of other biomolecules.

Drug–biomolecule interactions can be studied by comparison of absorption and emission spectra of the free

drug, free DNA, RNA, BSA, PAMAM-OH and drug–biomolecule complexes, which are generally altered.

Upon addition of NP drug to the biomolecules, the absorption and emission maxima of the biomolecules are

completely disappeared or changed. The absorption and emission maxima of the NP drug are typical results

in hyperchromism or hypochromism, hypsochromism (blue shift) and bathochromism (red shift). The gradual

change in the absorbance or the emission intensity with the addition of the drug to the biomolecules was attributed

to the sensing of the biomolecules. The spectral shifts showed that different functional groups are encapsulated

and these functional groups interacted with the biomolecules. The obtained results indicated that it is possible

to design the structure of these drug-biomolecule complexes by appropriately selecting the type, length and

functional substituent group in the drug.

Because of the intercalative mode involving a stacking interaction between the drug and the base pair of

biomolecules, the extent of the blue shift is consistent with the strength of intercalative interaction [31]. The

power of this electronic interaction is expected to decrease as the cube of the distance between the drug and the

biomolecule base reduces. By decreasing the distance between intercalated drugs and biomolecules, a spectral

shift apparently takes place. Thus, this is reliable with the combination of π-π electrons of the drug and the

DNA bases. Subsequently, the energy level of the π–π-electron transition decreases, which causes a red or blue

shift [32, 33]. In case of electrostatic interaction between the drug and the biomolecule, red or blue shift is

observed. This reflects some changes in biomolecule conformation and structure after drug– biomolecule

interaction is complete. The red or blue shift is an increase in absorbance of DNA upon denaturation. The two

strands of DNA are held together mainly by the stacking interactions, hydrogen bonds and hydrophobic effect

between the complementary bases. The hydrogen bond limits the resonance of the aromatic ring so the

absorbance of the sample is limited as well. When the DNA double helix is treated with denaturing agents, the

interaction force holding the double helical structure is disturbed. The double helix then separates into two

single strands which are in the random coiled conformation. At the moment, the base–base interaction gets

reduced, increasing the absorption and emission intensities of the biomolecule solution because many bases are

in free form and do not form hydrogen bonds with corresponding bases. Red or blue shift reveals the subsequent

changes of a biomolecule in its conformation and structure after the drug–biomolecule interaction is completed.

Further, the blue shift arises mainly due to the presence of charged cations which bind to biomolecules via

electrostatic interaction with the phosphate group of the DNA backbone and thereby causing a reduction and

overall damage to the secondary structure of DNA [34]. The blue shift may also be attributed to external contact

(electrostatic binding) [35] or to partial uncoiling of the helix structure of DNA, exposing more bases of the

DNA [36]. If there is a weaker interaction, then only hypochromic or blue shifts are observed without significant

changes of shifts in the spectral profiles [37].

The slight red shift can best be described by the decrease in π-π transition energy of the drugs due to their

ordered stacking between the DNA base pairs after intercalation. After binding to the biomolecules, the π-

orbital of the binding drug could pair with π- orbital of base pairs in the biomolecules. The coupling π- orbital

is generally partially filled by electrons, thus decreasing the transition probabilities, and hence resulting in the

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blue shift. The compression in the structure of either the drug alone and/or DNA after the formation of drug–

biomolecules complex can result in blue shift [38].

As discussed above, the various changes observed in the absorption and emission spectra indicated that the

drugs have interacted with DNA, RNA, BSA and PAMAM-OH molecules. This kind of sensing might have

caused the slight change in the conformation of drugs. The absorption and emission intensity of these solutions

showed moderate shifts towards the wavelength confirmed that the addition of biomolecule is sensing with

the drug.

Formation of Ag/NP/Biomolecules Nanoparticle

Absorption and emission spectra of Ag, NP, Ag/NP, Ag/biomolecules, and Ag/NP/biomolecule nanoparticles

are analyzed. Ag nanoparticle’s absorption and emission bond appear at 420, 250 nm and 474, 352 nm

respectively. Further, the yellow color was identified for the formation of Ag nanoparticles [39-45]. An addition

of NP solution to the Ag nano, the absorption maxima blue shifted from 420, 250 nm to 332, 318, 268, 260 nm

and the emission maxima blue shifted from 474, 352 nm to 354 nm [39-45].

By the addition of DNA solution to the Ag nanoparticles, the absorption maxima red shifted to 436, 262 nm

and the emission maxima blue shifted to 470, 423, 362 nm. With the addition of NP/DNA solution to the Ag

nanoparticles, no significant changes were noticed in the absorption maxima observed at 329, 316, 261, 230

nm while the emission maxima blue shifted to 440, 353 nm.

While adding RNA to the Ag nano solution, the absorption maxima red shifted to 445, 260 nm and emission

maxima shifted to 364, 325 nm respectively. Upon addition of NP/RNA solution to the Ag nanoparticles, no

significant changes were noticed in the absorption and emission maxima at 330, 318, 265 nm and 353 nm

respectively.

With an addition of BSA to the Ag nano solution, the absorption maxima red shifted to 454, 277 nm and the

emission maxima blue shifted to 350 nm respectively. Upon addition of NP/BSA solution to the Ag

nanoparticles, no significant changes were noticed in the absorption and emission maxima at 330, 318, 265,

257 nm and 353 nm respectively.

When dendrimer is added to the Ag nano solution, the absorption maxima red shifted to 427, 280 nm and the

emission maxima blue shifted to 330, 302 nm respectively. Upon addition of NP/PAMAM-OH solution to the

Ag nanoparticles, the absorption maxima red shifted to 450, 337, 262 nm and no significant changes were

noticed in the emission maxima at 352 nm. Due to the interaction of Ag nanoparticles with NP, DNA, RNA,

BSA and PAMAM-OH dendrimer, red or blue shift was noticed in the absorption and emission spectra.

Generally, due to interaction, tends to increase or decrease the intensity of the drug and biomolecules. The

spectral variation indicates to confirm the interaction between NP, biomolecules and Ag nanoparticles.

Molecular Docking of NP with biomolecules

The computer-simulated automated docking studies were performed using the widely distributed molecular

docking software Autodock 1.5.6. In DNA, RNA, BSA and dendrimer, the following protein data bank IDS

1bna, 2ke6, 3vo3, and 5d2a was used. Among the various conformers of docking results, only 10 conformers

were taken on the basis of the free energy of binding and score ranking. The minimum binding energy

conformer is shown in Figs.3 and 4. The binding energy ΔGb (kcal/mol), intermolecular energy (kcal/mol),

torsional energy, total internal energy, inhibition constant (Ki) (uM), van der Waals + H bond + desolvation

energy (kcal/mol), electrostatic energy (kcal/mol), ligand efficiency, unbound energy, refRMS are calculated

(Table 2).

In NP drug, the oxygen and hydrogen atoms were docked deeply within the grooves and amino acid of the

biomolecules and forming more intercalative sensing or hydrogen bonds with the biomolecules. In DNA, the

NP interacted with the nucleotide sites at DG10, DG11, DG12, DG14 and DG16 parts while in RNA, the NP

drug interacted with the nucleotide sites at A44, A45, G46, C47, U61. In BSA, the NP drug interacts at ASP814,

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GLU815, CYS817, GLU818 and ALA881. The NP drug interacts with dendrimer at ASN70. The binding

energy, intermolecular energy, total internal energy, van der Waals + H bond + desolvation energy, ligand

efficiency of NP with DNA are higher than those of RNA, BSA and dendrimer. The above results suggest that

sensing of NP with DNA is higher than with other biomolecules. The higher affinity is presumably attributed

to the formation of more and/or tighter hydrogen bonds between the several base pairs at the binding site owing

to the increased electronegativity of the hydrogen and oxygen. In other words, they possess the highest potential

binding affinity into the binding site of the 3D macromolecule.

Table 2. Naproxen with DNA, RNA, BSA and PAMAM-OH-Dendrimer interaction values.

Various Interactions

DNA

RNA

BSA

Dendrimer

Binding energy ΔGb (kcal/ mol)

7.14

4.38

5.47

5.49

Intermolec. Energy kcal/mol

8.33

5.57

6.66

6.69

Torsional energy

1.19

Total Internal energy

0.27

0.28

0.23

0.27

Inhibition constant (Ki) (uM)

5.85

618.88

97.96

94.1

vdW + H bond + desolv Energy kcal/mol

6.61

5.46

4.68

5.15

Electro static Energy kcal/mol

1.73

0.11

1.98

1.54

Ligand efficiency

0.42

0.26

0.32

Unbound energy

0.27

0.28

0.23

0.27

refRMS

26.16

30.39

46.3

66.3

(a) NP/DNA binding image (b) 3D Interactions (c) Hydrogen bond interactions

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(d) 2D Interactions (e) NP/RNA binding image (f) 3D interactions

(g) Hydrogen bond interaction (h) 2D interactions

Fig. 3. Naproxen with biomolecule interaction images for (a-d) NP/DNA binding image, (e-h) NP/RNA

binding images.

(a) NP/BSA binding image (b) 3D Interactions (c) Hydrogen bond interactions

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(d) 2D interactions (a) NP/ Dendrimer binding image (b) 3D Interactions

(g) Hydrogen bond interactions (h) 2D interactions

Fig. 4. Naproxen with biomolecule interaction images for (a-d) NP/BSA binding image, (e-h) NP/Dendrimer

binding images.

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Fig.5. Anticancer potential of naproxen with 1r51 protein

Fig.6. Anticancer potential of naproxen with 2oh4 protein.

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Anticancer Potential of naproxen

The anticancer potential of NP (ID No. 156391) was assessed through molecular docking studies, as depicted

in Figures 5 and 6. In the Figure, 9 and 10 shows the 3D and 2D interactions of the epidermal growth factor

receptor (EGFR) complex between epiregulin (EREG) (PDB ID:5WB7) and NP. The specific interactions

between NP and the target proteins are summarized below:

With the 1r51 protein, NP formed three conventional hydrogen bonds at Tyr275, Pro272 and Arg300. Further,

four alkyl interactions are observed at Lys270, Cys271, Val277 and Arg273 and two carbon-hydrogen bond

interactions are noticed at Lys 269 and Tyr261. The LibDock score is 83.22. With the 2oh4 protein, NP

exhibited a conventional hydrogen bond- Arg1049, Pi-alkyl- Ala1063, Ile1051 & Ala1048. The LibDock score

is 95.09.

Additional evaluation using the AutoDock method yielded the following ADMET (Absorption, Distribution,

Metabolism, Excretion, and Toxicity) profile for NP: Solubility level is 3; Blood-Brain Barrier (BBB)

penetration is 2; Extended hepatotoxicity model (EXT Hepatotoxic MD) is 10.4481; CYP2D6 inhibition

prediction is False; Hepatotoxicity prediction is True; Plasma Protein Binding (PPB) prediction is True. (Note:

Drug-induced hepatotoxicity refers to liver damage caused by pharmaceuticals or herbal agents, which is often

difficult to diagnose.

The PPB assessment for siRNA reflects the unbound drug fraction (fu) in plasma under equilibrium conditions.

This is a critical parameter in regulatory submissions, as the free drug hypothesis suggests that only the unbound

fraction is pharmacologically active at the target site during steady-state conditions. Overall, these results

indicate that NP demonstrates promising anticancer activity through interactions with both the 1r51 and 2oh4

EGFR protein targets.

CONCLUSION

Absorption, emission and molecular docking characteristics of the naproxen drug with biomolecules and silver

nanoparticles were analysed. With the addition of NP, the absorption and emission maxima of the biomolecules

completely disappeared, and no significant spectral shift was noticed in the NP drug. When biomolecule

concentrations increased, the absorption and emission intensities of the drug were gradually changed.

The negative ΔG0 values indicate the spontaneity of the binding between the drugs and biomolecules. The

intercalative binding, van der Waals force and hydrogen bonding play major roles in the sensing of the drugs

and biomolecules. Due to Ag nanoparticles interaction with NP/biomolecules, blue or red shift was noticed in

the absorption and emission spectra.

Molecular docking results indicated that the biomolecules interacted with the O and H groups of the NP drug.

The sensing behaviour of NP with DNA is higher than other biomolecules. NP drug demonstrates promising

anticancer activity through interactions with both the 1r51 and 2oh4 EGFR protein targets.

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