Structural and vibrational investigations and molecular docking studies of a vinca alkoloid vinorelbine

To shed light into the anticancer property of vinorelbine as microtubule destabilizer, the most favourable binding mode and the interaction details between vinorelbine and tubulin were r

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Structural and vibrational investigations and molecular docking studies of a vinca alkoloid, vinorelbine

Sefa Celik, Sevim Akyuz & Aysen E Ozel

To cite this article: Sefa Celik, Sevim Akyuz & Aysen E Ozel (2023) Structural

and vibrational investigations and molecular docking studies of a vinca alkoloid,vinorelbine, Journal of Biomolecular Structure and Dynamics, 41:19, 9666-9685, DOI:10.1080/07391102.2022.2145369

To link to this article: https://doi.org/10.1080/07391102.2022.2145369

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Published online: 11 Nov 2022

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Structural and vibrational investigations and molecular docking studies

of a vinca alkoloid, vinorelbine

Sefa Celika, Sevim Akyuzb and Aysen E Ozela

Vinorelbine, a vinca alkaloid, is an antimitotic drug that inhibits polymerisation process of tubulins to

microtubules, and is widely used in cancer chemotherapy Due to the importance of the structure-

activity relationship, in this work the conformational preferences of the vinorelbine molecule were

surched by PM3 method The obtained lowest energy conformer was then optimized at DFT/B3LYP/6-

31G(d,p) level of theory and the structural characteristics were determined Frontier orbital (HOMO,

LUMO) and molecular electrostatic potential (MEP) analyses were performed for the optimized

struc-ture The experimental FT-IR, Raman and UV-VIS spectral data of vinorelbine along with the theoretical

DFT/B3LYP/6-31G(d,p) calculations were investigated in detail The vibrational wavenumbers were

assigned based on the calculated potential energy distribution (PED) of the vibrational modes To

shed light into the anticancer property of vinorelbine as microtubule destabilizer, the most favourable

binding mode and the interaction details between vinorelbine and tubulin were revealed by molecular

docking studies of vinorelbine into the a,b-tubulin (PDB IDs: 4O2B; 1SA0; 7CNN) and binding free

ener-gies were calculated by the combination of Molecular Mechanics/Generalized Born Surface Area

(MMGBSA) and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) methods fMM/

PB(GB)SAg The calculated vinorelbine-7CNN binding free energy, using by MM/PB(GB)SA approach,

was found to be the best (-50.39 kcal/mol), and followed by vinorelbine-4O2B (-28.5 kcal/mol) and

vinorelbine-1SA0 (-17.59 kcal/mol) systems Moreover, the interaction of vinorelbine with the

cyto-chrome P450 enzymes (CYP), which are known to help in the metabolism of many drugs in the body,

was investigated by docking studies against CYP2D6 and CYP3A4 targets

ARTICLE HISTORY

Received 1 August 2022 Accepted 3 November 2022

KEYWORDS

Vinorelbine; density functional theory; molecular docking; FT-IR and Raman

1 Introduction

Vinorelbine is a vinca alkaloid that is produced

semi-synthet-ically and suppresses cellular growth by binding to tubulin,

like other vinca alkaloids, although it varies from them in

terms of its spectrum of antitumor action (Ngan et al., 2000)

It was shown by in vitro experiments that vinorelbine affects

on microtubule dynamic instability and treadmilling and

reported that its major effects were a slowing of the

micro-tubule growth rate, an increase in growth duration, and a

reduction in shortening duration (Ngan et al., 2000)

Vinorelbine has been used to treat non-small cell lung

cancer (NSCLC), as well as breast, ovarian, and cervical

can-cers (Altinoz et al., 2018; McQueen, 2010) It is also a vinca

plant-based antimicrotubule antineoplastic agent that has

been studied in both first and second-line NSCLC treatments

In the United States, the FDA (U.S Food and Drug

Administration) has authorized vinorelbine for NSCLC

treat-ment (Laurent & Shapiro, 2006) The antitumor activity of

vinorelbine has been demonstrated in several preclinical

studies against various cancer cell lines and by xenograft

tumor models (Waldman & Terzic, 2008) Vinorelbine has

become an important anticancer agent in adjuvant theraphy of of patients with NSCLC (stages 1B-III) and the palliative chemotheraphy in the NSCLC (stages IIIB and IV) offen in combination with cisplatin (Aronson, 2015) It also plays an important role in the treatment of advanced and metastatic breast cancer (Aronson, 2015; Gregory & Smith,

chemo-2000; Stravodimou et al., 2014) In Europe, vinorelbine has been approved for the treatment of NSCLC, breast cancer, and in some countries, prostate cancer (Debernardis

et al., 2009)

The human cytochrome P450 isoenzymes involved in in the liver metabolism of vinorelbine was investigated and determined that CYP3A4 was the main enzyme involved in the hepatic metabolism of vinorelbine (Beulz-Riche et al.,

2005) Chi et al investigated the structural mechanism for the binding of a vinca alcoloid, vinblastine, with tubulin by molecular docking studies (Chi et al., 2015)

Literature survey reveals that for vinorelbine no molecular structure analysis and vibrational assignments have been reported so far This study aimed to enlighten the molecular structure, electronic properties, and anticancer action mecha-nisms of vinorelbine To reveal the molecular structure,

CONTACT Sefa Celik scelik@istanbul.edu.tr Physics Department, Science Faculty, Istanbul University, Istanbul, Turkey

Supplemental data for this article can be accessed online at https://doi.org/10.1080/07391102.2022.2145369

2023, VOL 41, NO 19, 9666–9685

https://doi.org/10.1080/07391102.2022.2145369

conformational analysis on vinorelbine was performed and

the obtained most stable conformation was then optimized

at DFT/B3LYP/6-31G(d,p) level of theory The vibrational

wavenumbers of the molecule were experimentally observed

and compared with the computed values The vibrational

modes were determined based on the calculated potential

energy distribution (PED) The Frontier molecular orbitals

analysis of vinorelbine was performed to study the molecular

reactivity and stability Molecular Electrostatic Potential (MEP)

map was discussed to get information about the chemical

and site selectivity of vinorelbine

Vinorelbine exerts its cytotoxic effect on cancer cells by

binding to tubulin, which leads to cell cycle arrest in mitosis

The a,b-tubulin heterodimers have highly dynamic structure

and there are some differences in the crystal structures

tubu-lin-ligand complexes (Bueno et al., 2018) For this reason, to

elucidate the binding modes of vinorelbine against tubulin,

molecular docking studies were performed by using three

available tubulin crystal structures obtained from protein

data bank (PDB) as target proteins These targets are: 1)

Tubulin in complex with colchicine and with the stathnin-like

domain (PDB ID: 1SA0) (Ravelli et al., 2004), 2) tubulin

colchi-cine complex (PDB ID: 4O2B) (Prota et al., 2014) and 3)

tubu-lin-vinorelbine complex (PDB ID: 7CNN) Moreover, the

binding free energies were calculated by MM/PB(GB)SA

approach, which is the combination of Molecular Mechanics/

Generalized Born Surface Area (MMGBSA) and Molecular

Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA)

meth-ods (Wang et al., 2019) The purpose of this study is to find

the most favourable binding mode and reveal the interaction

details between vinorelbine and tubulin In a recent study,

the crystal structure of vinorelbine in complex with tubulin

was determined by Chengyong et al (2021; PDB ID: 7CNN)

In this study, to validate our docking protocol and to

high-light the importance of the initial geometry of the ligand in

the docking studies, vinorelbine was re-docked into the

vinorelbine binding site of PDB ID:7CNN target (Chengyong

et al., 2021) and for docking simulations, two different initial

structures of the ligand were used: 1) Vinorelbine structure

obtained from the published data of the crystal structure of

tubulin-vinorelbine complex (PDB ID: 7CNN) (Chengyong

et al., 2021) and 2) the optimized geometry of vinorelbine

Finally, since the side effects of vinca alkaloids are known

to be related to their metabolism (Lokwani et al., 2020), the

hepatic metabolism of vinorelbine in human, was

investi-gated theoretically by docking simulations against

cyto-chrome P450, CYP3A4 and CYP2D6 enzymes

2 Experimental and computational procedures

2.1 Experimental

Vinorelbine was acquired in solid form Santa Cruz

Biotechnology (CAS Number 71486-22-1) with reagent grade

and used as obtained The FT-IR spectrum of the KBr disc of

the sample was recorded on a Jasco 6300 FT-IR spectrometer

(2 cm 1 resolution), between 400 and 4000 cm 1 A Jasco

NRS 3100 micro-Raman spectrometer with a 532-nm diode

laser and a 1200 lines/mm diffraction grating was used to

record the Raman spectra For calibration the 520 cm 1 con phonon mode was used The UV-Visible spectrum of DMSO solution of vinorelbine was obtained using a Perkin Elmer-Lambda 25 spectrometer in the 190–900 nm region Spectral manipulations such as baseline adjustment, curve fitting and obtaining second derivative were performed using GRAMS/AI 7.02 (Thermo Electron Corporation) software package For curve fitting, second dervivative of the original spectrum was used as a guide, and curve fitting was done using Gaussian function The fitting was undertaken until reproducible and converged results were obtained with squared correlations better than r2 � 0.9998 The second derivatives of the spectra were obtained by using Savitzky- Golay function (two polynomial degrees, 17 points)

to convert Raman activity to Raman intensity For the etical computations, Lorentzian band forms with a band-width (FWHM) of 10 cm 1 were chosen

theor-The following scale factors for DFT/B3LYP/6-31G(d,p) level

of theory calculations were chosen to produce the best match for the experimental results: O-H stretch 0.87; N-H stretch 0.89; C ¼ O stretch 0.86; C-H stretch 0.91; N-H and C-H deformation 0.92; all others 0.98 These scale factors were chosen by optimization of the scale factors taken from the previous studies (Celik et al., 2016, 2021, 2022a, Celik, Vagifli, et al., 2022) by fitting the observed frequencies to the calculated ones

For docking studies, the crystal structures of a,b-tubulin (PDB IDs: 4O2B; 1SA0; 7CNN) (Chengyong et al., 2021; Prota

et al., 2014; Ravelli et al., 2004) and P450 enzymes CYP2D6 (PDB ID: 2F9Q) (Rowland et al., 2006), CYP3A4(PDB IDs: 1TQN, 1W0E, 1W0F, 1W0G and 2V0M) (Ekroos & Sj€ogren,

2006; Williams et al., 2004; Yano et al., 2004) were obtained from the protein data bank (http://www.rcsb.org/pdb) Molecular docking simulations were performed by the Autodock Vina program (Trott & Olson, 2010) and binding affinities were calculated The active sites of receptors were screened by using the CAVER program (Jurcik et al., 2018) In docking, vinorelbine was treated as flexible ligand by modify-ing its rotatable torsions, but the target protein was consid-ered to be a rigid receptor

The binding free energies of the vinorelbine tubulin (PDB

IDs: 4O2B, 1SA0 and 7CNN) systems were calculated by MM/

PB(GB)SA approach by the program developed by Wang

et al (2019)

3 Results and discussion

3.1 Structure

The most stable conformer obtained as a result of the

con-formation analysis was optimized using DFT/B3LYP level of

theory and the 6-31 G(d,p) basis set The optimized structure

of the vinorelbine molecule (C45H54N4O8) is shown in

Figure 1 The labeled wireframe representation of the

opti-mized molecular geometry of the vinorelbine molecule is

given in Figure S1 (Supplementary data file) The obtained

bond lengths and bond angles are tabulated in Table 1 and

the dihedral angles are given in Table S1

As seen in Table 1, the C-C bond lengths of the indole-

like rings of vinorelbine were computed in the range of

1.388 1.444 Å These bond lengths were experimentally

determined between 1.34 and 1.41 Å, in the crystal structure

of the indole molecule (Kaneda & Tanaka, 1976) and

between 1.360-1.412 Å in the crystal structure of the

Bisbenzylisoquinoline alkaloid methylwarifteine molecule

(Borkakoti & Palmer, 1978)

The C-C bond lengths of a phenyl ring are known to be

around 1.4 Å The mean C-C bond length of benzene crystal

was determined as 1.392 Å (Cox et al., 1958) In substituded

benzene molecules, these bond lengths were experimentally

determined in the 1.378-1.403 range (Campos et al., 1980) In

our study, the C-C bond lengths of the phenyl group of the

vinorelbine molecule were calculated in the range of 1.389-

1.411 Å, in agreement with the expected values

The C-N bond lengths (N11-C37 and N11-C48) and the

C-N-C bond angle in the indole-like ring of vinorelbine were

computed as 1.374 Å, 1.391 Å, and 110.3�, respectively In the

crystal structure of the indole molecule, the C-N bond

lengths and C-N-C bond angle were experimentally

deter-mined as 1.36 Å, 1.38 Å, and 110.5�, respectively (Kaneda &

Tanaka, 1976) Also, the C-C bond lengths (C37-C42, C42-C47, C47-C48) and C-C-C bond angles (C37-C42-C47 and C42-C47- C48) in the indole moiety were computed as 1.388, 1.444, 1.419 Å, and 106.5 and 107.6, respectively, the corresponding values were experimentally determined as 1.37, 1.41, 1.40 Å, and 105.8 and 109.8, respectively, in the crystal structure of ethyladenine-indole complex (Kaneda & Tanaka, 1976) The results showed that the computed geometrical parameters of vinorelbine were in conformity with the struc-tural data of similar compounds An X-ray crystallographic study on vinorelbine is not available For this reason, we compared optimized structure of vinorelbine in gas phase with the vinorelbine obtained from the crystal structure of tubulin-vinorelbine complex (PDB ID: 7CNN) (Chengyong

et al., 2021) Figure S2 shows comparatively the geometric structure of vinorelbine molecule, obtained from the crystal structure of tubulin-vinorelbine complex (PDB ID: 7CNN) with that of optimized structure, obtained by using DFT/B3LYP/6- 31G(d,p) level of theory To quantify the difference between the optimized geometry of vinorelbine and its experimental findings, obtained from tubulin-vinorelbine complex, we cal-culated the root-mean-square difrences of the two structures

by using the structures comparer utility of the Chemcraft program (Zhurko, 2005) Since the H atoms of vinorelbine, obtained from tubulin-vinorelbine complex, were not present (PDB ID: 7CNN) (Chengyong et al., 2021) The comparison between the two structures was made without considering the H atoms The weighted RMSD was found to be 6.025 Moreover, it was found that O atoms gave the largest RMSD among all kind of atoms of vinorelbine (RMSD ¼ 7.277) The oxygen and nitrogen atoms of vinorelbine (C45H54N4O8) are reactive sites that interact with tubulin amino acids, so the bond angles and bond lengths involving the O and N atoms

of vinorelbine in the tubulin complex are expected to differ from the calculated values for the single molecule It must

be considered that the number of oxygen atoms in bine is twice that of nitrogen atoms Sebhaoui et al (2021) compared molecular structures of 2-pyrone derivatives obtained from crystal structures with those of calculated with B3LYP in the gas phase, by using Chemcraft program

vinorel-In that study, it was reported that O atoms gave the largest RMSD among all kinds of atoms contained by investigated 2-pyrone derivatives

Molecular electrostatic potential

The molecular electrostatic potential relates with the dipole moment, electronegativity, and partial charges of a molecule

It provides a reliable analysis of chemical reactivity and bles to determine electrophilic and nucleophilic regions, as well as hydrogen-bonding interactions of the molecule (Kaya Kınayt€urk et al., 2021; Kutlu et al., 2021; Politzer & Murray,

ena-2002) The MEP analysis of the optimized structure of bine was performed using B3LYP/6-31G(d,p) level of theory The electrostatic potential map of a vinorelbine molecule is shown in Figure 2, along with a legend that shows how potential varies with color Dark red color represents the most negative (electron rich) and dark blue color shows the most positive (electron poor) regions, whereas, the yellow

vinorel-Figure 1 The optimized geometric structure of vinorelbine, as determined

using DFT/B3LYP/6-31G(d,p) level of theory

color represents slightly electron-rich and light blue, the

slightly electron-poor regions.The color code of vinorelbine

MEP varies between 1.909 V (dark red) and 1.909 V (dark

blue) Figure 2 shows that regions with positive potential are

predominantly located on hydrogen atoms, where possible

nucleophilic attack sites, and negative potential regions

around oxygen atoms, as possible sites for

electro-philic attack

Vibrational spectral analysis

The Vinorelbine molecule (C45H54N4O8) has 111 atoms in C1

symmetry point group, thus has 327 vibrational modes, both

IR and Raman active The analysis of the bands and the

assignments of fundamental wavenumbers were made based

on computed potential energy distributions (PED), the

mag-nitude and relative intensities of the observed bands and

group frequencies The wavenumbers of the observed and

calculated fundamental bands in IR and Raman spectra,

along with their proposed assignments were given in

Table 2

The experimental FT-IR and Raman spectra of vinorelbine

are given in Figures 3 and 4, respectively compared to the

simulated spectra To resolve the overlapping bands in the IR and Raman spectra, resolution enhance techniques, such as curve fitting and second derivative of the experimental spec-trum were used The Figure S3 represents curve fitted FT-IR spectrum of vinorelbine The Figure S4 shows the 1700-

150 cm 1 region of the Raman spectrum and 1800-400 cm 1 region of the FT-IR spectrum of vinorelbine together with their second derivative profiles As seen in Figure S4, the second derivative minima correspond to the peaks in the ori-ginal spectrum

Vinorelbine has both aromatic and aliphatic CH groups The CH stretching vibrations of the substituted benzene like molecules are observed in the region 3100–3000 cm 1 (Jiao

et al., 2022; Roeges & Baas, 1994), whereas methylene CH stretching vibrations are expected in 3000-2800 cm 1 (Hajduchova et al., 2018; Jiao et al., 2022) Methyl CH stretch-ings are observed higher than methylene and around 2980-

2870 cm 1 In our study the observed IR bands at 3078,

3058, 3052 and 3033 cm 1 were assigned to CH stretching vibrations of the phenyl rings of indole moiety (Silverstein

et al., 1981) The corresponding bands were predicted by DFT at 3092, 3059, 3048 and 3043 cm 1, respectively as pure

CH stretching vibrations with aromatic CH stretching

Table 1 The optimized geometry parameters of vinorelbine, calculated by DFT/B3LYP/6-31G(d,p) level of theory.�

O1-C19 1.436 N11-C37 1.391 C18-H60 1.092 C29-H74 1.103 C40-H83 1.092 C49-C50 1.525 C19-O1-C35 124.6 O1-C35 1.366 N11-C48 1.374 C18-H61 1.092 C29-H75 1.092 C40-H84 1.094 C49-H98 1.101 C17-O2-H72 107.7 O2-C17 1.410 N11-H91 1.009 C19-H62 1.089 C30-C33 1.401 C40-H85 1.089 C49-H99 1.099 C27-O3-C41 115.6 O2-H72 0.991 N12-C43 1.460 C20-C23 1.395 C30-H76 1.081 C41-H86 1.089 C50-C53 1.512 C33-O5-C45 119.5 O3-C27 1.339 N12-C44 1.479 C20-C28 1.389 C31-H77 1.095 C41-H87 1.093 C51-C55 1.389 C38-O7-C54 114.9 O3-C41 1.439 N12-C49 1.465 C21-H63 1.094 C31-H78 1.094 C41-H88 1.092 C51-H100 1.086 C14-N9-C21 104.9 O4-C27 1.217 C13-C14 1.569 C21-H64 1.105 C31-H79 1.095 C42-C44 1.507 C52-C56 1.389 C14-N9-C25 113.5 O5-C33 1.369 C13-C16 1.571 C22-C31 1.533 C32-C33 1.416 C42-C47 1.444 C52-H101 1.086 C21-N9-C25 114.2 O5-C45 1.419 C13-C18 1.567 C22-H65 1.093 C32-C34 1.544 C43-H89 1.097 C53-C57 1.540 C16-N10-C23 107.2 O6-C35 1.207 C13-C20 1.514 C22-H66 1.098 C34-C36 1.558 C43-H90 1.088 C53-H102 1.096 C16-N10-C29 117.9 O7-C38 1.360 C14-C15 1.553 C23-C30 1.398 C34-C37 1.531 C44-H92 1.096 C53-H103 1.100 C23-N10-C29 117.7 O7-C54 1.438 C14-H58 1.102 C24-C26 1.332 C34-C38 1.557 C44-H93 1.101 C54-H104 1.092 C37-N11-C48 110.3 O8-C38 1.208 C15-C19 1.588 C24-H67 1.088 C35-C40 1.515 C45-H94 1.097 C54-H105 1.090 C37-N11-H91 122.7 N9-C14 1.480 C15-C22 1.565 C25-C26 1.500 C36-C39 1.557 C45-H95 1.091 C54-H106 1.093 C48-N11-H91 126.5 N9-C21 1.467 C15-C24 1.521 C25-H68 1.098 C36-H80 1.090 C45-H96 1.097 C55-C56 1.411 C43-N12-C44 114.2 N9-C25 1.460 C16-C17 1.561 C25-H69 1.109 C36-H81 1.092 C46-C50 1.341 C55-H107 1.086 C43-N12-C49 109.4 N9-H72 1.794 C16-H59 1.100 C26-H70 1.087 C37-C42 1.388 C46-H97 1.091 C56-H108 1.086 C44-N12-C49 111.6 N10-C16 1.486 C17-C19 1.549 C28-C32 1.401 C39-C43 1.542 C47-C48 1.419 C57-H109 1.095 C14-C13-C16 113.7 N10-C23 1.404 C17-C27 1.543 C28-H71 1.085 C39-C46 1.515 C47-C51 1.406 C57-H110 1.095 C14-C13-C18 103.1 N10-C29 1.459 C18-C21 1.533 C29-H73 1.089 C39-H82 1.100 C48-C52 1.400 C57-H111 1.095 C14-C13-C20 112.2

�

Bond lengths (R) in Å and bond angle (A) in degree (o).

Figure 2 Molecular electrostatic potential (MEP) of vinorelbine obtained by DFT/B3LYP/6- 31 G(d,p) level of theory

Table 2 The experimental and calculated fB3LYP/6-31G(d,p)g wavenumbers

(cm -1 ) of vinorelbine and the PED distributions of the vibration modes

contributions, according to PED calculations In the IR spectra

of indole vapour, the CH stretching vibrations were observed

in the range 3128-3041 cm 1 (Klots & Collier, 1995)

Moreover, the aromatic CH stretching vibration of

4-(2-mor-pholinoethanoylamino)-benzenesulfonamide was observed at

3080 cm 1 (Durgun et al., 2016)

In the present work the observed 2989 cm 1 IR band was

attributed to alkene CH stretching motion The

correspond-ing mode was computed at 2991 cm 1 The CH2 and CH3

stretching vibrations were observed at 2961, 2944, 2931,

2924, 2875, 2840, 2817 cm 1 and computed at 2961, 2943,

2926, 2925, 2873, 2845, 2822 cm 1, respectively The CH

stretching wavenumbers are in accord to those given in the

literature for similar structures (Celik, Yilmaz, et al., 2022;

Celik et al., 2019; E�glence-Bakır et al., 2021; Mariappan & Sundaraganesan, 2015; Mıhc¸ıokur & €Ozpozan, 2017; Pangajavalli et al., 2017; Subramanian et al., 2011; Thirunavukkarasu et al., 2018)

The N-H stretching motion of indole was observed at

3529 cm 1 in vapor and at 3420 cm 1 in liquid state IR tra of indole (Klots & Collier, 1995) In the FT-IR spectrum of indole-3-aldehyde, this mode was observed at 3500 cm 1

spec-and was calculated at 3533 cm 1 using DFT/B3LYP/6-31G(d,p) theory (Muthu et al., 2013) In this study, the N-H stretching wavenumber of vinorelbine was computed as 3454 cm 1 In the IR spectrum of solid vinorelbine, the strong band

observed ca 3438 cm 1 can be attributable to this mode However, the contribution of OH stretching motion to this broad band can not be excluded

The C ¼ O stretching bands generally fall between 1740 and 1710 cm 1, in aliphatic aldehydes and ketones In many studies, C ¼ O bond stretching vibrations were observed in the range of 1755-1630 cm 1 (Celik et al., 2017; Devi & Gayathri, 2010; Pangajavalli et al., 2017; Thirunavukkarasu

et al., 2018) In this study, C ¼ O stretching vibrations were calculated at 1724 (PED contribution; 81%), 1705 (81%) and

1676 cm 1 (85%), as almost pure C ¼ O stretching mode This mode was observed at 1742, 1710 cm-1 (IR) and 1678 cm 1

(R) in the FT-IR and Raman spectra of vinorelbine The curve fitting analysis of the 1800-1700 cm 1 region of the FT-IR spectrum of vinorelbine resulted 4 band components at

1773, 1743, 1719 and 1710 cm 1 (see Figure S3) The 1743 and 1710 cm 1 band components were attributed to funda-mental C ¼ O stretching motion, in comparison to 1724,

1705 cm 1 computed values, respectively The 1773 and

1719 cm 1 components were probably overtone or ation bands In literature, the C ¼ O stretching vibrations were reported at 1666, 1618 cm 1 (IR) and 1652, 1626 cm 1 (R), for anti cancer drug sunitinib (Mıhc¸ıokur & €Ozpozan,

combin-2017) and this mode was observed at 1741, 1651 (IR) cm 1 and 1732, 1654 (R) cm 1 in the vibrational spectra of camp-tothecin (Subramanian et al., 2011) Our results are compat-ible with the literature

The phenyl group carbon–carbon stretching modes are expected in the range from 1650 to 1200 cm 1 (Socrates,

1980) The CC stretching vibrations of indole was observed

in the range of 1616-1276 cm 1 (Klots & Collier, 1995) In this study, the CC stretching vibrations of the phenyl ring of the indole moiety of vinorelbine were observed in the range of 1661-1539 cm 1, and the computed values fall in the range 1647-1555 cm 1, with 58-69% PED contributions The other

CC stretching vibrations were computed as mixed modes The CNH bending vibrational mode was calculated at

1432 cm 1 and observed at 1431 cm 1 in the IR and Raman spectra of vinorelbine This mode was observed at

1403 cm 1 in the IR spectrum of indole-3-aldehyde molecule and calculated at 1403 cm 1 as mixed character with contri-butions of mCC (32%), d(CNC) and mCN (18%) (Muthu et al.,

2013) The CNH bending vibrations were recorded at 1499,

1317 cm 1 and 1501, 1313 cm 1, in the IR and Raman tra of Gly-Tyr (Celik et al., 2017), respectively In the vibra-tional spectra of flucytosine the CNH bending vibration was

observed at 1420 (IR) (Gunasekaran et al., 2006) The CNH

bending wavenumber of isoniazid was calculated at

1466 cm-1 according to DFT(B3LYP)/6-311þþG(d,p)

calcula-tions and observed at 1473.8 and 1470.2 cm 1, in the Ar and

Xe matrixes, respectively (Borba et al., 2009)

The computed aliphatic CH bending vibrations fall in the

range 1489-1413 cm 1 The observed bands at 1489 cm 1 (IR,

R) and 1475 (IR), 1474 (R) cm 1 in the IR and Raman spectra of

vinorelbine were assigned to CH2 bending modes These

vibra-tions were computed at 1489 and 1476 cm 1 as

predomin-antly CH2 bending vibrations The observed bands at 1458 (IR)

and 1460 cm 1 (R), 1451 cm 1 (R), and 1412 (IR) were assigned

to antisymmetric CH3 bending vibrations The computed ues of these bands were as 1457, 1449 and 1413 cm 1, that found as predominantly daCH3 vibrations In the study on 4- [(2-hydroxy-3-methylbenzylidene)amino]benzene sulfonamide, the CH3 bending vibration was observed at 1481 cm 1 in the FT-IR spectrum and calculated at 1512 cm 1 using B3LYP/6- 311þþG(d,p) level of theory (Ceylan et al., 2015)

val-The mean absolute deviation, standard deviation, root mean square and correlation coefficient calculations for the overall spectrum of vinorelbine show that the theoretically computed values are in good agreement with experimental data (see Table 3) The Linear regression analyzes of

Figure 3 The experimental (a) and simulated (b) IR spectra of vinorelbine

Figure 4 The experimental (a) and simulated (b) Raman spectra of vinorelbine

calculated IR (a) and Raman (b) wavenumbers versus

experi-mental wavenumbers were shown in the supplementary file

Figure S5

Frontier molecular orbital analysis

The highest energy occupied orbital (HOMO) and the lowest

energy empty orbital (LUMO) are the molecular orbitals that

take part in chemical reactions or interactions with other

species The HOMO-LUMO energy difference (gap) provides

information about the reactivity of the molecule and the

absorbed/reflected light (Pearson, 1973)

The pictorial illustration of the frontier orbitals of

vinorel-bine, calculated by DFT/B3LYP/6-31 G(d,p) level of theory in

DMSO solvent, was given in Figure 5 The HOMO-LUMO

energy gap was predicted to be 4.679 eV The result indicates

the presence of a charge transfer interaction in the molecule

and reflects the biological activity of the compound The

HOMO-LUMO energy gap of a tubulin inhibitor anti cancer

peptide Taltobulin was predicted as 6.240 eV using a

concep-tual DFT methodology and MN12SX/Def2TZVP/H2O model

chemistry (Flores-Holgu�ın et al., 2019) For anti cancer agents

Cepharanthine (Celik et al., 2022b) and Sunitinib (Mıhc¸ıokur

& €Ozpozan, 2017) this gap was calculated as 4.998 eV fDFT/ B3LYP/6-311þþG(d,p)g and 3.31 eV fDFT/B3LYP/6-31G(d,p)grespectively Compounds comprising the sulfonamide group show a large number of biological activities (Maren, 1976; Scozzafava et al., 2013) and sulfonamides were among the first drugs to be widely used and used as chemotherapeutic agents against various diseases (Hansch et al., 1990) The HOMO-LUMO band gap of a sulfanomide derivative N-(2-((2- chloro-4,5-dicyanophenyl)amino)ethyl)-4-methylbenzenesulfo-namide molecule was calculated as 4.3617 eV by DFT/B3LYP/ 6-311þþG(d,p) level of theory (Dege et al., 2022) The results indicate that HOMO-LUMO energy gap of vinorelbine is com-patible with previous findings for bioactive molecules

To investigate the properties of electronic absorption and

to interpret the UV-VIS spectrum, the lowest singlet, and spin-allowed excited states of vinorelbine were calculated using Time-Dependent Density Functional Theory (TD-DFT), B3LYP functional and 6-31 G(d,p) basis set The energy differ-ence between the ground state energy level and the first excited state of vinorelbine was computed as 4.078 eV in gas phase and as 4.086 in DMSO The percentage of atomic orbital contributions to HOMO and LUMO was calculated using the GaussSum (Version 3.0) tool (O’boyle et al., 2008) The measured transition energies, oscillator strengths, and major contributions are listed in Table 4 The experimental UV-Vis spectrum of Vinorelbine in DMSO solution is shown in

Figure 6

Molecular docking analysis of vinorelbine with a,b-tubulin

Tubulin is an established target for the binding of anticancer agents that cause a cytotoxic effect by disrupting

Table 3 Mean absolute deviation, standard deviation, root mean square and

correlation coefficient (r) between the calculated and observed vibrational

wavenumbers of vinorelbine

Parameter

IR B3LYP/6-31G(d,p)

Raman B3LYP/6-31G(d,p) Mean absolute deviation 4.1 3.3