Literature DB >> 35663763

Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitor.

M Govindammal1, S Kannan2, P Srinivasan3, M Prasath1.   

Abstract

Quercitrin is an anti-lung cancer agent. It is a naturally occurring flavonoid and its derivatives are mainly present in nuts and beverages. It is mainly available as a glycoside, and the quercitrin glycosides are found to prevent the metastasis of cancer. Quercitrin is optimized with 6-311++G(d,p) basis set using the B3LYP method to attain its minimum energy structure. The vibrational studies of the Quercitrin compound were elucidated with reference to Potential Energy Distribution (PED). The geometrical parameters were obtained and correlated with experimental values. To examine the nature of the charge transfer mechanism of Quercitrin, the HOMO-LUMO energy gap is computed. The anti-cancer activity of Quercitrin has been explored using molecular docking study that are used to estimate how the ligand interacts with protein, specifically to identify the best-fit orientation of the ligand, its binding mode, and intermolecular interactions of amino acid residues in the binding region of B-RAF kinase protein. The binding affinity of the compound Quercitrin (-7.14 kcal/mol) was found using AutoDock and validated with a Glide XP score in Schrodinger tool (-8.01 kcal/mol). MD simulations of protein-ligand complexes were monitored for 100 ns, from which the RMSD, RMSF, Rg, H-bonds, and interaction energy calculations were executed. From these investigations, it is identified that the compound quercitrin has maintained good structural stability, compactness, higher Hydrogen bonds, and interaction energies than the Imidazopyridinyl benzamide inhibitor.
© 2022 The Author(s).

Entities:  

Keywords:  B-RAF kinase; DFT; Lung cancer

Year:  2022        PMID： 35663763      PMCID： PMC9160043          DOI： 10.1016/j.heliyon.2022.e09539

Source DB:  PubMed          Journal:  Heliyon        ISSN： 2405-8440


Introduction

Lung cancer is the crucial reason for morbidity and mortality worldwide in both sexes and is most widely recognized as a reason for malignancy-related deaths [1]. Non-Small Cell Lung cancer (NSCLC) is a highly aggressive and recurrent kind of lung cancer. Globally, NSCLC is considered responsible for about 85% of all lung cancers [2]. B-RAF is a kinase protein and a member of the RAF family of Ser/Thr kinase family which is highly downstream of the Ras/Raf/MEK/ERK signaling pathway [3, 4]. B-RAF mutations have been found in 3–4% of NSCLC [5]. If the MEK/ERK signaling pathway is activated in human cancer, B-RAF kinases are supposed to be a prominent therapeutic target. B-RAF is involved in complex activity such as phosphorylation/dephosphorylation process resulting in kinase activation/deactivation [6, 7]. Quercitrin is an active natural bioflavonoid, a plant derivative that mostly appears in the glycoside structure [8]. The bounded sugar moiety in the Quercitrin compound makes the Quercitrin aglycone soluble and improves the absorption and bioavailability. Quercitrin exhibits anti-cancer properties against NSCLC. It is reported to inhibit quercitrin–induced apoptosis in the NSCLC cell line A549 with an IC50 value of 50 μm [9]. Quercitrin displays an anti-oxidant property and has become the focus point for revealing the anti-cancer activity [10]. Vibrational spectroscopic studies have been carried out to recognize and examine the chemical bonding and intramolecular bonds of quercitrin. The vibrational analysis of Quercitrin was discovered using quantum chemical calculations using the DFT approach. The theoretical findings match up with the experimental results. The most reactive area of the Quercitrin is illustrated using the molecular electrostatic potential map (MEP). The chemical reactivity of quercitrin is determined by the Fukui function. The bio-availability compound was scrutinized with ADMET prediction analysis along with Lipinski's rule of five. A molecular docking evaluation was employed to explore the intermolecular interactions of quercitrin in the binding site of the B-RAF kinase protein. The analyses, such as HOMO-LUMO, MEP, and ADMET predictions, are utilized to find the anti-cancer behavior of Quercitrin against NSCLC.

Materials and methods

Experimental methods

Quercitrin was procured in solid form with a purity of ≥95% and no further purification of the compound has been made for spectral studies. The PERKIN ELMER (4000-400 cm−1) spectrometer with the KBr pellet technique was used to obtain the FT-IR spectrum of Quercitrin. Additionally, the FT-Raman spectrum was accomplished for Quercitrin in the region of 4000–100 cm−1 with a resolution of 2 cm−1 employing Brucker RFS 27- Nd: YAG laser source of 1064 nm at SAIF-IITM.

Computational methods

The Quercitrin compound was optimized using the DFT method employing the B3LYP level of theory by Gaussian09 software [11]. The geometrical parameters of the optimized geometry were generated using the Gaussview 0.5 software package [12]. The VEDA 4xx program package [13] was used to obtain the Potential Energy Distribution percentage (PED %) and fundamental vibrational assignments of Quercitrin. The biological properties of the ADME assessment of the compound were obtained using an online tool, the Molinspiration Cheminformatics server. The ligand (Quercitrin) and protein (B-RAF kinase) were docked with the aid of Autodock 4.2 [14]. The structural and interaction patterns of the protein-ligand complex are visualized and generated using the PyMol [15], Chimera [16], and Ligplot [17] software packages. The genetic algorithm and Lamarckian GA were employed to search for the appropriate conformers and for binding affinity. The number of points in the X, Y and Z dimensions are 24, 26, and 24 respectively. The center grid box in the X, Y and Z centres are -23.905, 5.081, and -6.037 respectively. The total grid points per map are 16875, with a spacing of 1 Å. The docking conformations are generated in AutoDock Vina, and those conformations are graded on the basis of binding free energy, by applying Eq. (1),where ΔGbind represents the binding free energy, ΔGvdw the van der Waals interaction, ΔGdesolv the desolvation effect, ΔGHbond the hydrogen bonding interaction, ΔGele the electrostatic interaction, ΔGinternal the internal energy, ΔGtorsion and ΔGunbound represents the torsional free energy, and unbound systems energy respectively. The AutoDock results were further validated with the Extra Precision Glide XP score in Maestro, the Schrodinger suite [18]. The molecular dynamics (MD) simulation of docked structures of protein-ligand complexes was carried out for a 100 ns time period using the GROMACS program, version 2019.5 [19]. With the SPC216 (simple point charge) water model, the molecular system was solvated in a cubic box [20]. Amber 99SB force field was executed and the system was examined at the same temperature of 300 K over a 100 ns period of time. The PBC (periodic boundary condition) was applied to the system and the ligand topology parameters were generated using the ACPYPE server [21]. The system was energy minimized and the position restrained MD was carried out for 1000 ps using NVT and NPT ensembles with the Parrinello-Rahman pressure coupling [22]. The RMSD, RMSF, radius of gyration and interaction energy were analyzed using the GROMACS program.

Results and discussion

Structural aspects

The Quercitrin structure was drawn utilizing the Chemdraw8.0 tool [23] and optimized with the DFT method to get the energy minimized structures using the B3LYP levels of theory [24, 25]. The Optimized geometrical parameters of the Quercitrin compound were generated using Gaussian 09 and GaussView5.0 as shown in Figure 1. With the crystal structure of Quercitrin not yet known, we have calculated the theoretical predictions on structural parameters of Quercitrin with available X-ray diffraction data [26] and the results are presented in Table 1. The Quercitrin's threshold converged at the limits of its maximum force value of 0.000010 (a.u) and displacement value of 0.000878 (a.u). The dipole moment value of the compound is found to be 8.2324 Debye. The quercitrin contains twelve C–H, twenty C–C, fifteen C–O, and eight O–H bonds. The C–C bond lengths of the phenol ring range from 1.359 to 1.369 Å. The ketone groups in Quercitrin have bond lengths of C(2)–O(12)→1.376/1.384∗Å, C(3)–O(11)→1.218/1.266∗Å, C(9)–O(10)→1.363/1.373∗Å, and O(1)–O(10)→1.366/1.373∗ (∗ denotes the Observed value). The highest bond length value, found in Quercitrin is C(16)–C(17) with 1.542 Å due to a double bond. The ketone group exhibits the bond angle of C(2)–C(1)–O(10) and the value is found to be 119.9/120.5°∗.
Figure 1

The scaled ball and stick model of optimized structure of Quercitrin molecule with atoms numbering scheme.

Table 1

Bond lengths and bond angles of quercitrin molecule compared with XRD data.

Bond Length (Å)CalculatedExpaBond Angle (o)CalculatedExpa
C(1)-C(2)1.3591.369C(2)-C(1)-O(10)119.9120.5
C(1)-O(10)1.3661.373C(2)-C(1)-C(25)128.9127.8
C(1)-C(25)1.4731.468O(10)-C(1)-C(25)111.1111.6
C(2)-C(3)1.4801.445C(1)-C(2)-C(3)122.9120.9
C(2)-O(12)1.3761.384C(1)-C(2)-O(12)121.1122.1
C(3)-C(4)1.4791.433C(3)-C(2)-O(12)115.8116.7
C(3)-O(11)1.2181.266C(2)-C(3)-C(4)113.7116.2
C(4)-C(5)1.4191.429C(2)-C(3)-O(11)121.5121.6
C(4)-C(9)1.4041.402C(4)-C(3)-O(11)124.8122.2
C(5)-C(6)1.3931.359C(3)-C(4)-C(5)123.9122.4
C(5)-O(24)1.3511.359C(3)-C(4)-C(9)119.6120.6
C(6)-C(7)1.4001.399C(5)-C(4)-C(9)116.5116.9
C(6)-H(33)1.0871.393C(4)-C(5)-C(6)120.6120.9
C(7)-C(8)1.387-C(4)-C(5)-O(24)118.5118.8
C(7)-O(23)1.3611.347C(6)-C(5)-O(25)120.8120.3
C(8)-C(9)1.3921.373C(5)-C(6)-C(7)120.5119.9
C(8)-H(34)1.081-C(5)-C(6)-H(33)119.5-
C(9)-O(10)1.3631.373C(7)-C(6)-H(33)120.0-
O(12)-C(14)1.4101.442C(6)-C(7)-C(8)120.5121.2
O(12)-H(50)2.289-C(6)-C(7)-O(23)122.0116.2
O(13)-C(14)1.4201.398C(8)-C(7)-O(23)117.5122.5
O(13)-C(18)1.4401.442C(7)-C(8)-C(9)118.2118
C(14)-C(15)1.5351.517C(7)-C(8)-H(34)121.0-
C(14)-H(35)1.098-C(9)-C(8)-H(34)120.8-
C(15)-C(16)1.5361.534C(4)-C(9)-C(8)123.7123
C(15)-O(22)1.4151.422C(4)-C(9)-O(10)121.5121.7
C(15)-H(36)1.092-C(8)-C(9)-O(10)114.8117.4
C(16)-C(17)1.5421.513C(1)-O(10)-C(9)122.0
C(16)-O(21)1.4401.416C(2)-O(12)-C(14)117.2116.1
C(16)-H(37)1.095-C(14)-O(13)-C(18)115.5116.3
C(17)-C(18)1.5361.542O(12)-C(14)-O(13)107.9112.3
C(17)-O(20)1.4251.426O(12)-C(14)-C(15)106.1105.3
C(17)-H(38)1.095-O(12)-C(14)-H(35)109.9-
C(18)-C(19)1.5291.511O(13)-C(14)-C(15)111.3112.9
C(18)-H(39)1.093-O(13)-C(14)-H(35)110.1-
C(19)-H(40)1.094-C(15)-C(14)-H(35)111.4-
C(19)-H(41)1.089-C(14)-C(15)-C(16)111.2109.4
C(19)-H(42)1.093-C(14)-C(15)-O(22)112.1107.7
O(20)-H(43)0.967-C(14)-C(15)-H(36)106.2-
O(21)-H(44)0.961-C(16)-C(15)-O(22)110.6110.6
O(22)-H(45)0.967-C(16)-C(15)-H(36)109.3-
O(23)-H(46)0.963-O(22)-C(15)-H(36)107.2-
O(24)-H(47)0.963C(15)-C(16)-C(17)111.8110.0
C(25)-C(26)1.4091.396C(15)-C(16)-O(21)106.0113.2
C(25)-C(30)1.4041.398C(15)-C(16)-H(37)108.2-
C(26)-C(27)1.3821.380C(17)-C(16)-O(21)112.4107.8
C(26)-H(48)1.083-C(17)-C(16)-H(37)108.5-
C(27)-C(28)1.4041.401O(21)-C(16)-H(37)109.9-
C(27)-O(32)1.3781.358C(16)-C(17)-C(18)112.1112.3
C(28)-C(29)1.390-C(16)-C(17)-O(20)108.8110.6
C(28)-O(31)1.3581.359C(16)-C(17)-H(38)109.4-
C(29)-O(30)1.391-C(18)-C(17)-O(20)109.6109.9
C(29)-H(49)1.083-C(18)-C(17)-H(38)110.3-
O(30)-H(50)1.079-O(20)-C(17)-H(38)106.5-
O(31)-H(51)0.966-O(13)-C(18)-C(17)107.1111.3
O(13)-C(18)-C(19)113.7106.5
O(13)-C(18)-H(39)103.1-
C(17)-C(18)-C(19)116.9111.6
C(17)-C(18)-H(39)106.5-
C(19)-C(18)-H(39)108.4-
C(18)-C(19)-H(40)109.3-
C(18)-C(19)-H(41)113.1-
C(18)-C(19)-H(42)109.2-
H(40)-C(19)-H(41)107.7-
H(40)-C(19)-H(42)108.0-
H(41)-C(19)-H(42)109.4-
C(17)-O(20)-H(43)106.9-
C(16)-O(21)-H(44)108.9-
C(15)-O(22)-H(45)105.7-
C(7)-O(23)-H(46)109.6-
C(5)-O(24)-H(47)108.8-
C(1)-C(25)-C(26)118.9119.4
C(1)-C(25)-C(30)122.6121.5
C(26)-C(25)-C(30)118.4118.4
C(25)-C(26)-C(27)120.6121.3
C(25)-C(26)-H(48)119.8-
C(27)-C(26)-C(28)119.6-
C(26)-C(27)-C(28)120.7119.5
C(26)-C(27)-O(32)124.5118.5
C(28)-C(27)-O(32)114.8122.3
C(27)-C(28)-C(29)118.9119.5
C(27)-C(28)-O(31)120.6114.9
C(29)-C(28)-O(31)120.5125.4
C(28)-C(29)-C(30)120.8125.4
C(28)-C(29)-H(49)118.6-
C(30)-C(29)-H(49)120.6-
C(25)-C(30)-C(29)120.5120.7
C(25)-C(30)-H(50)120.4-
C(29)-C(30)-H(50)119.0-
C(28)-O(31)-H(51)107.8-
C(27)-O(32)-H(52)110.0-

aExperimental values taken from ref [26].

The scaled ball and stick model of optimized structure of Quercitrin molecule with atoms numbering scheme. Bond lengths and bond angles of quercitrin molecule compared with XRD data. aExperimental values taken from ref [26].

Vibrational assignments

The Quercitrin, which is found to be more stable, pertains to C1 point symmetry. The DFT method is used to estimate the vibrational spectroscopic studies with a basis set of 6–311++G(d, p), which has a scaling factor of 0.961 and its PED % is calculated [27]. Table 2 illustrates the theoretical and experimental vibrational variables of the quercitrin. The FT-IR and FT-Raman spectra of Quercitrin are shown in Figures 2 and 3, respectively.
Table 2

The experimental (FT-IR and FT-Raman) and theoretical vibrational frequencies using DFT for quercitrin.

SpeciesExperimental Wavenumbers(cm−1)
Theoretical wave number (cm−1)
Vibrational assignments
FT-IRFT-RAMANUnscaledscaledIR intensities
RAMAN Activities
RelAbsRelAbs
W(150)38533703551311914OH stretching (92)
W(149)3850370068169712OH stretching (100)
W(148)38343684942219924OH stretching (92)
W(147)38173668581418722OH stretching (100)
W(146)378336361463418122OH stretching (100)
W(145)3611376436177718121OH stretching (100)
W(144)37633616307536OH stretching (100)
W(143)31223242311582374CH stretching (99)
W(142)30783221309500729CH stretching (100)
W(141)319430695113817CH stretching (99)
W(140)3185306161304CH stretching (97)
W(139)31433021113162CH stretching (98)
W(138)3139301719518923CH stretching (98)
W(137)30972976307789CH stretching (93)
W(136)30862966123617CH stretching (92)
W(135)3064294524613616CH stretching (98)
W(134)30462927491224429CH stretching (94)
W(133)3039292144109311CH stretching (95)
W(132)3036291731607CH stretching (84)
W(131)281630032886215263CH stretching (97)
W(130)16411660173316653247614517OC stretching (85)
W(129)160216041665160042410023929CC stretching (62)
W(128)16571593317293CC stretching (47)
W(127)165315881293178794CC stretching (26)
W(126)1557163515711944616520CC stretching (30)
W(125)15171546161715545413836100CC stretching (22)
W(124)1558149716739132CC stretching (42)
W(123)15361476236233CC stretching (38)
W(122)14451438151214535151CC stretching (26)
W(121)1494143672101CC stretching (21)
W(120)14191481142324858142CC stretching (41)
W(119)140214691412681681CC stretching (32)
W(118)1387144813926716152OC stretching (10)
W(117)143113754611243OC stretching (56)
W(116)13681428137235891OC stretching (10)
W(115)1417136230718422OC stretching (22)
W(114)14151359123506OC stretching (10)
W(113)14121357276293CC bending (20)
W(112)14061351164486OC stretching (30)
W(111)139513415120OC stretching (10)
W(110)138513312158110CC stretching (10)
W(109)13221382132829740OC stretching (20)
W(108)131513721318317121OC stretching (52)
W(107)136213093498225731OC stretching (36)
W(106)1354130141162OC stretching (66)
W(105)13341282246283CC stretching (22)
W(104)131812679021466CC stretching (13)
W(103)125613161265205243OC stretching (14)
W(102)1300124934882101CC stretching (32)
W(101)1293124314361CC stretching (22)
W(100)1274122533871OC stretching (49)
W(99)127312234210121CCC bending (10)
W(98)120512171267121736830CCC bending (28)
W(97)124311955012263CCC bending (12)
W(96)1175122511771112611314CCO bending (11)
W(95)1218117031875263HOC bending (56)
W(94)1214116633820HOC bending (63)
W(93)11581205115882162HOC bending (57)
W(92)119911522325571HOC bending (46)
W(91)1182113616840334HOC bending (54)
W(90)117211261944600HOC bending (45)
W(89)11201110116811231323171HOC bending (49)
W(88)11361092962330HCC bending (48)
W(87)1134108934840HCC bending (40)
W(86)11291085561320HCC bending (57)
W(85)1067111310701142730HCC bending (33)
W(84)1104106111627101HCC bending (23)
W(83)1098105617440HCO bending (69)
W(82)10821039912130HCO bending (23)
W(81)10711029611420HCO bending (40)
W(80)106610251383251HCC bending (44)
W(79)1004991104610051323171HCC bending (60)
W(78)1028988184101HCH bending (59)
W(77)970101497516461HCH bending (62)
W(76)10099691052551HCH bending (59)
W(75)9979584410142OCC bending (15)
W(74)94098294315310CCO bending (22)
W(73)930894451171CCC bending (25)
W(72)86591888215451CCO bending (13)
W(71)89485915430CCC bending (12)
W(70)832867833501210CCC bending (20)
W(69)85081714371CCC bending (16)
W(68)8078438104120CCO bending (14)
W(67)8247926161CCC bending (16)
W(66)7877858197873191OCC bending (37)
W(65)77480877734820OCC bending (44)
W(64)798767358283COC bending (11)
W(63)7907593181OCC bending (42)
W(62)722755726471110OCC bending (37)
W(61)7327045161CCC bending (14)
W(60)6827126853130OCC bending (11)
W(59)7056782030OCC bending (38)
W(58)6916644151COC bending (15)
W(57)6736474140OCC bending (18)
W(56)624638666640421020OCO bending (20)
W(55)63961413351OCC bending (12)
W(54)6026336086271OCC bending (51)
W(53)5926195958210OCC bending (10)
W(52)606582174152OCC bending (20)
W(51)57259657317420OCC bending (40)
W(50)5865632061OCC bending (35)
W(49)57355122591HOCC torsion (58)
W(48)5715488220HOCC torsion (78)
W(47)5265495283120HOCC torsion (75)
W(46)5345137210HOCC torsion (89)
W(45)487516496287182HOCC torsion (78)
W(44)503483791920HOCC torsion (88)
W(43)4904711022420HOCC torsion (83)
W(42)49047123510HCCC torsion (75)
W(41)469450511240HCCC torsion (67)
W(40)46845020520HCCC torsion (74)
W(39)46644819510HCCC torsion (79)
W(38)44843028710HCCC torsion (82)
W(37)4304136220HCOC torsion (33)
W(36)409393421020HCOC torsion (28)
W(35)40338815430HCCC torsion (50)
W(34)39137617451HCCC torsion (43)
W(33)37335927620HCCC torsion (49)
W(32)35934515430CCCC torsion (36)
W(31)3453324110CCCO torsion (36)
W(30)3433301082540CCCC torsion (51)
W(29)33732411300CCOC torsion (52)
W(28)3243122010CCCC torsion (29)
W(27)3123003100CCCC torsion (37)
W(26)30128911310CCCC torsion (37)
W(25)2962851030COCC torsion (44)
W(24)26725718420OCCC torsion (63)
W(23)26725619500COCC torsion (58)
W(22)25624625630OCOC torsion (81)
W(21)25024116410COCO torsion (50)
W(20)2392300000CCCO torsion
W(19)2332246110CCOC torsion (14)
W(18)22121321520CCCH out (67)
W(17)21921031740CCCH out (31)
W(16)217208711720CCCH out (26)
W(15)20519714320OCCC out (43)
W(14)1991924110OCCC out (28)
W(13)1811748200OCCC out (37)
W(12)1621721651010OCCC out (10)
W(11)1371310030OCCC out (11)
W(10)1141092100OCCC out (21)
W(9)93890000OCCC out (36)
W(8)92883100OCCC out (58)
W(7)7578750010CCOC out (22)
W(6)61580020COOC out (20)
W(5)46440040OCCC out (38)
W(4)37361010CCCC out (23)
W(3)29281030CCOC out (22)
W(2)24231020CCOC out (40)
W(1)14131030CCCC out (38)

1. Stretching, Bending, Torsion and Out.

2. Scaling Factor 0.961 for B3LYP6-311++G (d,p) [ref. 27].

3. Relative absorption intensity normalized with highest peak absorption equal to 100.

4. Relative Raman intensity normalized to 100.

Figure 2

Calculated and experimental FT-IR spectra of quercitrin.

Figure 3

Calculated and Experimental FT-Raman spectra of Quercitrin.

The experimental (FT-IR and FT-Raman) and theoretical vibrational frequencies using DFT for quercitrin. 1. Stretching, Bending, Torsion and Out. 2. Scaling Factor 0.961 for B3LYP6-311++G (d,p) [ref. 27]. 3. Relative absorption intensity normalized with highest peak absorption equal to 100. 4. Relative Raman intensity normalized to 100. Calculated and experimental FT-IR spectra of quercitrin. Calculated and Experimental FT-Raman spectra of Quercitrin.

O–H vibrations

The O–H hydroxyl stretching vibrations are tremendously effective for intra or intermolecular hydrogen bonding in the quercitrin. K. Muthu et.al reported the hydroxyl stretching vibrations in the 3600-3400 cm−1 range [28]. The O–H stretching vibrations of the Quercitrin, predicted by theoretical calculation, were observed at 3703, 3700, 3684, 3636, 3617, and 3616 cm−1 with a 100 % PED contribution. It is supported by the experimental FT-IR spectra observed at 3611cm−1.

C–H vibrations

The aromatic C–H stretching vibrations mostly appear in the range of 3100 to 3000 cm−1 [29]. Manjusha et.al reported the C–H stretching vibrations in the 2850-3000 cm−1 range [30]. In Quercitrin, C–H stretching vibrations occur from 3115 to 2886 cm−1. The experimental bands of FT-IR spectra were observed at 3122 and 2816 cm−1 and FT-Raman was observed at 3078 cm−1. The maximum PED contribution is 100%. Moreover, HCC bending bands are registered at 1067 and 1004 cm−1 in FT-IR and 991cm−1 in FT-Raman. Theoretically, HCH bending bands appear at 983,970 cm−1.

C–O vibrations

The stretching vibrations of C–O and the carbonyl C=O group are commonly disclosed in the range of 1740–1660 cm−1 [31]. The C–O stretching bands of the Quercitrin are noticed theoretically at 1665, 1392, 1375, 1372, 1362, 1359,1351, 1341, 1328, 1318, 1309, 1301, 1265, and 1225 cm−1 for the 6–311 G (d,p) basis set. The experimental values noticed at 1452, 1242, 1175, 1128, and 1003 cm−1 for FT-IR spectra and values at 1177 and 1226 cm−1 for FT-Raman spectra are in great concurrence with the values predicted using theoretical calculations with the 6-311G++ (d,p) basis set. These values are supported by the average potential energy distribution value of 85%. The blended vibration positions at 774,722, 682, 592, and 572cm−1for FT-IR are assigned to the OCC bending vibration. The other COC bending vibrations are observed at 624 in FT-IR and 638 cm−1 in FT-Raman. The CCO bending vibrations are recorded at 865, 807 and 787cm−1in FT-IR and at 1175 and 940cm−1in FT-Raman.

C–C vibrations

In carbon-carbon stretching vibrations, the bands between 1300–1000 cm−1 are designated as C–C ring stretching vibrations [32, 33]. The theoretical C–C stretching vibration for Quercitrin is reported at 1600, 1593, 1653, 1635, 1617, 1558, 1536, 1512, 1494, 1481, 1467, 1357, 1331, 1282, 1267, 1249, and 1243 cm−1. For the Quercitrin, the experimental CC stretching vibration values in FT-IR are observed at 1600, 1557, 1517, 1445, and 1419 cm-1, and the FT-Raman values are 1604, 1546, 1438, and 1402 cm-1.

Frontier molecular orbitals (FMO's)

FMOs assume a significant part during molecular interaction. The HOMO-LUMO energy gap and other FMO energies of the Quercitrin were plotted and represented in Figure 4. The FMOs fundamental descriptors are represented in Table 3 and Figure 4, [34, 35, 36]. The calculated HOMO energy value is -4.198eV, the LUMO value is -0.154 eV, and the bandgap energy value is 4.044 eV, for the quercitrin compound. It shows good charge transfer inside the molecule, and its biological activity is high [37]. The chemical softness of the quercitrin was found to be 0.247 eV. The low softness values of the quercitrin confirm the high stability and reactivity of the molecule. The chemical hardness of the quercitrin was computed to be 2.022 eV. The chemical potential and electrophilicity index values of quercitrin show that the molecule is a good bioactive drug.
Figure 4

Frontier molecular orbital of the Quercitrin molecule.

Table 3

Global chemical reactivity descriptors of the Quercitrin.

Parameters (eV)values
HOMO energy (EHOMO)-4.1984
LUMO energy (ELUMO)-0.1542
Energy gap (eV)4.0442
Ionization potential(I)4.1984
Electron affinity(A)0.1542
Electronegativity (χ)2.1763
Chemical potential (μ)-2.1763
Chemical Hardness (η)2.0221
Chemical softness (S)0.2472
Electrophilicity (ω)1.1711
Frontier molecular orbital of the Quercitrin molecule. Global chemical reactivity descriptors of the Quercitrin.

Molecular electrostatic potential

The molecular electrostatic potential surface Using the Gaussview 5.0 tool, for the quercitrin is depicted in Figure 5 (a) [38,39]. The MEP surface is exposed by various colors due to the increasing electron density in the order of red < orange < yellow < green < sky blue < blue. The 3D colour code MEP map ranges between-7.797 × 10−2 (red colour) and 7.797 × 10−2 (blue colour) for the Quercitrin, whereas the red color indicates the nucleophilic attack, which is the strongest attraction and the blue colour expresses electrophilic attack, which is the strongest repulsion. In the quercitrin, the negative region is more focused around the O(10), O(11), O(12), O(13), O(20), O(21), O(22), O(23), O(24), O(31), and O(32) atoms. Figure 5(b) depicts the contour map for Quercitrin, which clearly shows the density around various atoms.
Figure 5

a) Molecular Electrostatic Potential surface map of Quercitrin and b) Contour map of electrostatic potential of the total density of the Quercitrin.

a) Molecular Electrostatic Potential surface map of Quercitrin and b) Contour map of electrostatic potential of the total density of the Quercitrin.

Local reactivity descriptors

The Fukui function is an important aspect of developing a pharmaceutical product since it is used to identify the electron density based on local reactivity descriptors, which are used to predict the chemical reactivity of the molecule [40, 41, 42, 43]. The atoms may possess a positive or negative mulliken charge in accordance with the number of electrons surrounding them. Figure 6 depicts the histogram of the computed Mulliken charge of the Quercitrin without hydrogen atoms, as well as all the oxygen atoms that have a negative charge and carbon atoms C1 to C9, C14, C15, C17, C27, and C28 that have a positive charge, while the molecule's other carbon atoms have negative charges. C3 has the highest positive value (0.389) of all the carbon atoms, whereas the oxygen atom has the highest negative value (−0.433) and the results are reported in Table 4. The computed fk+ value shows the possible site for nucleophilic attack (due to positive value) and is in the order of C1, C2, C6, C8, O24, C27, C28, C30, O31, and O, and the fk− value shows the possible site for electrophilic attack (due to negative value) and is in the order of C4, C7, C9, C18, and C25.
Figure 6

The histogram of calculated Mulliken charge of Quercitrin molecule expect hydrogen.

Table 4

Condensed Mulliken atomic charges, Fukui function fk and descriptors (sf)k and (ωf)k values for Quercitrin.

Atom. NoMulliken atomic charges
Fukui Function
Local softness
Electrophilicityindex
qN+1qNqN-1fk+fk-(sf)+(sf)-(ωf)+(ωf)-
C10.3180.2910.2400.0270.0510.0070.0130.0320.060
C20.0980.020-0.0160.0780.0360.0190.0090.0910.042
C30.3890.3720.2500.0170.1220.0040.0300.0200.143
C4-0.214-0.214-0.1770.010-0.0370.010-0.0090.000-0.044
C50.1900.1710.0980.0190.0720.0050.0180.0230.085
C6-0.107-0.142-0.1250.035-0.0170.009-0.0040.041-0.020
C70.1680.1600.1690.008-0.0090.002-0.0020.009-0.011
C8-0.053-0.094-0.1170.0400.0240.0100.0060.0470.028
C90.2120.2180.269-0.007-0.051-0.002-0.013-0.008-0.060
O10-0.337-0.354-0.5140.0170.1600.0040.0400.0200.187
O11-0.250-0.305-0.3440.0550.0390.0140.0100.0640.046
O12-0.358-0.383-0.4190.0260.0350.0060.0090.0300.041
O13-0.390-0.387-0.291-0.003-0.096-0.001-0.024-0.003-0.113
C140.2880.3030.264-0.0150.039-0.0040.010-0.0170.046
C150.0230.0280.093-0.005-0.065-0.001-0.016-0.006-0.077
C160.002-0.0010.0100.003-0.0110.001-0.0030.003-0.013
C170.0700.0740.062-0.0030.011-0.0010.003-0.0040.013
C18-0.032-0.0190.050-0.013-0.069-0.003-0.017-0.015-0.081
C19-0.283-0.284-0.3230.0010.0390.0000.0100.0010.046
O20-0.376-0.396-0.3940.019-0.0010.0050.0000.023-0.001
O21-0.433-0.426-0.407-0.007-0.019-0.002-0.005-0.008-0.022
O22-0.392-0.393-0.3970.0000.0040.0000.0010.0000.005
O23-0.327-0.353-0.4230.0270.0690.0070.0170.0310.081
O24-0.279-0.301-0.3790.0220.0790.0050.0190.0260.092
C25-0.188-0.202-0.1560.015-0.0470.004-0.0120.017-0.055
C260.011-0.023-0.0820.0340.0590.0080.0140.0390.069
C270.1490.1170.1450.032-0.0290.008-0.0070.038-0.033
C280.2060.1730.1550.0330.0180.0080.0040.0390.021
C29-0.082-0.107-0.1340.0250.0270.0060.0070.0300.032
C30-0.020-0.056-0.1010.0360.0450.0090.0110.0420.053
O31-0.286-0.354-0.4310.0670.0770.0170.0190.0790.091
O32-0.374-0.412-0.4510.0380.0380.0090.0090.0450.045
The histogram of calculated Mulliken charge of Quercitrin molecule expect hydrogen. Condensed Mulliken atomic charges, Fukui function fk and descriptors (sf)k and (ωf)k values for Quercitrin.

ADMET, drug-likeness properties and bioactivity score

Lipinski's rule of five [44, 45] and ADMET prediction [46] are both applied to assess the bioavailability of bulk material in drug discovery and development. In this study all the molecular characteristics of the Quercitrin were examined using the Molinspiration cheminformatics tool. Since the H-bond acceptor range is 11 (>10) and the H-bond donor range is 7 (>5) and TPSA 190 (>140), Quercitrin does not obey Lipinski's rule of five, as shown in Table 5 [47]. From ADMET, it is found that the compound quercitrin is orally available to humans, and the results are represented in Table 6. The AMES test's toxicity demonstrates that it is a non-carcinogenic and non-mutagenic molecule. The title compound was seen as a non-inhibitor for hERG (human ether -a-go-go gene), which proposes that it does not hinder any potassium channels.
Table 5

Prediction of drug-likeness properties for Quercitrin.

DescriptorsProperties
Hydrogen bond donor (HBD)7
Hydrogen bond acceptor (HBA)11
Partition coefficient (MilogP)0.64
Molecular weight (MW)448.34
Topological polar surface area (TPSA) (Å2)190.2
Number of atoms52
Number of rotatable bonds3
Table 6

Prediction of ADMET profiles of Quercitrin.

ABCDEFGHIJ
0.0393Non52.70976.443-4.573SuitableQualifiedMutagenViolatedNon-inhibitor

A:ADMET_BBB.

B: P-glycoprotein inhibitor.

C: Human intestinal absorption (HIA+, %).

D: Plasma protein binding (PPB, %).

E: ADMET_SK logP.

F: Lipinski's rule.

G:CMC-like rule.

H:Ames_test

I: Lead-like rule.

J: hERG- I&II inhibitor.

Prediction of drug-likeness properties for Quercitrin. Prediction of ADMET profiles of Quercitrin. A:ADMET_BBB. B: P-glycoprotein inhibitor. C: Human intestinal absorption (HIA+, %). D: Plasma protein binding (PPB, %). E: ADMET_SK logP. F: Lipinski's rule. G:CMC-like rule. H:Ames_test I: Lead-like rule. J: hERG- I&II inhibitor. Molinspiration is a web server tool utilized to predict the bioactivity score of the Quercitrin against regular human targets. The values are given in Table 7 which shows it as a moderately active compound. Bioactive scores for kinase protein, nuclear receptor ligands, and enzyme inhibitors were 0.08, 0.17, and 0.37, respectively. The projected values for GPCR, ion channel modulators, and protease inhibitors are -0.01, -0.08, and -0.06, respectively: These expected values are relatively active. Based on these findings, we can conclude that quercitrin has the potential to be used as an anti-cancer drug in the future.
Table 7

Bioactivity score of Quercitrin.

CompoundGPCRIon channel modulatorKinase inhibitorNuclear receptor ligandProtease inhibitorEnzyme inhibitor
Quercitrin-0.01-0.080.080.17-0.060.37
Bioactivity score of Quercitrin.

Molecular docking study

The optimized Quercitrin structure is converted to PDB format and docked with the B-RAF protein (RCSB with PDB ID 6B8U) [48]. The resolution of the corresponding protein has a lower value of 2.68Å so that we can get an optimum structure for the B-RAF protein. The active site of the B-RAF protein comprises the residues Glu 501, Cys 532, Asp 594, and Phe 595; respective binding energy values are shown in Table 8. The amino acids Phe 595, Gln 530, Cys 532, and Ser 536 of B-RAF protein forms strong conventional hydrogen bond interactions with atoms H(44), H(45), H(46), and H(51) of the Quercitrin with a distance of 2.2, 2.1, 2.3, and 2.2Å, respectively Figure 7 (a). The residues Trp 531, Ala 481, and Ile 463 of B-RAF protein form pi-pi stacked interaction with Quercitrin which is shown in Figure 7 (b). Figure 7 (c) represents the Quercitrin docked into the binding cavity (2D view, Ligplot) of the B-RAF protein. The compound which has numerically higher binding energy is found to possess increased binding affinity towards target protein [49]. This result reveals that quercitrin interacts well with the B-RAF kinase protein and fits well into the binding cavity of the B-RAF target protein. The binding affinity of the compound Quercitrin, which has a -7.14 kcal/mol using AutoDock, was validated with the Glide XP score in Schrodinger software (−8.01 kcal/mol). In addition, the binding score of Imidazopyridinyl benzamide bound with B-RAF protein was also calculated using AutoDock (−5.21 kcal/mol) and Schrodinger's Glide XP (−6.41). From these docking results, it is found that quercitrin has a numerically higher binding energy and is found to be a potent anti-cancer agent than Imidazopyridinyl benzamide.
Table 8

Molecular docking results and Hydrogen bonding distances between B-RAF protein and inhibitors such as Quercitrin and Imidazopyridinyl benzamide.

CompoundsBonded residuesBond distance (Å)Binding energy Kcal/mol
Reference RMSD (Å)
AutodockSchrodinger maestro xpGlide
QuercitrinPhe 595Ser 536Gln 530Cys 5322.22.22.12.0-7.14-8.011.816
Imidazopyridinyl benzamidePhe 595Asp 594Glu 501Cys 5323.12.92.82.5-5.21-6.411.780
Figure 7

a) The position of the ligand Quercitrin in the binding cavity of the B-RAF Protein b) 2D view of distance for hydrogen bond interaction of Quercitrin with amino acid residues of B-RAF Protein and c) The ligplot showing intermolecular interaction of Quercitrin molecule in the active site of B-RAF Protein.

Molecular docking results and Hydrogen bonding distances between B-RAF protein and inhibitors such as Quercitrin and Imidazopyridinyl benzamide. a) The position of the ligand Quercitrin in the binding cavity of the B-RAF Protein b) 2D view of distance for hydrogen bond interaction of Quercitrin with amino acid residues of B-RAF Protein and c) The ligplot showing intermolecular interaction of Quercitrin molecule in the active site of B-RAF Protein.

Molecular dynamics simulations

Analysis of structural stability, fluctuations and compactness of the protein

The structural stability of the Quercitrin and Imidazopyridinyl benzamide inhibitors bound to B-RAF protein was performed and compared using the Root Mean Square Deviation (RMSD) as shown in Figure 8 (a). For the last 20 ns, the Quercitrin has maintained RMSD value of around 0.20 nm. Though both the inhibitors maintain good stability of the protein, quercitrin is found to possess a low RMSD value and has shown higher stability of the protein in comparison with the Imidazopyridinyl benzamide inhibitor. The fluctuations of amino acid residues of B-RAF protein bound to Quercitrin and Imidazopyridinyl benzamide inhibitors were carried out using Root Mean Square Fluctuations (RMSF) analysis as shown in Figure 8 (b). The residue at position 493 of the Imidazopyridinyl benzamide bound B-RAF protein shows higher fluctuations at 0.53 nm, whereas the Quercitrin bound protein has 0.29 nm. On comparing the fluctuations of the two inhibitors, the Quercitrin bounded protein has low fluctuations and shows higher stability of the protein structure. The compactness of the protein can be identified from the analysis of the radius of gyration (Rg). From Figure 9, it is clearly known that the Quercitrin bounded protein has a lower value of Rg value than the Imidazopyridinyl benzamide bounded B-RAF protein. The Rg value of the Quercitrin-bound protein remained at 1.91 nm for the final 40 ns of MD simulation, whereas the Rg value of the Imidazopyridinyl benzamide-bound B-RAF protein ended at 1.96 nm.
Figure 8

a) Root Mean Square Deviation (RMSD) and b) Root Mean Square Fluctuation (RMSF) of B-RAF protein bounded to Quercitrin and Imidazopyridinyl benzamide inhibitors.

Figure 9

Radius of gyration (Rg) of the B-RAF protein bounded to Quercitrin and Imidazopyridinyl benzamide inhibitors.

a) Root Mean Square Deviation (RMSD) and b) Root Mean Square Fluctuation (RMSF) of B-RAF protein bounded to Quercitrin and Imidazopyridinyl benzamide inhibitors. Radius of gyration (Rg) of the B-RAF protein bounded to Quercitrin and Imidazopyridinyl benzamide inhibitors.

Analysis of hydrogen bonding and interaction energy analysis

The hydrogen bonds between the protein and ligands (Quercitrin and Imidazopyridinyl benzamide) were monitored throughout the MD simulation of 100 ns as shown in Figure 10. From Figure 10, it is evident that the Quercitrin has maintained 3 to 4 hydrogen bonds throughout the MD simulation, whereas the Imidazopyridinyl benzamide maintains 2 to 1 hydrogen bond. The total interaction energy, which is the sum of electrostatic and van der Waals (vdW) interactions, between the B-RAF protein and ligands (Quercitrin and Imidazopyridinyl benzamide), is shown in Figure 11 and Table 9. According to Table 9, quercitrin has a numerically higher interaction energy of 299.59 kj/mol (−71.60 kcal/mol) than Imidazopyridinyl benzamide, which has a numerically lower interaction energy of 269.39 kj/mol (−64.38 kcal/mol). For the two ligands, the vdW (−223.33 kj/mol (−53.37 kcal/mol) for Quercitrin and -169.63 kj/mol (−40.54 kcal/mol) for Imidazopyridinyl benzamide) interaction is found to be higher than electrostatic (−76.24 kj/mol (−18.22 kcal/mol) for Quercitrin and -99.76 kj/mol (−23.84 kcal/mol) for Imidazopyridinyl benzamide)) interactions. From this analysis, it is clearly known that quercitrin has higher affinity and is more bound to B-RAF protein than Imidazopyridinyl benzamide inhibitors.
Figure 10

Hydrogen bonding interactions of Quercitrin and Imidazopyridinyl benzamide with B-RAF protein.

Figure 11

Total interaction energy between the inhibitors (Quercitrin and Imidazopyridinyl benzamide) and B-RAF protein.

Table 9

Total interaction energy of Quercitrin and Imidazopyridinyl benzamide inhibitors bounded to B-RAF protein. Energies are in kj/mol.

S. No.CompoundsElectrostaticvdWTotal interaction energy
1Quercitrin-99.76-163.63-269.39
2Imidazopyridinyl benzamide-76.24-223.33-299.59
Hydrogen bonding interactions of Quercitrin and Imidazopyridinyl benzamide with B-RAF protein. Total interaction energy between the inhibitors (Quercitrin and Imidazopyridinyl benzamide) and B-RAF protein. Total interaction energy of Quercitrin and Imidazopyridinyl benzamide inhibitors bounded to B-RAF protein. Energies are in kj/mol.

Conclusion

The Quercitrin was structurally drawn and optimised to its lowest energy conformation, and bond length and bond angles were calculated and compared to experimental XRD data. The experimental and observed results of the Quercitrin compound's vibrational spectra (those based on PED %) were compared. The charge transfer inside the molecule is clearly described by the HOMO-LUMO, MEP, and Mulliken analyses. The molecular docking calculations were validated with two docking tools, AutoDock and Schrodinger's Glide XP. The binding affinity of the Quercitrin compound has a numerically higher binding affinity -7.14 kcal/mol (AutoDock) and -8.01 kcal/mol (Glide XP score in Schrodinger software) than the Imidazopyridinyl benzamide inhibitor. In addition, MD simulations of protein-ligand complexes were monitored for 100 ns, from which the RMSD, RMSF, Rg, H-bonds, and interaction energy calculations were executed. Quercitrin is found to have a low RMSD value and has shown higher stability of the protein compared to Imidazopyridinyl benzamide inhibitor. From RMSF analysis, the Quercitrin bounded protein has low fluctuations and shows higher stability of the protein structure. Throughout the 100 ns of MD simulation, Quercitrin maintained 3 to 4 hydrogen bonds, whereas Imidazopyridinyl benzamide maintained 2 to 1 hydrogen bond. From these investigations, it is identified that the compound quercitrin has maintained good structural stability, compactness, higher Hydrogen bonds, and interaction energies than the Imidazopyridinyl benzamide inhibitors. Finally, it is concluded that quercitrin bounds well in the binding domain of B-RAF kinase protein.

Declarations

Author contribution statement

Govindammal M: Conceived and designed the experiments; Performed the experiments; Analyzed and interpreted the data; Contributed reagents, materials, analysis tools or data; Wrote the paper. Kannan S: Performed the experiments; Analyzed and interpreted the data; Contributed reagents, materials, analysis tools or data. Srinivasan P: Contributed reagents, materials, analysis tools or data. Prasath M: Conceived and designed the experiments; Analyzed and interpreted the data; Wrote the paper.

Funding statement

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Data availability statement

Data included in article/supplementary material/referenced in article.

Declaration of interests statement

The authors declare no conflict of interest.

Additional information

No additional information is available for this paper.
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