Research

, Volume: 15( 3) DOI: 10.37421/0974-7516.2021.15.006

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Molecular structure, spectroscopic properties, Molecular docking analysis, and in vitro anticancer activity studies on of Gabapentin compounds.

*Correspondence:

Uvarani R
Department of Physics
Thiruvalluvar Government Arts College
Tamilnadu, India
E-Mail: anbuuvanithin@gmail.com

Abstract

Abstract

To investigate their electronic structures, Potential Energy Curves (PECs) of S₀ and S₁ states and vibrational spectral properties of gabapentin based derivatives namely GPN₁-GPN₄ are calculated by employing the Density Functional Theory (DFT) and Time- Dependent Density Functional Theory (TD-DFT) methods of DFT at 6-311G⁺⁺(d,p) basis set using Gaussian 09 software. The vibrational assignments, ₁H and ₁₃C NMR chemical shifts of the complexes computationally and compared with experimental data. The calculated geometric parameters (bond lengths, bond angles, torsion angles), the mapped Molecular Electrostatic Potential (MEP), local reactivity descriptors and the Potential Energy Curves (PECs) of S₀ and S₁ states are scanned by varying H₁₈-N₇-H₁₉ distance, etc. The molecular docking results suggest that the GPN₂ compound might exhibit inhibitory activity against Ca²⁺/CAMCaV2.2 IQ domain inhibitor.

Keywords

DFT; MEP analysis; Spectral properties; PECs; Molecular docking analysis

Introduction

Gabapentin or Aminomethyl Cyclohexanacetic Acid is a novel Antiepileptic Drug (AED) at present approved for the treatment of partial seizures neuropathic pain (nerve pain) [1], hot flashes, and restless legs syndrome conditions, such as diabetic neuropathy, central neuropathic pain, and painful diabetic peripheral neuropathy, post herpetic neuralgia [2]. Whilst gabapentin is considered to be better tolerated with fewer side effects than other antiepileptic drugs, treatment of nerve pain with oral gabapentin is still often limited by adverse effects such as posttraumatic stress disorder [3], dizziness, alcohol withdrawal, somnolence, hot flashes associated with prostate cancer treatment [4], and postoperative pain after cancer surgery [5, 6]. The topical gabapentin formulations or localized drug delivery has been controlled the adverse effect for NP whilst drug [5]. Furthermore, a recent approach is supported by in vivo study that has shown topical gabapentin formulations to be efficacious in rodent and porcine models for static or dynamic mechanical post-herpetic neuralgia and vulvodynia [6]. However, there is no licensed product comprising gabapentin available as a generic mediation in the United States or, somewhere else. This topical product is available as a “biological special” although, with reported compounds used as a treatment for seizures and neuropathic pain [7]. The bioavailability of gabapentin is comparatively light and strong doses (i.e. higher doses have lower bioavailability than lower doses). The bioavailability of gabapentin is approximately 27%-60% following 200 mg (threshold), 200 mg-600 mg (lower dose), 600 mg-900 mg (common), and 900 mg-1200 mg (higher dose) is about 5 hours-8 hours. Gabapentin is making unsaturated fats including olive oil and vegetable oil considerably boost the total amount of absorption for the reason eating a high heavy food considerably increases gabapentin's bioavailability and that meals measured down and thus decreasing gabapentin transporter saturation by increase gabapentin absorption [8]. In the present investigation, we describe the molecular structure, potential energy curves analysis and quantum chemical calculations have been performed for 2-(1-aminomethyl-cyclohexyl)acetic acid (GPN₁), methyl 2-(1-aminomethylcyclohexyl) acetate (GPN₂), 2-(1-(aminomethyl-cyclohexyl) acetamide (GPN₃), 2-(1-(aminomethyl-cyclohexyl) acetyl chloride (GPN₄). The detailed experimental FT-IR and FT-Raman spectra have been recorded and the calculated fundamental vibrational wavenumbers of Potential Energy Distribution (PED) have not been done so far. Further, the ¹³C and ¹H Nuclear Magnetic Resonance (NMR), (UV-VIS) spectra, Molecular Electrostatic Potential (MEP) surface map, and frontier molecular orbital analysis were simulated and visualized. The chemical reactivity, stability, hardness, and softness values were performed by utilizing the HOMO-LUMO energies of the title molecules. For interesting molecular docking analysis of gabapentin-based different anchoring groups moiety followed by studying the in vitro biological and anticancer activities.

Experimental details

Gabapentin and solvent materials were supplied from Alfa Aesar chemical companies with no further purification. The FTRaman spectrum of the compound was also recorded using Bruker RFS 27 spectrometer with 1064 nm lines of Nd: YAG laser source as excitation wavelength was obtained in the region from 4000 to 50 cm^-1. The Fourier transform infrared spectra are collected using Thermo Nicolet NEXUS 870 FT-IR spectrometer in the range of 400 cm^-1 to 4000 cm^-1 making KBr pellets of title the compound. The ¹H and ¹³C NMR spectra were measured on Bruker FT-400 MHz spectrometer at room temperature and with CDCl₃ as a solvent.

Computational method

We studied the structural, electronic properties and the spectroscopic properties of GPN₁-GPN₄ was all the calculations presented here have been performed at the Becke‟s three-parameter hybrid exchange functional combining with Lee-Yang- Parr gradient-corrected correlation functional DFT/B3LYP/6-311G⁺⁺(d,p) basis set using quantum chemical calculations implemented with the help of Gaussian 09 Wprogram [9] package. The Gauss-View 5.0 can graphically display a variety of Gaussian results such as ground state optimized structure, molecular orbitals, NMR shielding density, MEP surface map, and animation of the normal modes corresponding to vibrational frequencies. The harmonic vibrational wavenumbers and all vibrational assignments were performed by the potential energy distribution calculated by using the VEDA 4 program [10]. The TD-DFT calculations of the title compounds were carried out using the PCM model with the same basis set considered for ground state optimizations. Electrostatic potential surface maps of the molecules have also been presented to view most negative electrostatic potential, most positive electrostatic potential, and zero potential regions. ₁H and ₁₃C NMR isotropic chemical shifts were calculated via the GIAO approach by applying DFT/B3LYP method with of 6-311G⁺⁺ (d,p) [11, 12] basis set using in DMSO as a solvent were analyzed. The important chemical properties such as chemical hardness, softness, electron affinity electrophilicity index, ionization potential, and electronegativity. Molecular docking analysis was performed using AUTODOCK 4.2 [13] and PyMOL molecular graphics system to predict the binding pose, distance from the best mode (Å) of the title complexes.

Result and Discussion

Molecular geometry

The ground state optimized structural parameters or certain coordinates such as bond distances, bond angles, and dihedral angles of 1-4 complexes calculated by using DFT/B3LYP/6-311G⁺⁺(d,p) level of theory and accordance with atom numbering scheme is represented in (FIG. 2).

In this present work, geometry optimization parameters of molecules have been employed without symmetry constrain. The ground state optimized structure of GPN₁-GPN₄ belongs to the C₁ symmetry point group and has Global minimum energy of about E=558.0371,-597.2752,-538.2119, and -942.4537 Hartrees respectively. The calculated molecular parameter characterizes a good estimate and they are the bases of calculating other parameters including chemical structure, chemical kinetics, thermodynamic and spectroscopic properties. The optimized result of our calculations very high bond distances strong bond which is found to be C₂-O₁, C₄-C₂ bond distance of the ring varies in the narrow range 1.2359-1.5631 and smaller value of bond distances weak bond C₄-C₂, C₆-N₇ is 1.1079-1.1968Å. These bond angles mainly depend on the state of electronegativity (donate electrons) of the central atom. If the electronegativity of the central atom decreases, the bond angle also decreases. The bond distances, bond angles, and dihedral angles that show that the molecule is nearly perfectly planar are presented in Table 1.

Vibrational spectral analysis

The fundamental vibrational wavenumbers of the most stable GPN₂ compound work to 32 atoms and 90 and belongs to the Cs symmetry point group for theoretical calculations. The comparative experimental and theoretical FT-IR and FT-Raman spectra of the title compound are shown in FIG. 3 and FIG. 4.

The FT-IR and Raman vibrational pattern includes many stretching, bending, and torsional vibrations that create many signals. The calculated vibration wave numbers were usually higher than the observed vibrational modes. This is expected because the theoretical calculations of the isolated molecule considered in the gas phase while the experimental measurements were carried out in the solid phase. On the other hand, the selected theoretical wavenumbers are harmonic while the experimental ones are anharmonic frequencies are listed in Table 2.

Table 2: The experimental and computed vibrational frequencies of the GPN₂ compound.

C-H vibration modes

The C-H stretching is considered characteristic wavenumbers. In such differences are usually observed for C-H vibrations. The aromatic ring shows the occurrence of C-H stretching vibration modes in the range 3100 cm^-1-3000 cm^-1 region [14,15], which is the normal bands in the region for ready identification of C-H symmetric and asymmetric stretching vibrations. The title compounds observed C-H stretching vibration modes are assigned 3175, 3051, 2967, 2941cm^-1 in FT-IR and 3170, 3063, 2958, 2933 cm^-1 in FT-Raman spectra, and the calculated scaled DFT/6311⁺⁺G (d,p) values are 3188, 3083, 3081, 3061, 3058 cm^-1 have been bands assigned to C-H stretching vibrations respectively.

Aromatic ring vibration

Benzene or aromatic ring is commonly used in organic chemistry. Although we write benzene is a special six-carbon ring (hexagon) that includes three double bonds, each of the carbon represents the delocalized electrons of the molecule. The fundamental vibrational oscillations of an aromatic ring are not isolated but involve the entire molecule. Fortunately, the force constants do vary with the molecular structure in a fairly expected approach and therefore it is possible to different types of C-C bonds. Generally, the aromatic ring C=C and C-C stretching vibrations, known as semicircle stretching modes are normally found between 1625 cm^-1-1400 cm^-1. The aromatic structure shows the presence of C-C stretching vibrations assigned at 1530 cm^-1, 1510 cm^-1, and 3092 cm^-1 in FT-IR spectra and 1518 cm^-1 in FT-Raman spectra, and the corresponding values are 1521 cm^-1, 1512 cm^-1, 1508 cm^-1, 1484 cm^-1.

CH₃ vibration modes

The CH₃ stretching vibrations modes for the assignments of CH₃group frequencies, fundamentally nine normal vibration modes can be associated to each Methyl group [16] namely, CH₃ ss-symmetric stretch; CH₃ ips-in-plane stretch; CH₃ opsout- of-plane stretch; CH₃ ipb-in-plane bending ; CH₃ opb-out-of-plane bending vibrations; CH₃ in-plane rocking, CH₃ oprout- of-plane rocking; CH₃ipb-in-plane bending; tCH₃-twisting modes; CH₃sb-symmetric bending and the aromatic ring outof- plane bending modes of methyl group vibrations would be expected to be depolarized. In CH₃groups are normally referred to as electron-donating substituents in the molecular system. The in-plane stretch is usually at higher frequencies than the symmetric stretch. The methyl C-H vibrations appear at lower frequencies than aromatic C-H stretching vibrations. The calculated wavenumber of in-of-plane bending and out-of-plane bending modes of CH₃ values are 1495, 1474, 1462 cm^{- 1}. The observed CH₃ opb and ipb were assigned 1489, 1466, 1460 cm^-1 in FT-IR and 1470 cm^-1 FT-Raman spectra. The CH₃ group vibrations computed DFT/6311⁺⁺ G (d,p) methods also show good agreement with the experimental data. The twisting vibration frequencies are assigned within the characteristic range and reported. The methyl group out-of-plane bending vibrations are also assigned and identified.

NH vibration modes

The NH group gives rise to five or six fundamental vibration modes including asymmetric stretching (νas), symmetric stretching (νs), the in-plane deformations (scissoring, δsis and rocking, δroc) and the out-of-plane deformation (wagging, γwag and twisting, γtwi). The molecule under study possesses one N-H out-of-plane bending, one symmetric N-H stretching, and hence expected one N-H asymmetric stretching vibrations. The N-H group stretching wavenumbers are usually observed in the region 3500-3300 cm^-1 [17]. The asymmetric and symmetric stretching modes of the NH group are observed at 3634 cm^-1 in the FT-IR and N-H stretching vibrations were identified in FT-Raman at 3612, 3590 cm^-1 respectively. The theoretical values for these stretching vibrations of GPN₂ were calculated at 3799, 3684 cm^-1 with an average PED contribution of 100%. However, good agreement between calculated and experimental spectra is observed for frequencies.

Frontier molecular orbitals analysis

The HOMO and LUMO levels are very common quantum chemical parameters that play a role in determining the way the molecule interacts with another molecule. The difference between HOMO-LUMO energy gaps is important parameters such as chemical stability, reactivity, and electronic charge transfer properties of the molecules. It determines the energy required for the charge transition from the main stable in the ground state to an excited state in a molecule. FIG. 5, shows the behaviors of the HOMO and LUMO molecular orbital diagram and respective calculated energy values of the frontier orbital energies of the studied compounds are summarized in Table 3.

It was shown that for electron-withdrawing different functional substituted gabapentin GPN₁, GPN₂, GPN₃, and GPN₄ the HOMO level electron cloud is predominantly localized on the ring which has a lone pair of the benzene ring and OH, OCH₃, NH₂, Cl atoms bonded to ring with the highest density on carbons atoms. In HOMO orbital characterized by π-bonding over the whole molecule except C-C, C-C, C-C, C-N, C-O, C-H, H-O, and LUMO revealed anti-bonding orbital with no electron projection at these regions from C-C, C-C, C-C, C-N, C-O, C-H, H-O. As a result, it is expected that the energy difference between the HOMO and LUMO (HOMO-LUMO energy gap) displays the chemical activity of the molecule and the calculated energy gap of the title compounds is 4.26 and 4.81 eV at the DFT/B3LYP levels, respectively. Likewise, these frontier molecular orbital formations of electron density localizations on HOMOs and LUMOs are supported by the nature of the transition is π→π*. This suggests the importance of considering these orbitals, especially GPN₂ and their corresponding eigen values upon studying their charge transfer properties. Also, the HOMO and LUMO energy values are used to compute global chemicals reactivity descriptors such as ionization potential (I), the electron affinity (A), Global electrophilicity (ω), the absolute electronegativity (χ), the chemical hardness (η) and softness (S) have been calculated at the same level theoretically by using HOMO and LUMO (ΔE) energy difference and are presented in Table 3.

Table 3: Molecular Properties end energy gap (eV) between molecular orbitals involved in electronic transitions of GPN₁-GPN₄ compounds.

NLO analysis

The calculated NLO properties such as molecular dipole moment, linear polarizability, and first-order hyperpolarizability of a molecular system, the quantum chemical calculations were performed by using DFT/B3LYP method with 6-311G⁺⁺ (d,p) level using Gaussian 09W program package. The molecules with large values of electronic dipole moment, polarizability, and hyperpolarizability are a measure of non-linear optical properties of the molecular system, which is linked with the electron cloud movement through π conjugated build of an electron. The theoretically calculated total molecular dipole moments (μ) of 1.2072 for GPN1, 4.7808 for GPN2, 2.8620 for GPN3, 1.6353 for GPN4 Debye, polarizability is equal to 1.073x10-23, 1.190x10-23, 1.086x10-23, 1.232x10-23 esu and first hyperpolarizability (β) of title compounds is 4.707x10- 31, 5.758x10-31, 7.246x10-31, 2.695x10-31 esu, respectively as shown in Table 4, and thus results show that the title compounds is the best material for efficient nonlinear optical application.

Table 4: Polarizability ^atot(x10-24esu) and Hyperpolarizability ß (x10-31esu) of GPN₁-GPN₄ compounds calculated at the DFT/6-311⁺⁺G (d, p) level.

Molecular electrostatic potential analysis

The Molecular electrostatic potential maps are a helpful tool in understanding the physicochemical property relationship of a molecule since it shows the molecular properties including molecular shape, size, and color grading [18]. It is a calculation technique frequently used to analyzing the possible hydrogen binding site of the molecule by calculating the charge transfer interaction of a molecule. The most electronegative regions of MEP are related to electrophilic reactivity and the positive ones to nucleophilic reactivity for electron-donating and electron-accepting reaction at this visual presentation by using Gauss view 5.0 software MEP surface and molecular contour map is drawn for the title molecules as shown in FIG. 6 and FIG. 7.

The fitted electrostatic point charges alongside the electric potential V(r) calculated at DFT/B3LYP/6-311G⁺⁺ (d, p) are given in Table 5.

Table 5: ESP charges (e) and Electrostatic Potential V(r) values of GPN₁- GPN₄ compounds.

As seen from Fig, the Intermediate potentials are assigned colors according to the following color regions: blue >green>red >yellow>orange. Different colors on the MEP surface map show electrostatic potential values of title compounds. The potential increases from red to blue. The regions with a negative electrostatic potential were found around the O atom of acetic acid whereas the regions with a positive potential were found around the H atoms.

Nuclear magnetic resonance analysis

In this study predicted chemical shifts of pharmaceuticals, the Gauge-Independent Atomic Orbital (GIAO) method [19] methods with optimized geometry using basis sets 6-311G⁺⁺(d,p) with B3LYP methods, have been interested in scientists, the compute the ₁H and 13_C chemical shifts are calculated and compared with experimental. In Table 6, the predicted ₁H and ₁₃C NMR chemical shifts are summarized by using the DFT/B3LYP\6-31G (d) methods in DMSO as a solvent.

Table 6: Experimental and calculated ₁₃C chemical shift [d (ppm)] of GPN₁- GPN₄ compounds.

The Root-Mean-Square Deviations (RMSDs) between the experimental values with the corresponding computational values were performed by using DFT/B3LYP/6-311G⁺⁺ (d,p) level theory. The experimental and theoretical NMR obtained from DFT has been shown in FIG. 8.

In our present investigation, chemical shift values of carbon atoms were determined in the range of 23.371016-220.8632 ppm, which agrees with literature values. The high chemical shift value of carbon atoms are compared to other aromatic carbons gives signals in overlapped areas of the spectrum with chemical shift values ranging from 25 ppm to 100 ppm. The oxygen atom in the methanol group results in the de-shielding of aromatic carbon atoms shows a downfield chemical shift of 181.911148 ppm (GPN₁), 196.446335 ppm (GPN₂), 213.636029 ppm (GPN₃), and 220.8632 ppm (GPN₄). Which are theoretically observed at 171.0 ppm, 173.1 ppm, 179.3 ppm, 178.7ppm, and show that the carbon atoms of methanol, methoxymethane, amino, and chloride groups in bioactivity. The scaled values are in good agreement with the experimental data. The ₁H NMR chemical shifts show a singlet different function groups observed peaks upfield at 2.044854 ppm for OCH₃, 2.683420 ppm for OH group, 2.020196 ppm for OCH₃, and at 1.969190 ppm for Cl group and theoretically computed chemical shifts spectral assignments are listed in Table 7, The proton numbered H₂₁, H₂₂ hydrogen atoms directly attached to the electronegative nitrogen shifts are shown in FIG. 9, respectively.

Table 7: Experimental and calculated ₁H chemical shift [d (ppm)] of GPN₁- GPN₄ compounds.

Mulliken charge analysis

Mulliken charges and natural atomic charges play an important role in the application of quantum chemical calculation such as electronic structure, dipole moment, molecular polarizability, and a lot of properties of molecular systems [20]. The electronic charge distribution over the atoms suggests the structure of electron-donor and electron-acceptor pairs involving the electronegativity equalization and charge transfer in the molecule. The Mulliken atomic charges and bar diagram representing the charge distribution is displayed in FIG. 10 and FIG. 11.

The Mulliken atomic charges of the title molecule have been calculated by DFT/B3LYP method using 6-311G⁺⁺ (d,p) levels of theory are collected in Table 8, from which it could be seen that the carbon atoms showed the highest positive charge is noted in C₁₃, C₂ and the lowest negative value is obtained in C₆, C₁₀, C₆, C₇, C₉ atoms. Among all the hydrogen atoms show net positive charge, respectively.

Table 8: Values of the Milliken atomic charges (ZA).

Potential energy curves (PECs)

The conformational analysis [21, 22] of the gabapentin compounds is carried out through the potential energy surface scan (PES) in the present study by using DFT method 6-311G⁺⁺ (d,p) level of theory. The conformational stability of GPN₁, GPN₂, GPN₃ and GPN₄ in the S₀ and S₁ states are calculated by potential surface scanning the amide group around the H₁₈- N₇-H₁₉ bond is found to be 1.02 Å to 2.2 Å. The potential energy surface scan of the different conformers as a function of the angle of rotation is shown in FIG. 12.

It can be seen that there are no proton transfer reaction stationary points for the amide group form of Gabapentin derivatives in the S₀ state. The PES scan of the GPN₁-GPN₄ is 1.21, 1.24, 1.02, and 1.25 kcal/mol, which indicates that the potential barriers are small enough for proton transfer in the S₁ state. Moreover, the S1 state of reverse proton transfer barriers is 1.51, 1.52, 1.46, and 1.48 kcal/mol, respectively.

Molecular docking

It is generally believed that the small molecule drug contacts with active amino acid residues of the target enzyme to inhibit the activity of an enzyme. The PDB structures (www.rcsb.org) [3DVE] were downloaded and energy minimization of the protein structure [23]. Molecular docking analysis can help us to identify the binding types and the most important residues at the basis of the Ca²⁺/CAM-CaV2.2 IQ activities, which paves new ways to design and synthesis a series of highly selective and potent Ca²⁺/CAM-CaV2.2 IQ domain inhibitors. The four compounds with high, medium, and low activity can form hydrogen bonds with the protein. In Amino acids (GPN₁) Ile 85 forms a-alkyl interaction with a benzene ring and MET 145 (H-N-H), MET 76 (O=O-H) conventional hydrogen bonds with the amino radical and carboxylic acid group. Ile 85 forms alkyl interaction with a benzene ring and MET 145 (H-N), THR 146 (N-H) forms a-alkyl interaction with the amino radical group. In PHE 12 donor hydrogen bond with benzene ring interaction and TYR 1858 (N-H) forms pi-alkyl interaction with amine ring. In the compound, GPN₄ forms H-bonds with Ile 85 a-alkyl interaction with a benzene ring, and MET 145 (N-H), MET 76 (O=N-H) form conventional hydrogen bonds with the amine group. These are the non-covalent interaction of the ligands GPN₁- GPN₄ with the substrate and are detailed in FIG. 13 and FIG. 14.

The docked ligands form stable complexes with Ca²⁺/CAM-CaV2.2 IQ domain inhibitor which gives a good binding affinity value of -4.8kcal/mol for the GPN₂ compound. These binding affinity values of different poses of ligands with the same protein are tabulated in Table 9, These preliminary results suggest that the GPN₂ compound might exhibit inhibitory activity against Ca²⁺/CAM-CaV2.2 IQ domain inhibitor.

Table 9: The Docking, Bond distance, score, and H-bond interaction of best-fit ligands.

Conclusions

In the present study, the molecular geometry of the title molecules suggests that the different anchoring group‟s moiety plays an important role in the intermolecular charge transfer interaction. The spectroscopic techniques such as FT-IR, FT-Raman for GPN₂ have been carried out by employing DFT/B3LYP method with 6-311G⁺⁺ (d, p) level supported by PED contributions. The calculated normal modes of vibrations are in good agreement with the experimental results. The molecular electrostatic potential map shows that the regions with negative electrostatic potential sites are on electronegative O atoms and positive potential sites are around the hydrogen and carbon atoms. HOMO-LUMO energy gap and chemical stability descriptors of the title compounds were calculated. The result of the comparison between the experimental and calculated values of ₁H and ₁₃C NMR chemical shifts was calculated for title compounds. To further determine the scanning S₀ and S₁ states are calculated by potential surface scanning the amide group around the H₁₈-N₇-H₁₉ bond. Molecular docking studies show that the GPN₂ compound might exhibit inhibitory activity against Ca²⁺/CAM-CaV2.2 IQ domain inhibitor and strong affinity, distance from best mode (Å), suggesting that the compound may be candidates as anticancer drugs.

Acknowledgment

We are thankful to the sophisticated analytical instrumentation facility (SAIF) St. Joseph„s college, Thiruchirappalli, India for providing generous support in taking spectral measurements.

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