4.1 Experimental details
Cipla Laboratories has kindly provided the drugs Imatinib and Thalidomide. “They are used to make spectral measurements. The Perkin Elmer spectra Two FTIR-ATR spectrophotometer is used to record the spectra of the Imatinib and Thalidomide in the range 4000-450 cm-1 with a resolution of less than 1 cm-1”[17]. Tables 1 and 2 detail the frequency profiles from the experiments.
Tables 1 and 2 present a condensed overview of the observed frequencies. Meanwhile, Figures 6a, 6b and 8a, 8b exhibit the FT-IR spectra of Imatinib and Thalidomide. The “Perkin Elmer LAMBDA 35 UV/Vis DRS/DTS spectrophotometer was employed to record the UV-Vis spectra. The UV-Visible absorption spectra” were meticulously measured within an ethanol solution, encompassing wavelengths ranging from 190 to 1100 nm [18]. Fig.7 and Fig.9 depict the UV-Vis spectra of Imatinib and Thalidomide.
4.2 FT-IR Spectrum Analysis of Imatinib
Standard analyses of Imatinib's FT-IR spectra suggest that the anti-cancer drug has several functional groups, which can be categorized into distinct classifications. “The title drug's CH stretching groups” correlate to Imatinib's FT-IR frequencies 3340, 3321, and 3315 cm-1, which were shown to have a substantial region of absorption.[19]. The CH3ss (Symmetrical Stretchings) stretching mode was ascribed a wavenumber of 3303 cm-1. “The stretching groups of CHmeln can be recognized in the “FT-IR spectra” of the cancer drug as bands 2920, and 2851 cm-1 in the “Infrared Spectrum”. [20][21]. The C=O mode is designated as a frequency band of 1655 cm-1 in Imatinib's infrared spectrum [22].
The stretchings of βCH and βHCH with bands of 1558 cm-1 and 1535 cm-1, severally, as well as νC-C of Imatinib at 1440 cm-1 are assigned [23]. While studying “the infrared spectra of the” titular cancer agent, the modes of in-plane bending” CH3ib and CH3ir were allotted to 1491 cm-1, and 1481 cm-1 discovered in Imatinib's “FT-IR spectra” was imputed to βCH3ob and βCH3or, severally [24].
The 1466 and 1374 cm-1 wavenumbers in the molecule's infrared spectrum can be used to explain Imatinib's CH2 rocking modes. The bands at wavenumber 1424 and 1270 cm-1 in “the FT-IR spectrum” of cancer agents were CH2Twisting modes. At a wavenumber of 1416 cm-1 in "the infrared spectrum”, the βCH2, also known as CH2Scissoring, has been identified [25].
Imatinib's FT- IR Spectrum matches to the wavenumber area of 1388 cm-1 that was assigned to the βNCH2. In contrast, the stretching modes of C=N and C-N, which have wavenumbers of 1361 and 1316, 1308 and 1181 cm-1, severally, the βNCH has a wavenumber of 1338 cm-1. “The IR spectrum” of Imatinib the bands at 1143, 1130, 1037, 981, 945, 922, 916, 891, and 883 cm-1; these bands were linked to the anti-cancerous drug's νC-C, and νC-Cring[26].
The results show that “the ring trigonal deformation, ring symmetric deformation, ring asymmetric deformation, and ring torsion modes” correspond to wavenumbers 861, 781, 765, and 751 cm-1 shown on Imatinib's infrared spectra, respectively[24]. The frequency areas 851, 829, 816 and 791 cm-1 of the “FT-IR spectra, the ωCH has been assigned to the out-of-plane bending modes”(ω) of Imatinib. While the τ Ring Trigonal deformation was “ascribed to the frequency” of 804 cm-1, βCH2 wagging might be “allotted to the wavenumber” of 842 cm-1. Three ωCCs, “with frequencies” of 695, 646 and 597 cm-1, are assigned from the Imatinib IR spectrum [27]. “The FT-IR spectra” of Imatinib, which has a frequency of 712, 666, and 618 cm-1 attributed to ωCCN. From “the FT-IR spectra” of Imatinib, “the wavenumbers” 558 and 522 cm-1 are connected to τ Ring symd and τ Ring asymd that are present in the drug. The frequencies 712, and 618 cm-1 of Imatinib's infrared spectra were identified as ωCCN, and the torsion modes corresponded to the cancer drug's molecule, namely τNCNC, τCCCH, and τCCNC are assigned to the bands of 481, 471 and 458 cm-1 of Imatinib's infrared spectra [28].
4.3 Electron absorption spectra of Imatinib
A “Perkin Elmer LAMBDA 35 UV/Vis DRS spectrophotometer” with a range of scannings “190-1100 nm and bandwidth of 0.5 – 4 nm” has been utilized to record Imatinib's “UV-vis absorption spectra. As may be seen in Fig.5, Imatinib's UV-Vis spectrum was recorded”.
The peak absorbed by a substance corresponds to the electron shift over the HOMO and LUMO, from “the theory of molecular orbitals” [29]. In the realm of molecular orbital theory, the absorption characteristics of a molecule are explained by “the electron transitions between the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO). When the molecule absorbs light, electrons move from the HOMO to the LUMO, creating an excited state”. The energy necessary for this transition corresponds to specific wavelengths in “the absorption spectrum”. The “HOMO-LUMO” gap serves as a crucial indicator of a molecule's electronic structure[22]. A smaller gap signifies that less energy is required for electronic transitions, making the molecule more responsive to lower-energy radiation.
Furthermore, in conjugated molecules, the HOMO-LUMO gap illustrates the energy needed for “internal charge transfer between electron-donating and electron-accepting groups” within the molecule. This concept is fundamental in the development of organic materials for optoelectronic devices. Essentially, the movement of electrons between these orbitals underlies a molecule's electronic behaviour and holds substantial importance in various technological contexts [30]. The peaks absorption associated with the wavelength shown in Fig.5 is 210, 246, 279, 301, 337, 372, 397, 429 and 459 nm, and the energy interval corresponding to the shifts of electrons are 5.91, 5.05, 4.45, 4.13, 3.69, 3.34, 3.17, 2.90, and 2.71 eV. The variance in energy levels can impact a molecule's ability to bind with specific receptors or proteins, thereby affecting their functioning and contributing to its anticancer properties. Molecules with larger energy gaps tend to be less polarized and possess a higher hardness, indicating low chemical reactivity and enhanced stability.
4.4 FT-IR Spectrum Analysis of Thalidomide
Standard analyses of Thalidomide's FT-IR spectra suggest that the anti-cancer drug has several functional groups, which can be categorized into distinct classifications. “The title drug's CH stretching groups” correlate to Thalidomide's FT-IR frequencies 3341, 3332, 3329, 3317, 3310, 3285, 3278, 3266, 3252, 3229, 3208, 3193, 3097, 2914 and 2902 cm-1, which were shown to have a substantial region of absorption.[19]. The NH stretching mode was ascribed a wavenumber of 3393 cm-1. “The stretching groups of CHmeln can be recognized in the “FT-IR spectra” of the cancer drug as bands 3354, and 3346 cm-1 in the “Infrared Spectrum”. [20][21]. The C=O mode is designated as a frequency band of 1772, 1732, 1708 and 1695 cm-1 in Thalidomide's infrared spectrum [22].
The stretchings of βCH and βHCH with bands of 1434 cm-1 and 1410 cm-1, severally, as well as νC-C of Thalidomide at 1668, 1611 and 1471 cm-1 are assigned [23][24].
The 1296 and 1092 cm-1 wavenumbers in the molecule's infrared spectrum can be used to explain Thalidomide's CH2 rocking modes. The bands at wavenumber 1345 and 1198 cm-1 in “the FT-IR spectrum” of cancer agents were CH2Twisting modes. At a wavenumber of 1385 cm-1 in "the infrared spectrum”, the βCH2, also known as CH2Scissoring, has been identified [25].
Thalidomide's FT- IR Spectrum matches to the wavenumber area of 1388 cm-1 that was assigned to the βNCH2. In contrast, the stretching modes of C-N, have wavenumbers of 1361 and 1316, 1308 and 1181 cm-1, and the βNCH has a wavenumber of 1283 cm-1. “The IR spectrum” of Thalidomide the bands at 1327, 1258, 1208, and 1113 cm-1; these bands were linked to the anti-cancerous drug's νC-C, and νC-Cring[26].
The results show that “the ring trigonal deformation, ring symmetric deformation, ring asymmetric deformation, and ring torsion modes” correspond to wavenumbers 1176, 1019, 859, and 803 cm-1 shown on Thalidomide's infrared spectra, respectively[24]. The frequency areas 1032, 1001, 949 and 915 cm-1 of the “FT-IR spectra, the ωCH has been assigned to the out-of-plane bending modes”(ω) of Thalidomide. While the τ Ring Trigonal deformation was “ascribed to the frequencies” of 1141 and 990 cm-1, βCH2 wagging might be “allotted to the wavenumber” of 842 cm-1. Three ωCCs, “with frequencies” of 728 and 649 cm-1, are assigned from the Thalidomide IR spectrum [27]. “The FT-IR spectra” of Thalidomide, which has frequencies of 756, and 631 cm-1 attributed to ωCCN. From “the FT-IR spectra” of Thalidomide, “the wavenumbers” 699 and 566 cm-1 are connected to τ Ring symd and τ Ring asymd that are present in the drug[30]. While studying “the infrared spectra of the” titular cancer agent, the modes of out-of-plane bending” CCO were allotted to 606 and 552 cm-1 discovered in Thalidomide's “FT-IR spectra” was imputed to ωCCO. The frequencies 712, and 618 cm-1 of Thalidomide's infrared spectra were identified as βCCO and βOCO, severally. The torsion modes corresponded to the cancer drug's molecule, namely τCCCO and τCCCN are assigned to the bands of 532 and 469 cm-1 of Thalidomide's infrared spectra [28].
4.5 Electron absorption spectra of Thalidomide
A “Perkin Elmer LAMBDA 35 UV/Vis DRS spectrophotometer” with a range of scannings “190-1100 nm and bandwidth of 0.5 – 4 nm” has been utilized to record Thalidomide's “UV-vis absorption spectra. As may be seen in Fig.9, Thalidomide's UV-Vis spectrum was recorded”.
The peak absorbed by a substance corresponds to the electron shift over the HOMO and LUMO, from “the theory of molecular orbitals” [29]. In the realm of molecular orbital theory, the absorption characteristics of a molecule are explained by “the electron transitions between the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO). When the molecule absorbs light, electrons move from the HOMO to the LUMO, creating an excited state”. The energy necessary for this transition corresponds to specific wavelengths in “the absorption spectrum” [22]. The “HOMO-LUMO” gap serves as a crucial indicator of a molecule's electronic structure. A smaller gap signifies that less energy is required for electronic transitions, making the molecule more responsive to lower-energy radiation.
Furthermore, in conjugated molecules, the HOMO-LUMO gap illustrates the energy needed for “internal charge transfer between electron-donating and electron-accepting groups” within the molecule. This concept is fundamental in the development of organic materials for optoelectronic devices. Essentially, the movement of electrons between these orbitals underlies a molecule's electronic behaviour and holds substantial importance in various technological contexts [30]. The peaks absorption associated with the wavelength shown in Fig.9 is 210, 246, 281, 301, 336, and 373 nm, and the energy intervals corresponding to the shifts of electrons are 5.91, 5.05, 4.42, 4.13, 3.69, 3.34 eV. The variance in energy levels can impact a molecule's ability to bind with specific receptors or proteins, thereby affecting their functioning and contributing to its anticancer properties. Molecules with larger energy gaps tend to be less polarized and possess a higher hardness, indicating low chemical reactivity and enhanced stability.
4.6 Molecular Docking Analysis of Imatinib
In the field of medicinal chemistry, “computational techniques like molecular docking are employed to foresee how drugs may attach to receptor-binding sites and interact with one another”. These insights have paved the way for an exploration of the chemical components governing “ligand-protein interactions” in crucial therapeutic targets and the development of structure-based virtual screening for potential pharmaceuticals. Precisely predicting “the binding affinities and preferences of two molecules” is a particularly challenging aspect of the docking process. To obtain the most optimal docking solutions, docking algorithms evaluate binding affinities across various positions within receptor binding sites and ligand orientations. This evaluation involves comparing the ligand to its respective macromolecular partner (in this case, proteins) to determine the most favourable binding configuration. The final docking solution is then selected from a range of potential positions. Therefore, it becomes imperative to generate a substantial number of unique poses for the ligand within the protein's binding site, encompassing a variety of structural patterns and orientations. The present investigation involved the utilization of molecular docking with the Tyrosine Kinase Sh2 Domain and “Tyrosine-Protein Kinase ABL1” proteins [31][32]. The structure database of the 1AB2 and 7N9G (target proteins) was “acquired from the protein data bank” (RCSB) [33]. The quality of the proteins is determined by comparing them to hydrogen bonds and Ramachandran plots, as illustrated in Fig.10a, 10b and Fig.13a, 13b for the two proteins, severally. These plots demonstrate that all residues are accessible within the authorized range. Imatinib molecular docking investigations were carried out with the 1AB2 and 7N9G target proteins using the program “AutoDock 1.5.6 and BIOVIA from Discovery Studios” [34][35][36][37]. Ligand-target interaction was found in two separate postures for the two proteins, with affinities of binding -8.2 and -8.2 kcal-mole-1 and binding -10.1 and -11 kcal-mole-1 for the two proteins, respectively, as observed in Fig.11a), 11b), 11c), Fig. 12a), 12b), 12c) and Fig.14a), 14b), 14c) and Fig. 15a), 15b), 15c) of the two target proteins. Tables 3, 4, 5 and 6 summarize “the root mean square deviation (RMSD)” and distinct types of binds between Proteins and Ligands i.e specific atoms, and group epitopes, as well as the precise itinerary and place of docking interactions of the Ligand and Proteins distinctly. The “low binding affinity of the molecule” signifies that it is an “effective anti-hypercoagulant and covalently binds” to Tyrosine Kinase Sh2 Domain and Tyrosine-Protein Kinase ABL1 proteins over an extended time [22]. In the docking studies of the Imatinib with Tyrosine Kinase Sh2 Domain (PDB ID: 1AB2), the observation noted that hydrogen atoms established the highest number of interactions with the target. The atom H46 makes a hydrogen (conventional) bond with 1AB2 (C: SER368:OG). The atom N22 makes a hydrogen (conventional) bond with 1AB2 (B: ASP295:OD2) and the atom H42 forms two hydrogen (conventional) bonds with 1AB2 (C: GLU513:OE1) and 1AB2 (C: GLU513:OE2) of the target Tyrosine Kinase Sh2 Domain (PDB ID: 1AB2). These hydrogen bonds are crucial for the stabilization of the ligand-receptor complex, involving interactions between hydrogen atoms and electronegative atoms of the receptor. The (C10-C15 ring) forms two electrostatic (Pi-Anion) bonds these involve interactions between the electron-rich pi-system of the ligand's aromatic rings and anions on the receptor. with the 1AB2(B: ASP295:OD1) and 1AB2(C:GLU513:OE2), the atom (C2-C7 ring) makes one hydrophobic (Pi-Sigma) bond Pi-sigma interactions involve the interaction between the pi-electron cloud of the ligand and the sigma electron cloud of the receptor, contributing to hydrophobic stabilization with 1AB2(B:LEU303:CD1). The (C17-C22 ring) makes one hydrophobic (Pi-Pi Stacked) with 1AB2(C:HIS314) this interaction involves the stacking of aromatic rings, contributing to the stability of the ligand-receptor complex and the (C17-C22 ring) forms a hydrophobic (Pi-Alkyl) bond pi-alkyl interactions involve the interaction between the pi-electron cloud of the ligand and alkyl groups on the receptor, promoting complex stability with 1AB2(C:PRO315) of the target Tyrosine Kinase Sh2 Domain (PDB ID: 1AB2) in pose–1. The atom H46 makes a hydrogen (conventional) bond with 1AB2 (C:SER368:OG) and the H42 atom makes a hydrogen (conventional) bond with 1AB2 (C:GLU513:OE2) of the target Tyrosine Kinase Sh2 Domain (PDB ID: 1AB2). The C35 atom made a carbon-hydrogen bond with 1AB2 (B:THR325:OG1) and the C37 atom made a carbon-hydrogen bond with 1AB2 (B:THR325:OG1) of the target Tyrosine Kinase Sh2 Domain (PDB ID: 1AB2). The (C10-C15 ring) makes a Pi-Anion (electrostatic) bond with the 1AB2 (B:ASP295:OD1) and the (C12-C17 ring) makes a Pi-Anion (electrostatic) bond with the 1AB2 (B:ASP295:OD2). The (C17-C22 ring) makes one hydrophobic (Pi-Pi Stacked) with 1AB2(C:HIS314) and the (C10-C15 ring) forms a hydrophobic (Pi-Pi T-shaped) bond this T-shaped pi-pi interactions are a specific type of aromatic interaction that enhances the stability of the ligand-receptor complex with 1AB2 (C:HIS509) of the target Tyrosine Kinase Sh2 Domain (PDB ID: 1AB2) in pose-2. The interactions between these components play a “pivotal role in determining the binding affinity and specificity” of Imatinib to the Tyrosine Kinase Sh2 Domain. Understanding these interactions at the molecular level provides valuable insights for drug design and rational modification of ligands to enhance their effectiveness in targeting specific proteins involved in diseases These molecular insights help in the development of novel drugs with enhanced specificity, potency, and reduced side effects, ultimately advancing the field of pharmacology and drug discovery. In the docking studies of the Imatinib with the target (PDB ID: 7N9G), it was identified that the nitrogen N28 atom has made a hydrogen (conventional) bond with 7N9G (B:MET337:HN). The atom H42 makes a “hydrogen (conventional) bond" with 7N9G (B:ASP344:OD2), the atom C32 makes a hydrogen (conventional) bond with 7N9G (A:TYR276:OH) and the atom C23 makes a hydrogen (conventional) bond with 7N9G (B: MET337: O) of the target (PDB ID: 7N9G). These hydrogen bonds are crucial for the stabilization of the ligand-receptor complex, involving interactions between hydrogen atoms and electronegative atoms of the receptor. The (C10-C15 ring) forms an electrostatic (Pi-Anion) bond with the 7N9G (B:ASP344:OD2), these involve interactions between the electron-rich pi-system of the ligand's aromatic rings and anions on the receptor. The (C11-N22 ring) makes one hydrophobic (Pi-Sigma) bond with 7N9G (B:LEU267:CB), Pi-sigma interactions involve the interaction between the pi-electron cloud of the ligand and the sigma electron cloud of the receptor, contributing to hydrophobic stabilization. The (C2-C7 ring) makes one hydrophobic forms a hydrophobic (Pi-Pi T-shaped) bond with 7N9G (A:TYR276) this T-shaped pi-pi interaction is a specific type of aromatic interaction that enhances the stability of the ligand-receptor complex. (Pi-Pi Stacked) with 1AB2(C:HIS314) this interaction involves the stacking of aromatic rings, contributing to the stability of the ligand-receptor complex. The (C17-C22 ring) forms two hydrophobic (Pi-Alkyl) bonds with 7N9G (B:LEU267) and 7N9G (B:VAL275) of the target (PDB ID: 7N9G) in pose-1, pi-alkyl interactions involve the interaction between the pi-electron cloud of the ligand and alkyl groups on the receptor, promoting complex stability. The atom N28 formed a hydrogen (conventional) bond with 7N9G (B:MET337:HN) and the atom H42 formed a hydrogen (conventional) bond with 7N9G (B:ASP344:OD2) of the target (PDB ID:7N9G), these bonds play a significant role in maintaining the specific shape and structure of biological molecules. In ligand-protein interactions, they contribute to the precise binding of ligands to their target protein, ensuring the formation of stable complexes necessary for biological functions. The atom C23 makes a carbon-hydrogen bond with 7N9G (B: MET337: O) of the target (PDB ID:7N9G), the carbon-hydrogen bond is significant in hydrophobic interactions, where nonpolar ligand or protein groups avoid water molecules by associating with each other. This interaction is vital in stabilizing the hydrophobic core of proteins and the nonpolar regions of small molecules. The (C2-C7 ring) forms an Electrostatic (Pi-Cation) bond with 7N9G (A:LYS266:NZ), Pi-Cation interaction is crucial in molecular recognition processes. In ligand-protein interactions, it contributes to the stabilization of ligands binding to aromatic residues in the protein, enhancing the affinity and specificity of the complex. The (C10-C15 ring) forms an Electrostatic (Pi-Anion) bond with 7N9G (B:ASP344:OD2) of the target (PDB ID:7N9G), Pi-Anion interaction is essential for recognizing and binding ligands containing negatively charged groups. They provide additional stability to complexes, especially when the ligand or protein contains aromatic systems and charged moieties. The (C11-N22 ring) forms a hydrophobic (Pi-Sigma) bond with the 7N9G (B: LEU267:CB), Pi-Sigma interactions drive the association of nonpolar groups, such as aromatic rings, contributing to the stability of protein-ligand complexes. They are vital for burying hydrophobic portions of the ligand and protein away from the surrounding aqueous environment. The (C23-C28 ring) formed three Hydrophobic (Alkyl) bonds with 7N9G (B:LEU267), 7N9G (B:VAL275) and 7N9G (B:ALA288) of the target (PDB ID:7N9G) in pose-2, hydrophobic (Alkyl) interactions are essential for maintaining the structural integrity of proteins. In ligand binding, they help in the proper orientation and stabilization of Imatinib, especially when the ligand has hydrophobic moieties that can interact with nonpolar regions of the target (PDB ID:7N9G).
These bonds are tabulated in Tables 2, 3, 4 and 5, respectively. The hydrogen bonding interactions found with active receptors are documented in Tables 2, 3, 4 and 5. After binding to Tyrosine Kinase Sh2 Domain and Tyrosine-Protein Kinase ABL1 proteins, ABL activation is strongly related to cancer cell survival and proliferation and is overexpressed in a variety of tumours. By attaching to the ATP pocket in the BCR-ABL protein's active site, imatinib prevents the target protein from being phosphorylated downstream. Effective catalytic activity in ABL was revealed to depend on this SH2 domain binding to the N-lobe. The Imatinib docking study supports establishing the precise region of bonding interactions with the Tyrosine Kinase Sh2 Domain and Tyrosine-Protein Kinase ABL1 proteins as well as the new mode of action of the Imatinib with cancerous cells. Through the careful alteration of the regulatory and reciprocating residues of the designated cancer agent, these results will aid in the eradication of undesirable effects, the design of quicker modes of action, and the production of more effective anti-cancer treatments.
4.7 Functional Group Analysis of Imatinib
4.7.1 C=N group
Imatinib's structure and mode of action are significantly influenced by the functional group C=N. The drug's structure includes the C=N functional group, which enables it to bind selectively with the target enzyme, in this case, a mutant version of “the Abl tyrosine kinase enzyme” in the case of imatinib. The C=N group interacts with amino acid residues in the enzyme's active site through hydrogen bonding and "other interactions," which reduces the enzyme's activity.
The C=N group makes it easier for imatinib to attach to the target enzyme specifically. Because it lessens the possibility of unwanted interactions with other proteins or enzymes in the body, this specificity is essential in the treatment of cancer. Imatinib efficiently slows down the advancement and division of cancerous cells by reducing the action of the mutant tyrosine kinase enzyme linked to CML and GISTs, resulting in disease remission and better patient outcomes. Imatinib's success in targeting cancer cells with the C=N functional group has established the trajectory for the advancement of other targeted therapies.
The N22 atom makes a hydrogen (conventional) bond with 1AB2 (B:ASP295:OD2) of Tyrosine Kinase Sh2 Domain (PDB ID: 1AB2) and Nitrogen atom N28 makes a hydrogen (conventional) bond with 7N9G (B:MET337:HN) of Tyrosine-Protein Kinase ABL1 (PDB ID: 7N9G). The atom C32 makes a hydrogen (conventional) bond with 7N9G (A:TYR276:OH) and atom C23 makes a hydrogen (conventional) bond with 7N9G (B:MET337:O). It has served as a model for designing drugs that specifically target the molecular drivers of various diseases, leading to more effective and less toxic treatments. The C=N functional group in Imatinib is a key structural element that contributes to the drug's specificity and effectiveness in targeting cancer cells by inhibiting the activity of specific tyrosine kinase enzymes. Its significance lies in its role in the success of Imatinib as a targeted therapy for certain types of cancer and its impact on drug development strategies.
4.7.2 N-H group
Imatinib, a tyrosine kinase inhibitor used to treat many leukaemias, contains an N-H functional group that is important for the drug's mode of action and selectivity. Why is the N-H functional group in Imatinib important? Imatinib's N-H group can generate hydrogen bonds with certain amino acid residues in target kinase enzymes including Abl and c-Kit. The atom H46 C23 makes a hydrogen (conventional) bond with 1AB2 (C: SER368:OG), and atom H42 C23 makes two hydrogen (conventional) bonds with 1AB2 (C:GLU513:OE1) and (C:GLU513:OE2) of the target Tyrosine Kinase Sh2 Domain (PDB ID: 1AB2). The atom H42 makes a hydrogen (conventional) bond with 7N9G (B:ASP344:OD2) of “the target Tyrosine-Protein Kinase ABL1” (PDB ID: 7N9G).
By increasing the drug's propensity for attaching to its target, this interaction stimulates a potent and focused interaction. The N-H functional group, like the C=N functional group, adds to the drug's enzyme selectivity. Imatinib makes sure that it largely inhibits the activity of the mutant kinase enzymes linked to cancer while protecting other enzymes in the body by establishing hydrogen bonds with certain amino acid residues in the enzyme's active region.
Imatinib's therapeutic impact depends on its capacity to suppress the activity of tyrosine kinase enzymes, particularly those with mutations that promote the proliferation of cancer cells. The N-H group takes part in the molecular interactions that result in kinase inhibition, which inhibits the growth of cancer cells and encourages tumour regression.
The N-H functional group's specificity helps to limit off-target effects, which lowers the risk of negative responses or medication toxicity. The development of imatinib as a targeted therapy for gastrointestinal stromal tumours (GISTs) and chronic myeloid leukaemia (CML) has transformed cancer care. It has proven that it is possible to create medications that directly target the molecular causes of illnesses, resulting in more efficient and safe therapies.
Imatinib's N-H functional group, which forms hydrogen bonds with important amino acid residues in target kinase enzymes, is essential to the drug's mode of action and selectivity. This interaction makes the medicine more effective at binding to mutant kinases and inhibiting their activity, giving it a very effective and tailored treatment for a number of malignancies.
4.7.3 Benzene ring
Imatinib has a benzene ring, which is important for the drug's structure, function, and therapeutic efficacy for a number of reasons. The drug's structure, namely the benzene ring, has a role in how well it interacts with particular target proteins, notably tyrosine kinase enzymes. Imatinib is made to stop the activity of mutant versions of the c-Kit receptor tyrosine kinase and Abl kinase, both of which are important in the development and proliferation of cancer cells. The benzene ring plays a role in these proteins' molecular recognition and binding.
It is well known that benzene rings are hydrophobic. Imatinib's hydrophobic interactions with the benzene ring are essential for securing the medication inside the hydrophobic pockets of the target kinase enzymes. The (C10-C15 ring) forms two electrostatic (Pi-Anion) bonds with 1AB2 (B:ASP295:OD1) and (C:GLU513:OE2). The (C10-C15 ring) forms one hydrophobic (Pi-Sigma) bond with 1AB2 (B:LEU303:CD1), the (C17-C22 ring) makes one (hydrophobic) Stacked Pi-Pi bond with 1AB2 (C:HIS314) and the (C17-C22 ring) makes a Pi-Alkyl (hydrophobic) bond with 1AB2 (C:PRO315) of the target Tyrosine Kinase Sh2 Domain (PDB ID: 1AB2). The (C10-C15 ring) makes a (electrostatic) Pi-Anion bond with 7N9G (B:ASP344:OD2). The (C11-N22 ring) forms one hydrophobic (Pi-Sigma) bond with 7N9G (B:LEU267:CB), the (C2-C7 ring) makes a (hydrophobic) Pi-Pi T-shaped bond with 7N9G (A:TYR276), the (C23-C28 ring) forms three Alkyl (hydrophobic) bonds with 7N9G (B:LEU267), (B:VAL275), and (B:ALA288) of the “target Tyrosine-Protein Kinase ABL1” (PDB ID: 7N9G).
This increases the drug's binding affinity and specificity for its target, resulting in the drug-protein complex being stabilised. The presence of the benzene ring helps to the specificity of the medication. It aids in ensuring that Imatinib preferentially interacts with the mutant kinase enzymes that drive cancer cell development, while minimising interactions with other proteins or enzymes in the body. This selectivity is critical for minimising side effects and unsettling responses.
The capacity of imatinib to suppress the activity of tyrosine kinase enzymes, aided in part by the benzene ring, is critical to its therapeutic impact. Imatinib inhibits cancer cell growth by disrupting the signalling pathways mediated by these kinases, resulting in disease remission. Imatinib's benzene ring is important for molecular recognition, hydrophobic interactions, selectivity, and kinase inhibition. It helps the medicine target and block mutant kinase enzymes linked to particular malignancies, making it a highly effective and revolutionary treatment.
4.8 Molecular Docking Analysis of Thalidomide
The present investigation involved the utilization of molecular docking with the Cereblon Isoform 4 protein[38]. The structure database of the (PDB ID: 4V2Y) (target protein) was “acquired from the protein data bank” (RCSB)[39]. The quality of the proteins is determined by comparing them to hydrogen bonds and Ramachandran plots, as illustrated in Fig.15a, 15b these plots demonstrate that all residues are accessible within the authorized range. Imatinib molecular docking investigations were carried out with the 4V2Y target protein using the program “AutoDock 1.5.6 and BIOVIA from Discovery Studios”[40]. The quality of the proteins is determined by comparing them to hydrogen bonds and Ramachandran plots, as illustrated in Fig.16a, 16b for the two proteins. Ligand-target interaction was found in two separate postures for the protein, with affinities of binding -6.3 and -6.2 kcal-mole-1 and binding -for the protein, as observed in Fig.17a), 17b), 17c), Fig. 18a), 18b), 18c) of the target protein. Tables 7 and 8 summarize “the root mean square deviation (RMSD)” and distinct types of binds between Protein and Ligand i.e specific atoms, and group epitopes, as well as the precise itinerary and place of docking interactions of the Ligand and Proteins distinctly. The “low binding affinity of the molecule” signifies that it is an “effective anti-hypercoagulant and covalently binds” to Cereblon Isoform 4 protein over an extended time[41].
In the docking studies of the Thalidomide with Cereblon Isoform 4 protein (PDB ID: 4V2Y), the observation noted that oxygen atoms established the highest number of interactions with the target. The atom O11 makes a hydrogen (conventional) bond with 4V2Y (C:ARG117:HE). The atom O19 makes a hydrogen (conventional) bond with 4V2Y (C:ARG25:HH11) and the atom O18 forms two hydrogen (conventional) bonds with 4V2Y (A:ARG57:HH22) and 4V2Y (C:GLN26:HE22) of the target Cereblon Isoform 4 protein (PDB ID: 4V2Y). The atom H24 makes a hydrogen (conventional) bond with 4V2Y (A:GLU45:OE2) These hydrogen bonds are crucial for the stabilization of the ligand-receptor complex, involving interactions between hydrogen atoms and electronegative atoms of the receptor. The (C4-C9 ring) forms an electrostatic (Pi-Anion) bond these involve interactions between the electron-rich pi-system of the ligand's aromatic rings and anions on the receptor with the 4V2Y(C:ASP116:OD2) of the target Cereblon Isoform 4 protein (PDB ID: 4V2Y) in pose–1. The atom O19 makes a hydrogen (conventional) bond with 4V2Y (C:ARG25:HH11) and the O18 atom makes a hydrogen (conventional) bond with 4V2Y (C:GLN26:HE22) of the target Cereblon Isoform 4 protein (PDB ID: 4V2Y). The O10 atom makes a hydrogen (conventional) bond with 4V2Y (B:THR325:OG1), the H24 atom made a hydrogen (conventional) bond with 4V2Y (B:GLY42:O) and The O11 atom makes a hydrogen (conventional) bond with 4V2Y (C:ARG25:CD) of the target Cereblon Isoform 4 protein (PDB ID: 4V2Y). The (C4-C9 ring) makes a Pi-Anion (electrostatic) bond with the 4V2Y (C:ASP116:OD2) of the target Cereblon Isoform 4 protein (PDB ID: 4V2Y) in pose-2. These bonds are tabulated in Tables 7 and 8, respectively.
4.9 Functional Group Analysis of Thalidomide
The molecular structure of thalidomide consists of a phthalimide ring, which serves as its core structure. The functional groups present in thalidomide include.
4.9.1 Phthalimide Ring
The central core of thalidomide's structure is composed of two benzene rings linked by an imide group, specifically C6H4(CO)2NH. The imide functional group consists of a carbonyl group (C=O) that is bonded to two nitrogen atoms. The presence of the phthalimide ring in thalidomide is of significant importance in understanding its mechanism of action, specifically in relation to its immunomodulatory and anti-inflammatory effects. The mechanism of action of Thalidomide is intricate and encompasses multiple pathways. Although the precise mechanisms are not yet comprehensively understood, it is widely believed that the phthalimide ring plays a crucial role in facilitating certain effects of thalidomide. The following are several key aspects regarding the significance of the phthalimide ring.
The inhibition of tumour necrosis factor-alpha (TNF-α), a pro-inflammatory cytokine involved in multiple inflammatory processes, is a well-documented effect of TNF-Alpha Inhibition, Thalidomide, and its derivatives. The presence of the phthalimide ring is considered to be essential for this particular activity. Thalidomide has been observed to demonstrate anti-inflammatory effects by modulating TNF-α levels. Consequently, it has been utilised in the treatment of specific autoimmune diseases where TNF-α is implicated[14].
Immunomodulation, The presence of the phthalimide ring in thalidomide is responsible for its immunomodulatory effects. Research has demonstrated that Thalidomide has an impact on the production of several cytokines, such as interleukin-2 (IL-2) and interferon-gamma (IFN-γ). The immunomodulatory properties exhibited by thalidomide and its analogues have resulted in their utilisation for the treatment of various medical conditions, including multiple myeloma and leprosy.
Angiogenesis Inhibition, Thalidomide has anti-angiogenic characteristics, which enable it to impede the development of fresh blood vessels. The use of this characteristic has been harnessed in the management of some types of malignancies, where the suppression of angiogenesis may effectively restrict the proliferation of tumours. Thalidomide's anti-angiogenic effect is linked to the presence of the phthalimide ring. Central Nervous System Effects: Thalidomide has the capability to pass across the blood-brain barrier, and the presence of the phthalimide ring in its structure may play a role in facilitating this capacity. This feature is applicable in situations when there is a desire or requirement to evaluate the impact on the central nervous system (CNS).
4.9.2 Aromatic Rings
Two aromatic rings, each having six carbon atoms and alternating single and double bonds, make up thalidomide. The phthalimide structure has these benzene rings. Some of thalidomide's pharmacological effects and mechanisms of action, such its capacity to bind to specific biological targets, are a result of its structural aromatic rings. There are several routes involved in thalidomide's complicated mechanism of action. The importance of thalidomide's aromatic rings is discussed here.
Binding to Biological Targets, A planar structure provided by thalidomide's aromatic rings allows it to engage with certain biological targets. Cereblon (CRBN) is one of the proteins that thalidomide and its analogues bind to. Many of thalidomide's actions, including its immunomodulatory capabilities, are believed to be dependent on its interaction with CRBN.
CRBN-Mediated Degradation of Proteins, The interaction between thalidomide and cereblon is associated with the ubiquitin-proteasome system. The CRBN protein, when coupled to thalidomide, selectively targets certain proteins for ubiquitination, which leads to their eventual destruction by the proteasome. This process has ramifications for the modulation of immune responses and the management of certain illnesses.
Immunomodulation, the presence of aromatic rings in thalidomide enhances its immunomodulatory effects by affecting its interaction with proteins that play a role in immunological function. Thalidomide has been used to address medical disorders marked by heightened immune response, such as multiple myeloma and leprosy.
Anti-Inflammatory Effects, The anti-inflammatory actions of thalidomide are attributed to its interaction with proteins implicated in inflammation, maybe mediated by the aromatic rings. This is important in the management of autoimmune disorders and inflammatory illnesses.
Thalidomide's ability to inhibit angiogenesis may be attributed to the presence of aromatic rings. Thalidomide hinders angiogenesis, a process crucial for the development of new blood vessels, hence effectively restraining the proliferation of certain cancers [42].
It is important to acknowledge that the precise interactions and binding sites of thalidomide with its targets are subjects of current research, and the exact mechanisms may differ based on the particular biological context. These components correspond to the benzene rings present in the phthalimide structure. The comprehension of this concept has resulted in the advancement of thalidomide derivatives that offer improved therapeutic advantages and minimised adverse effects. The presence of aromatic rings plays a crucial role in the pharmacological properties of thalidomide, as they are intricately involved in the intricate interactions between thalidomide and different cellular components.
4.9.3 Carbonyl Group
Thalidomide is composed of a carbonyl group (C=O) located within the phthalimide ring. This particular functional group holds significant importance due to its pharmacological activity. The presence of the carbonyl group within the structure of thalidomide is of considerable importance in relation to its pharmacological properties, as it serves as a critical component in the drug's mechanism of action. The mechanism of action of Thalidomide involves its interaction with specific proteins, modulation of immune responses, and impact on various cellular processes. The following are key aspects highlighting the significance of the carbonyl group in thalidomide.
Binding to Biological Targets, The carbonyl group, which constitutes a carbonyl (C=O) functional group within the phthalimide ring, plays a crucial role in the drug's capacity to engage with specific biological targets. Thalidomide has been observed to exhibit binding affinity towards cereblon (CRBN), a protein that is involved in maintaining protein homeostasis and regulating cellular function.
Cereblon-Mediated Activities, the carbonyl group, which constitutes a carbonyl (C=O) functional group within the phthalimide ring, plays a crucial role in the drug's capacity to engage with specific biological targets. Thalidomide has been observed to exhibit binding affinity towards cereblon (CRBN), a protein that is involved in maintaining protein homeostasis and regulating cellular function.
Immunomodulatory Effects, The immunomodulatory features of thalidomide are attributed to its interaction with cereblon and the subsequent impact it has on the body. The medicine has been used in the management of illnesses marked by aberrant immune responses, such as multiple myeloma and leprosy.
Anti-Inflammatory Actions, Thalidomide's anti-inflammatory actions are attributed to the involvement of the carbonyl group and the phthalimide ring. Thalidomide may decrease the inflammatory response seen in autoimmune disorders and associated illnesses by regulating the activity of certain proteins involved in inflammation.
Anti-Angiogenic Properties, the carbonyl group also affects Thalidomide's capacity to hinder angiogenesis, which is the process of forming new blood vessels. This characteristic is significant in the management of certain malignancies, since blocking angiogenesis may effectively regulate the development of tumours. The carbonyl moiety, in conjunction with other structural components, contributes to the drug's overall mode of action.
4.9.4 Amine Group
The phthalimide structure contains an amine group (NH). Nitrogen's inclusion in this group enhances the collective chemical characteristics of thalidomide.
The presence of the amine group in thalidomide's structure is also significant in determining its pharmacological characteristics and mode of action, notably in its interactions with biological targets. The mechanism of action of Thalidomide is complex and involves the manipulation of several cellular processes. The amine group in thalidomide has many important implications.
Protein Binding and Interactions, the presence of the amine group in thalidomide facilitates its capacity to establish connections with certain proteins. Thalidomide has the ability to attach itself to cereblon (CRBN), a protein that plays a role in cellular activities and maintaining protein balance. The amine group, in conjunction with other structural components, is likely implicated in these binding interactions.
Cereblon-Mediated Pathways, The interaction between thalidomide and CRBN is linked to the regulation of the ubiquitin-proteasome system. The amine group likely facilitates the interaction between thalidomide and CRBN, resulting in subsequent impacts on the breakdown of certain proteins by ubiquitination.
Immunomodulatory Effects, The immunomodulatory effects of thalidomide are attributed to its interaction with CRBN and its influence on the ubiquitin-proteasome system. The medicine has been used in the management of disorders characterised by dysregulated immune responses, such as multiple myeloma and leprosy.
Anti-Inflammatory Actions, thalidomide's anti-inflammatory properties are attributed to the involvement of the amine group, along with other structural aspects. Thalidomide regulates the function of certain proteins linked to inflammation, resulting in a decrease in the inflammatory reaction seen in specific autoimmune disorders.
Angiogenesis Inhibition, The amine group may also play a role in Thalidomide's capacity to suppress angiogenesis, which is the process of forming new blood vessels. Angiogenesis inhibition is significant in the management of some types of malignancies since it aids in regulating tumour development.
It is crucial to take into account the comprehensive molecular structure of thalidomide and the various functional groups, such as the amine group, that play a role in its pharmacological effects. Furthermore, the stereochemistry of thalidomide plays a crucial role in determining its specific activities. The (R)-enantiomer is known to exhibit immunomodulatory effects, whereas the (S)-enantiomer has been found to be associated with teratogenic effects. The comprehension of this concept has resulted in the advancement of thalidomide derivatives that offer improved therapeutic advantages and minimised adverse effects.