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Tumor Discovery Bioinformatics insights into CCL2 mutations

the local structural environment and the overall protein online tool, which revealed significant insights into their
conformation. I-TASSER was used to generate a 3D model binding interactions. Native CCL2 displayed binding
of the CCL2 protein based on the cysteine (C59) and affinity to CCR2, with the top 10 minimum docking
glycine (G59) structures. The model was selected due to scores being −176.10, −160.30, −159.82, −156.20, −155.16,
its high C-score, indicating a high confidence level in the −153.10, −152.99, −151.07, −150.53, and −150.21 kcal/mol
predicted structure. This computational method enabled (Figure 9A). The lowest score of −176.10 kcal/mol indicates
the prediction of the protein tertiary structure. According the most favorable binding interaction. Similarly, mutant
to I-TASSER modeling results, the predicted structure of CCL2 also exhibited robust binding affinity to CCR2, with
the native CCL2 protein has a C-score of −1.20, a TM-score top docking scores of −175.86, −172.30, −168.52, −161.03,
of 0.56 ± 0.15, and an RMSD of 6.4 ± 3.9 Å. Similarly, the −160.64, −159.83, −159.64, −158.47, −155.39, and −153.79
mutant CCL2 protein was predicted to have a comparable kcal/mol (Figure 9B). Although the mutant CCL2 had
structure, with a C-score of −1.10, a TM-score of 0.54 ± slightly higher minimum docking scores than the native
0.14, and an RMSD of 6.2 ± 3.7 Å. These values suggest CCL2, the scores indicate strong binding interactions. The
that both models have a moderate confidence level and comparison of the native and mutant CCL2 forms revealed
a correct global topology, despite some local structural that the mutant CCL2 had a marginally better minimum
variations. docking score (−175.86 kcal/mol) than the native form
The mutation of a cysteine (C) to glycine (G) in the (−176.10 kcal/mol) (Figure 9), suggesting a slightly higher
CCL2 protein substantially affected both its secondary binding affinity for CCR2. However, the overall similarity
and tertiary structures. This is mainly due to the differing in the docking scores indicates that the mutation alters the
side-chain properties of these amino acids, which can alter binding affinity of CCL2 to CCR2. These findings suggest
local interactions and disrupt hydrogen bonding networks. that mutant CCL2 has a strong binding affinity for the
In addition, the mutation’s impact on electrostatic CCR2 receptor and that the mutation impacts CCL2’s
interactions and hydrophobic forces can alter the protein’s ability to interact with its receptor. Further experimental
overall folding and stability. These structural alterations validation and structural analysis are required to fully
can significantly influence the protein’s function, solubility, elucidate the functional implications of this mutation on
and susceptibility to aggregation. 78,79 CCL2–CCR2 signaling.
In the present study, we observed changes in the bond 4. Discussion
distances between the amino acids in the CCL2 protein.
The native CCL2 structure with K58 and C59 had bond CCL2 interacts with CCR2 through its N-terminal β strand,
distances of 9.6 and 6.5 Å, respectively. In contrast, the which is a critical component of the chemokine receptor
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mutant G59 structure with K58 and P60 had bond distances binding process. The CCL2–CCR2 signaling pathway
of 11.7 and 7.1 Å, respectively. The observed changes in plays a crucial role in the pathophysiology of various
bond distances suggest notable structural differences in disorders, including chronic obstructive pulmonary
the mutant protein compared to the native structure. The disease, asthma, cystic fibrosis, and cancer. In the context
mutant protein displays structural variations compared to of cancer, the interaction between CCL2, which is released
the native protein, as indicated by distance measurements by cancer cells, and CCR2 in the tumor microenvironment
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and C-scores (Figure 8A and B). Cysteine at position 59 is essential for the progression and metastasis of cancer.
is a positively charged amino acid that participates in Previous research has shown that CCL2 promotes tumor
electrostatic interactions. Substituting cysteine with glycine growth and metastasis by recruiting macrophages and
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eliminates this positive charge, disrupting electrostatic immune cells to the tumor microenvironment. The
interactions. Furthermore, cysteine can form disulfide CCL2–CCR2 axis is a critical factor in the progression of
bonds, which can alter the protein’s overall structure. These various cancers, including prostate, pancreatic, breast, lung,
changes can significantly affect the protein’s function, kidney, bladder, and colorectal cancers. In prostate cancer,
stability, and interactions with other molecules. 80,81 These CCL2 promotes tumor growth and migration through the
findings highlight the structural variations in CCL2 among PI3K/Akt signaling pathway and contributes to resistance
proteins and critical mutations, providing crucial insights against castration and chemotherapy, making it a potential
into their functional implications. therapeutic target. In pancreatic ductal adenocarcinoma,
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high levels of CCL2 correlate with a poor prognosis and
3.10. Molecular docking of native and mutant CCL2 facilitate angiogenesis, and CCR2 inhibitors have shown
with CCR2 promise in enhancing treatment outcomes. In breast
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The molecular docking results of native and mutant CCL2 cancer, CCL2 enhances cell migration and is implicated
with the CCR2 receptor were obtained using the HDOCK in triple-negative breast cancer, suggesting that targeting

Volume 3 Issue 4 (2024) 17 doi: 10.36922/td.3891