Cordycepin Triphosphate as a Potential Modulator of Cellular Plasticity in Cancer via cAMP-Dependent Pathways: An In Silico Approach

Abstract

Cordycepin, or 3'-deoxyadenosine, is an adenosine analog with a broad spectrum of biological activity. The key structural difference between cordycepin and adenosine lies in the absence of a hydroxyl group at the 3' position of the ribose ring. Upon administration, cordycepin can undergo an enzymatic transformation in specific tissues, forming cordycepin triphosphate. In this study, we conducted a comprehensive analysis of the structural features of cordycepin and its derivatives, contrasting them with endogenous purine-based metabolites using chemoinformatics and bioinformatics tools in addition to molecular dynamics simulations. We tested the hypothesis that cordycepin triphosphate could bind to the active site of the adenylate cyclase enzyme. The outcomes of our molecular dynamics simulations revealed scores that are comparable to, and superior to, those of adenosine triphosphate (ATP), the endogenous ligand. This interaction could reduce the production of cyclic adenosine monophosphate (cAMP) by acting as a pseudo-ATP that lacks a hydroxyl group at the 3' position, essential to carry out nucleotide cyclization. We discuss the implications in the context of the plasticity of cancer and other cells within the tumor microenvironment, such as cancer-associated fibroblast, endothelial, and immune cells. This interaction could awaken antitumor immunity by preventing phenotypic changes in the immune cells driven by sustained cAMP signaling. The last could be an unreported molecular mechanism that helps to explain more details about cordycepin's mechanism of action.

Keywords: adenylate cyclase; cordycepin; mechanism of action; molecular docking; molecular dynamics; purine metabolites; tumor microenvironment.

Figure 1

Hierarchical clustering of COR-TP. Molecules clustered according to their physicochemical characteristics. 1. Di- and triphosphate nucleotides. 2. Glucose-related metabolic intermediates, non-phosphorylated purine metabolites, monophosphate nucleotides, arginine-derived metabolites, and cyclic nucleotides. 3. Palmitic acid. 4. Intermediary metabolites of glycolysis and TCA cycle. 5. Polyamines and other arginine-derived metabolites. 6. Aromatic amino acids and other intermediates of the TCA cycle. 7. Branched-chain amino acids and ketone bodies. 8. Other amino acids and creatine-related metabolites. ATP: adenosine triphosphate; ADP: adenosine diphosphate; AMP: adenosine monophosphate; cAMP: cyclic adenosine monophosphate; ADO: adenosine; COR-TP: cordycepin triphosphate; INO: inosine; ITP: inosine triphosphate; IDP: inosine diphosphate; IMP: inosine monophosphate; GUA: guanosine; GTP: guanosine triphosphate; GDP: guanosine diphosphate; GMP: guanosine monophosphate, cGMP: cyclic guanosine monophosphate; ADMA: asymmetric dimethylarginine; SDMA: symmetric dimethylarginine; L-ASS: L-argininesuccinate; F1,6BP: fructose-1,6-bisphosphate; G6P: glucose-6-phospate; F6P: fructose-6-phospate; GLU: glucose; FUM: fumarate; CP: creatine phosphate; PEP: phosphoenolpyruvate; PYR: pyruvate; ACETO: acetoacetate; OXA: oxaloacetate; SUCC: succinate; KETOG: alpha-ketoglutarate; PAL: palmitic acid; NG-MMA: NG-monomethyl-L-arginine; L-HARG: L-homoarginine; 1,3BPG: 1,3-bisphosphoglycerate; 3PG: 3-phosphoglycerate; CITR: citrate; ISOCITR: isocitrate; GLI3P: glycerol-3-phosphate; MAL: malate; G3P: glyceraldehyde 3-phosphate; DHAP: dihydroxyacetone; L-CAR: L-carnitine; L-ORN: L-ornithine; L-LYS: L-lysine; PUT: putrescine; CAD: cadaverine; AGM: agmatine; SPD: spermidine; SPR: spermine; L-CIT: L-citrulline; L-ARG: arginine; L-ALA: L-alanine; L-ASN: L-asparagine; L-ASP: L-aspartate; L-CYS: L-cysteine; L-GLN: L-glutamine; GLUT: L-glutamate; L-GLY: L-glycine; L-HIS: L-histidine; L-ILE: L-isoleucine; L-LEU: L-leucine; L-MET: L-methionine; L-PHE: L-phenylalanine; L-PRO: L-proline; L-SER: L-serine; L-THR: L-threonine; L-TRP: L-tryptophan; L-TYR: L-tyrosine; L-KYN: L-kynurenine; L-VAL: L-valine, CREA: creatine; GAC: guanidinoacetate; LAC: lactate; ACET: acetate; 3OHB: 3-O-hydroxybutyrate.

Figure 2

Docking scores (kcal/mol) of different targets with COR and derivatives compared to affinities of endogenous metabolites. ADK: adenosine kinase; sAC: soluble adenylate cyclase; tmAC: transmembrane adenylate cyclase; PNP: purine nucleoside phosphorylase; MAT: methionine adenosyl transferase; ADA: adenosine deaminase; NT5C2: cytosolic 5′-nucleotidase II; ENPP3: ectonucleotide pyrophosphatase/phosphodiesterase 3; DNMT3A: DNA methyltransferase 3 alpha; DNMT1: DNA methyltransferase 1; A₁R: adenosine receptor 1; A_2AR: Adenosine receptor 2A; A_2BR: Adenosine receptor 2B.

Figure 3

Binding modes of COR, 3′-dINO, and ADO with different targets like ADK (site 1), ADA, A_2AR, and A_2BR.

Figure 4

Binding modes of ATP and COR-TP with different targets like CD39, ENPP3, and sAC, as well as ADP, and COR-DP with CD39.

Figure 5

RMSD of the α carbons of the protein–ligand complexes, compared to protein alone.

Figure 6

RMSD of ligand atoms relative to protein.

Figure 7

RMSD of the ligand atoms relative to their original position.

Figure 8

Summary of ligand interactions with ADCY05. (A) COR-TP interactions; (B) ATP interactions. (C) Amino acid residues with which COR-TP interacts; (D) amino acid residues with which ATP interacts. Green represents hydrogen bonds; purple represents hydrophobic interactions; pink represents ionic interactions; and blue represents water-mediated interactions.

Figure 9

Summary of ligand interactions with ADCY10. (A) COR-TP interactions; (B) ATP interactions. (C) Amino acid residues with which COR-TP interacts; (D) amino acid residues with which ATP interacts. Green represents hydrogen bonds; purple represents hydrophobic interactions; pink represents ionic interactions; and blue represents water-mediated interactions.

Figure 10

Free energy profile obtained by metadynamics using the distance of the ligand-catalytic site centers of mass as a collective variable.

Figure 11

Effects of cAMP-mediated signaling on TME that COR-TP could disrupt by decreasing tmAC and sAC activity. (A) In CAF, cAMP-mediated signaling can activate PKA and Epac, which can phosphorylate CREB and C/EBPβ, respectively. This increases the expression of IL-6 and Wnt5a, which favors the proliferation of tumor cells and angiogenesis in endothelial cells. (B) In endothelial cells, the cAMP-PKA-CREB axis induces the activation of HDAC2, which represses the expression of TSP-1, a potent angiogenesis inhibitor. (C) In tumor cells, cAMP activates PKA and Epac. PKA activates CREB, leading to the transcription of genes involved in proliferation and survival. Epac, in turn, activates Rap1, which activates the MAPK pathway and mTOR through AKT, inhibiting apoptosis. (D) In immune system cells, cAMP signaling activates Epac, inhibiting NF-κB. The cAMP-PKA-CREB axis also favors the inhibition of NF-κB, decreasing the proliferation, activation, and release of pro-inflammatory cytokines. In addition, tolerogenic processes in immune cells are favored, significantly reducing their antitumor activity. psGPCRs: proton-sensing G protein-coupled receptors; A_2AR: Adenosine receptor 2A; A_2BR: Adenosine receptor 2B; EP2: Prostaglandin E2 (PGE₂) receptor 2; EP4: Prostaglandin E2 (PGE₂) receptor 4; β-AR: β-adrenergic receptor; TSP-1: thrombospondin 1; CREB: cAMP response element-binding; C/EBPβ: CCAAT/enhancer-binding protein beta; Wnt5a: Wnt Family Member 5A; CRE: cAMP response element; sAC: soluble adenylate cyclase; tmAC: transmembrane adenylate cyclase.