Survey of ribose ring pucker of signaling nucleosides and nucleotides

Abstract

The ribose of protein-bound nucleosides and nucleotides displays preferred conformations (usually either North or South), which can be exploited to design enhanced analogs having chemically fixed conformations. We introduce a computational protocol for assembling data from the protein database (PDB) on the ribose and ribose-like conformation of small molecule ligands when complexed with purinergic signaling proteins (including receptors, enzymes and transporters, and related intracellular pathways). Some targets prefer exclusively North (adenosine and P2Y₁ receptors, CD73, adenosine kinase ATP/ADP-binding site, adenosine deaminase), others prefer South (P2Y₁₂ receptor, E-NTPDase2) or East (adenosine kinase substrates), while others (P2XRs) allow various conformations.

Keywords: G protein-coupled receptor; Nucleoside; enzyme; nucleotide; transporter.

Figure 1.

A. Schematic representation of the nucleosidic substructure used as query by the script, in the form of SMARTS string. Six substructures are searched, involving three possibilities for the ribose-like ring (identified by three different colors in the image) combined to a purine-like or pyrimidine-like scaffold. B. Schematic representation of the dihedral angles ν₀, ν₁, ν₂, ν₃, ν₄.

Figure 2.

Representation of the ribose conformations of purinergic receptors, shown on the pseudorotational cycle (P on polar axes, ν_max on x and y axes). The plots on the left and on the right depict the data on a per-ligand (residue name according to PDB file) and per-protein (species and gene name) basis. A and B. A₁ and A_2AARs (all human). Nucleoside ligands in (A) are labeled as: ADN (adenosine), NEC (NECA), UKA (UK432097), NGI (CGS21680). GDP is also present in one of the structures (5G53), where it is bound to a G_s protein. C and D. P2Y₁ and P2Y₁₂Rs (all human). Nucleotide ligands in (C) are labeled according as: 2ID (MRS2500), 6AD (2MeSADP), 6AT (2MeSATP). E and F. Ribose conformations at P2XRs (all species, as indicated) are shown for human P2RX3, Danio rerio (zebrafish) P2RX4, Ailuropoda melanoleuca (giant panda) P2RX7, Gallus gallus (chicken) P2RX7; with ligands: ATP, 6AT (2MeSATP), 128 (TNP-ATP (spiro-trinitrobenzene-ATP)), CTP.

Figure 3.

Three dimensional views of selected bound ligands, identified by PDB ID and color in the legend (compound abbreviations are reported in Figure 2, 4 and 5 legends). A. Superposition of ADN-bound human ARs A₁ (6D9H, orange) and A_2A (2YDO, lime). ADN appears in the (N) conformation. B. Overlay of nucleotides bound to rat E-NTPDase2. The superposition shows the following nucleotide ligands: ANP (4BR5, white), UNP (4BR2, green), AU1 (4BR0, pink), GNP (4BQZ, cyan), ANP (3CJA, orange), AMP (3CJ9, lime), AMP (3CJ7, purple). The compounds appear in the (S) conformation. C. Superposition of the C-terminal domain of human 5′-nucleotidase bound to the ligands: ADN (4H2F, orange; 4H2G, lime), A12 (4H2I, pink), 0YQ (4H1Y, cyan). The compounds appear in the (N) conformation. D. Superposition of adenosine kinase bound to ADN (1BX4, orange; 5KB5, cyan), 5I5 (chain A 2I6A, lime) and HO4 (chain A 4OIL, purple). The compounds appear in the (E) conformation. E. Superposition of hADA1 bound to 3DI (3IAR, orange), mADA bound to 1DA (1ADD, cyan), PUR (1FKW, purple; 1UIP, lime) and 9DI (chain A 3KM8, pink). The compounds are all (N)-(E). The red spheres represent a conserved water molecule interacting with the ribose moiety. F. Superposition of NDPK-A bound to ADP (chain A 1UCN, orange; chain A 2HVD, cyan; chain A 2HVE, purple), NDPK-B bound to GDP (chain A 1NUE, lime; chain A 3BBF, pink), and NDPK-C bound to ADP (chain A 1ZS6, green). The compounds are all (N).

Figure 4.

Representations of the ribose conformations associated with enzymes that hydrolyze P2R agonists, shown on the pseudorotational cycle (P on polar axes, ν_max on x and y axes). The plots on the left and on the right depict the data on a per-ligand (residue name according to PDB file) and per-protein (species and gene name) basis. A and B. E-NTPDases: Structures of rat ENTPD2 are shown, and the bound nucleotides are: AMP, ANP (phosphonoamino-phosphoryl-oxy-phosphoryl-adenosine), GNP (phosphonoamino-phosphoryl-oxy-phosphoryl-guanosine), AU1 (phosphonoamino-phosphoryl-adenosine), UNP (phosphonoamino-phosphoryl-oxy-phosphoryl-uridine). C and D. Ligands at the nucleotide-binding pocket of E-NPPs: AMP, TMP, 5GP (GMP), C5P (CMP), A (AMP), 4BW (3′3′-cGAMP), B4P (bis(adenosine)-5′-tetraphosphate), UD1 (UDPGlcNAc), ZAN (5′-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]-amino}phosphoryl]adenosine), APC (diphospomethyl phosphonic acid adenosyl ester). ENPP1 data include mouse structures, ENPP3 data include mainly rat structures, with the addition of one human structure (6C02, APC ligand), while ENPP4s include human structures. E and F. 5′-Nucleotidase (all human). Compounds: 0YQ (PSB11552), ADN (adenosine), A12 (phosphomethyl phosphonic acid adenosyl ester).

Figure 5.

Representation of the ribose conformations of compounds bound to adenosine kinase (human and mouse), shown on the pseudorotational cycle (P on polar axes, ν_max on x and y axes). The plots on the left and on the right depict the data on a per-ligand (residue name according to PDB file) and per-protein (species and gene name) basis. A and B. Data relative of all the ligands. C and D. Data of the compounds bound to the substrate-binding site. E and F. Data of the compounds bound to the ATP/ADP-binding site. The compounds are labelled as: ADN (adenosine), ADP, 5I5 (7-(5-deoxy-beta-D-ribofuranosyl)-5-iodo-7H-pyrrolo[2,3-D]pyrimidin-4-amine), HO4 (5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine)

Figure 6.

Representation of the ribose conformations of compounds bound to other enzymes, shown on the pseudorotational cycle (P on polar axes, ν_max on x and y axes). The plots on the left and on the right depict the data on a per-ligand (residue name according to PDB file) and per-protein (species and gene name) basis. A and B. Data relative to human and and mouse adenosine deaminase. Compounds are labelled as: 3DI (2′-deoxyadenosine), 1DA (1-deaza-adenosine), PUR (purine riboside), 9DI (9-deaza-inosine). C and D. Data relative to human nucleoside-diphosphate kinases, isoforms 1, 2 and 3. Compounds are labelled as: ADP, GDP, DG (2'-deoxyguanosine-5′-monophosphate), DA (2′-deoxyadenosine-5′-monophosphate).