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Structural Basis of Type II Topoisomerase Inhibition by the Anticancer Drug Etoposide

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Science  22 Jul 2011:
Vol. 333, Issue 6041, pp. 459-462
DOI: 10.1126/science.1204117

Abstract

Type II topoisomerases (TOP2s) resolve the topological problems of DNA by transiently cleaving both strands of a DNA duplex to form a cleavage complex through which another DNA segment can be transported. Several widely prescribed anticancer drugs increase the population of TOP2 cleavage complex, which leads to TOP2-mediated chromosome DNA breakage and death of cancer cells. We present the crystal structure of a large fragment of human TOP2β complexed to DNA and to the anticancer drug etoposide to reveal structural details of drug-induced stabilization of a cleavage complex. The interplay between the protein, the DNA, and the drug explains the structure-activity relations of etoposide derivatives and the molecular basis of drug-resistant mutations. The analysis of protein-drug interactions provides information applicable for developing an isoform-specific TOP2-targeting strategy.

Type II topoisomerases (TOP2s) alter DNA topology and play roles in replication, transcription, recombination, and chromosome condensation and segregation (1, 2). These two-fold symmetric enzymes transiently cleave a pair of opposing phosphodiester bonds four base pairs apart, which generates a TOP2-DNA cleavage complex. Passage of a second DNA segment through this enzyme-bridged “DNA gate” and its resealing complete the topological change of the DNA (3, 4). TOP2’s DNA cleavage activity is a double-edged sword; failure to reseal the enzyme-mediated DNA break can lead to cell death (5). Several potent anticancer drugs and antibiotics exploit this harmful aspect of TOP2 and promote the formation of cytotoxic DNA lesions by increasing the steady-state level of cleavage complexes (69). However, despite the extensive use of TOP2-targeting drugs in anticancer chemotherapy, the lack of three-dimensional structures of any drug-stabilized cleavage complexes has left the structural bases of drug actions and resistance largely unresolved and has hampered the development of isoform-specific TOP2-targeting agents (10). To these ends, we determined the high-resolution crystal structure of the DNA-binding and cleavage core of the human TOP2 β isoform (residues 445 to 1201; hereinafter abbreviated hTOP2βcore) in complex with DNA and the anticancer drug etoposide.

A ternary cleavage complex was prepared by mixing purified hTOP2βcore with a 20–base pair DNA duplex and etoposide (Fig. 1, A and B). The DNA substrate contained a preferred 5′-CNNNNG-3′ cleavage site (the arrow) in the middle, flanked by nucleotides matching a deduced semiconsensus sequence (table S1). The crystal structure of the etoposide-stabilized cleavage complex was determined at 2.16 Å resolution (table S2) (11). The asymmetric unit comprised one DNA duplex enclosed symmetrically by the dimeric hTOP2βcore (Fig. 1C). All DNA base pairs, two etoposide molecules, and six Mg2+ ions are clearly visible in the electron density maps (fig. S1). The observation of phosphotyrosyl linkages between the two active-site tyrosine residues (Y821 and Y821′) and the scissile phosphates at the expected positions, accompanied by the rupture of phosphodiester bonds, confirms the formation of the cleavage complex. This high-resolution structure reveals the detailed interplay between the protein, the DNA, and the drug (fig. S2).

Fig. 1

Structure of the hTOP2βcore-DNA cleavage complex stabilized by the anticancer drug etoposide. (A) Linear domain organization of hTOP2β. The middle fragment (residues 445 to 1201), corresponding to hTOP2βcore, was used in this study. The nomenclature of the TOP2 domains is adopted from the yeast enzyme (19). Key drug-interacting residues whose mutations may confer drug resistance to antibiotics (for bacterial TOP2s) or anticancer agents (for eukaryotic TOP2s) are shown in red. (B) The palindromic DNA substrate used for crystallization. The cleavage sites are indicated by arrows. Positive and negative numbers (+1 to +12 and −1 to −8) designate nucleotides downstream and upstream of the scissile phosphate, respectively, with the +1 nucleotide forming a phosphotyrosyl linkage with Y821. The −1/+5 base pairs (in red) highlight the nucleotide preference for this position. (C) Orthogonal views of the ternary cleavage complex. DNA is in blue, one hTOP2βcore monomer is in gray, and the other follows the scheme shown in (A).

The overall structure of the hTOP2βcore dimer adopts a more open quaternary conformation than in other DNA-bound structures reported for bacterial and yeast TOP2s (1217), with significant changes in the relative orientations between the main DNA-contacting domains of the two monomers (Fig. 2), which reduce the buried surface area per monomer from ~1800 Å2 [as seen in the yeast structure (14)] to less than 800 Å2. Because the active center of TOP2 is assembled in trans with the catalytic tyrosine (located in the WHD domain) and the Mg2+-chelating triad of acidic amino acid residues (E477, D557, and D559; situated in the TOPRIM domain), each from different monomers (18), the increase in distance between the active-site tyrosine and the Mg2+-chelating residues suggests that etoposide stabilizes the cleavage complex in part by disfavoring the religation of cleaved DNA ends via decoupling of key catalytic residues (Fig. 2A and figs. S3 and S4).

Fig. 2

The etoposide-stabilized cleavage complex represents a distinct quaternary conformation of TOP2 with decoupled catalytic residues. (A) Surface representation of hTOP2βcore (oriented and colored as in Fig. 1C) as observed in the etoposide-stabilized ternary cleavage complex (left). Note the presence of holes along the dimer interface, which indicate a looser packing between the two monomers. (B) Surface representation of yeast TOP2core in the closed conformation as observed (left) in a protein-DNA binary complex [PDB no. 3L4K (14)]. For each structure, selected residues from the enclosed region are shown in an enlarged view (right) to illustrate the spatial relation between the catalytic tyrosine and the Mg2+-binding triad; the distance between catalytic tyrosine and one aspartate (D557 of hTOP2β and the equivalent D526 of yeast TOP2) of the metal-binding triad is indicated. Residues from different monomers are colored differently, with labels belonging to the second monomer flagged by a prime. The quaternary structural difference between hTOP2βcore and yeast TOP2core can be explained by a sliding of the two A'α3 helices about the structural dyad.

If one assumes that etoposide simply traps a preexisting conformation of the TOP2 cleavage complex, this drug-bound structure may represent a functionally relevant quaternary conformation. With the two monomers moving away from each other, the distances between the 3′ ends of the two cleavage sites and between the two DNA-intercalating isoleucines (I872 and I872′) are longer than those observed in closed structures (table S3 and fig. S5). The structure thus represents a putative intermediate between a closed postcleavage state (12, 14) and the open conformation (19).

The two etoposide molecules bind between the base pairs (+1/+4 and −1/+5) immediately flanking the two cleaved scissile phosphates (Fig. 3A), with the drug’s polycyclic aglycone core (rings A to D) sitting between base pairs, and the glycosidic group and the E ring protruding toward the DNA major and minor grooves, respectively. The insertion of etoposide abolishes the stacking interaction between the +1/+4 and −1/+5 base pairs. The 3′-OH of the −1 nucleotide is held ~8 Å away from the enzyme-linked scissile phosphate, which effectively blocks religation of the cleaved phosphodiester bond (Fig. 3B).

Fig. 3

Detailed views of the etoposide-binding site(s). (A) A cartoon-and-stick representation shows the insertion of two etoposide molecules into two cleavage sites. (B) Close-up stereo representation of the etoposide-binding site. DNA is shown in blue, and two hTOP2βcore monomers are colored differently. Labels belonging to the second monomer are flagged by a prime. Mg2+ and water molecules are shown as green and red spheres, respectively. The distance between the Y821′-linked scissile phosphate and the 3′-OH is indicated. (C) Chemical structure of etoposide. Drug-interacting residues are indicated. The interactions mediated by side-chain and main-chain atoms are shown as solid and dashed lines, respectively. Atoms involve in drug-DNA interactions are shaded gray.

The bound etoposide interacts extensively with both protein and DNA (Fig. 3, B and C). All parts of the aglycone core contribute to drug-DNA interaction by being located between base pairs. The A, B, and D rings also mediate drug-protein interactions. The E ring is anchored both by interacting with G478, D479, and L502 and by being sandwiched between R503 and the deoxyribose ring of the +1 nucleotide. Albeit less extensive, hydrogen bonding and van der Waals interactions are observed between the drug’s glycosidic group and the +5 guanine base, and with Q778 and M782 from helix A′α4 (fig. S6). Clearly, etoposide is stabilized by a new set of interactions in the cleavage complex differing from those observed in the drug-enzyme binary complex (20).

Unlike planar DNA intercalators that stack against base pairs on both sides (21), the aglycone moiety stacks only with the +5 guanine base because of its skewed orientation relative to the DNA backbones and pronounced E ring–induced reposition and buckling of the +1/+4 base pair (Fig. 3, A and B, and fig. S7). Such a DNA deformation is localized and does not propagate toward the symmetry-related active site, which supports the idea that two etoposide molecules are needed to stabilize a double-stranded break (22). The nonplanar conformation adopted by etoposide, owing to the 1,4-trans arrangement of the E ring and glycosidic group, strongly suggests that its insertion between base pairs would be facilitated by the presence of a nicked DNA backbone. The interactions observed between etoposide and the surrounding amino acid residues further highlight the enzyme’s central role in stabilizing the bound drug (Fig. 3C). The active involvement of TOP2 in promoting and stabilizing the interaction between etoposide and DNA further agrees with the notion that the drug displays low affinity toward free DNA and is a poor DNA intercalator (23).

Numerous etoposide analogs have been synthesized and characterized in search of a more effective drug with fewer clinical side effects (24, 25). By revealing the binding mode of etoposide, our structure provides molecular insights for observed structure-activity relations. E-ring modifications—such as the replacement of the 3′- and 5′-methoxyl group by hydrogens and the substitution of 4′-hydroxyl by a hydrogen (20) or by a methoxyl group—cause a decrease in drug activity (26). The negative impact exerted by the hydrogen substitution on drug activity is readily explained by the loss of crucial hydrogen bonds and van der Waals interactions between the E ring and nearby residues. The adverse effect of placing a bulkier methoxy substituent on C4′ is likely due to stronger steric repulsion with D479 and a concomitant loss of favorable interactions (Figs. 3C and 4A). Although modifications of the spatially constrained E ring usually compromise drug function, enhancement of TOP2-poisoning activity can be achieved by a hydroxyl substitution on either the 3′- or 5′-methoxyl group (27). This can be rationalized by the mediation of additional hydrogen bonds.

Fig. 4

Interactions observed in the etoposide-binding site suggest the structure-activity relations of etoposide derivatives, the sequence preference for drug-stabilized cleavage site, and the molecular basis of drug resistance. (A and B) Interactions mediated by the C1 (E ring) and C4 substituent (glycosidic group) of etoposide. Distances between pairs of key interacting atoms are indicated. (C) The conserved PLRGKXL segment in the TOPRIM domain plays a key role in etoposide binding by harboring R503. The reported drug-resistant mutation sites are shown in green. The red dashed line highlights a key hydrogen bond between the +5 guanine base and the main-chain carbonyl of R503. (D) Spatial locations of the drug-resistant mutation sites reported for prokaryotic and eukaryotic TOP2s. A TOP2βcore monomer is shown as gray ribbons, DNA as cyan ribbons, and etoposide as dark blue sticks. Residues involved in drug-binding, DNA-binding, and catalytic functions are shown as red, yellow, and green spheres, respectively. The remaining residues with unidentified mechanism of drug resistance are shown as black spheres. Relevant citations for the selected drug-resistant mutations are listed in table S4.

The finding that the glycosidic moiety rests in a spacious binding pocket with relatively few interactions (Figs. 3C and 4B) explains why it can be either modified or replaced to produce derivatives with enhanced TOP2-poisoning activities, as observed in TOP-53 and F14512 (28, 29). Modeling analysis shows that, compared with the glycosidic group, the aminoalkyl chain of TOP-53 and the spermine moiety of F14512 at C4 may strengthen the ligand-protein and ligand-DNA interaction, respectively, and lead to tighter ligand binding. Although other positions of the aglycone core that line the DNA major groove side are available for modifications, it appears that those non-C4 substitutions would cause steric conflicts and impair the drug-binding site. Therefore, we favor the use of C4 substitutions for generating new bioactive etoposide derivatives.

The structure also suggests a molecular basis for a cytosine at the −1 position being strongly favored at etoposide-stabilized DNA cleavage sites (30). The etoposide-mediated base-stacking interaction was only observed between the A- and B-ring portions of the aglycone core and the +5 guanine base (Fig. 3B). Because the size of the fused A and B ring approximates that of a bicyclic purine base, the presence of a purine may offer a larger surface for interaction. Guanosine is favored over adenosine because its 2-NH2 forms a hydrogen bond with the backbone carbonyl of R503, which anchors this key drug-contacting residue for interacting with the bound etoposide (Fig. 4C). The preference for having a guanosine at position +5 in turn specifies a cytosine at the −1 position.

Mutations in TOP2 have conferred resistance to TOP2-targeting anticancer drugs and antibiotics (7, 16). These drug-resistant mutation sites (Fig. 4D and table S4) can be classified into three groups on the basis of their potential mechanisms of resistance. Group 1—clustering around the E ring (P501, L502, R503, and E522) and glycosidic moiety (G776, E777, Q778, A779, and M782)—likely decreases drug-binding affinity by eliminating key drug-protein interactions or by introducing structural changes in the drug-binding pocket. Group 2 is composed of residues participating in DNA-binding (K505, L507, R510, H514, A668, P732, K814, Q922, A924, and V925). By reducing the enzyme’s affinity toward DNA, these mutants likely produce less cleavage complex and thus compromise drug action. Group 3 contains mutations that reduce the catalytic activity of TOP2: Residues G465, K466, R496, and G550 may impair the communications between the adenosine triphosphatase (ATPase) and the TOPRIM domain (31); P819 and Y821 are key active-site residues. Notably, group 1 mutations may display resistance to some drugs but hypersensitivity to others. In contrast, mutations in groups 2 and 3 usually exhibit a cross-resistance to all drugs.

All vertebrates have two highly similar, yet functionally distinct, TOP2 isoforms (9). The α isoform is particularly important for DNA replication and is usually present at high levels in fast-growing cancer cells (32, 33), whereas the β isoform is mainly involved in transcription-related processes (34, 35). Although the inhibition of both TOP2 isoforms contributes to the drug-induced death of cancer cells, targeting the β isoform has been implicated in deleterious therapy-related secondary malignancies (10, 36). Although most drug-contacting residues are conserved between isoforms, we noted that a key drug-interacting residue, Q778 (Figs. 3C and 4B), is replaced with methionine (M762) in the α isoform. Such a change in residue polarity may be exploitable in developing new isoform-specific anticancer drugs.

Supporting Online Material

www.sciencemag.org/cgi/content/full/333/6041/459/DC1

Materials and Methods

Figs. S1 to S7

Tables S1 to S4

References

References and Notes

  1. Materials and methods are available as supporting material on Science Online.
  2. Atomic coordinates and structure factors have been deposited in the Protein DataBank (PDB) under accession code 3QX3. This work was supported by the National Science Council (99-2113-M-002-008-MY3 to N.C.; 99-2320-B-002-058-MY3 and 100-2325-B-002-019 to T.L.), National Taiwan University College of Medicine (99R311001 to N.C. and T.L.), and National Health Research Institute (EX100-9939NI to T.L.). We thank T.-S. Hsieh for stimulating discussion, and critical reading and editing of the manuscript. Portions of this research were carried out at beamline BL13B1 of the National Synchrotron Radiation Research Center (Taiwan) and beamline SP12B2 of the SPring-8 (Japan). We thank the Protein Crystallography teams at both facilities for assistance during data collection. The National Taiwan University has applied for a patent concerning use of the hTOP2βcore–DNA structure in drug development.

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