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Metal-Mediated Diradical Tuning for DNA Replication Arrest Via Template

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Metal-Mediated Diradical Tuning for DNA Replication Arrest Via Template Metal-mediated diradical tuning for DNA replication PNAS PLUS arrest via template strand scission Meghan R. Portera, Sarah E. Lindahla, Anne Lietzkeb, Erin M. Metzgera, Quan Wangb, Erik Hencka,b, Chun-Hsing Chenc, Hengyao Niub,1, and Jeffrey M. Zaleskia,1 aDepartment of Chemistry, Indiana University, Bloomington, IN 47405; bDepartment of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405; and cMolecular Structure Center, Indiana University, Bloomington, IN 47405 SEE COMMENTARY Edited by Richard Eisenberg, University of Rochester, Rochester, NY, and approved June 30, 2017 (received for review December 27, 2016) − 2− A series of M(PyED)·X(X= 2Cl ,SO4 ) pyridine–metalloenediyne damage cellular DNA in a fashion that leaves DNA polymerase complexes [M = Cu(II), Fe(II), or Zn(II)] and their independently unable to either repair the damage or replicate the DNA. synthesized, cyclized analogs have been prepared to investigate their Double-stranded DNA, and more recently the machinery involved potential as radical-generating DNA-damaging agents. All complexes in DNA replication and repair, have been prominent targets for the possess a 1:1 metal-to-ligand stoichiometry as determined by electronic development of novel, metal-based cancer therapeutics. The impor- absorption spectroscopy and X-ray diffraction. Solution structural tance of the geometry/stereochemistry of the metal center cannot be analysis reveals a pπ Cl → Cu(II) LMCT (22,026 cm−1) for Cu(PyED)·2Cl, overstated because this determines the orientation of ancillary ligands indicating three nitrogens and a chloride in the psuedo-equatorial with respect to the DNA duplex and can be used to tune the reactivity plane with the remaining pyridine nitrogen and solvent in axial and binding modes of these metal-containing therapeutics. Metal- positions. EPR spectra of the Cu(II) complexes exhibit an axially elon- loinserters and metallointercalators exploit noncovalent interactions gated octahedron. This spectroscopic evidence, together with den- of planar aromatic ligands to inhibit DNA repair because they show sity functional theory computed geometries, suggest six-coordinate unwinding of DNA to π-stack between base pairs, groove binding, or structures for Cu(II) and Fe(II) complexes and a five-coordinate envi- insertion into a destabilized site (12, 13). Covalent interactions can be ronment for Zn(II) analogs. Bergman cyclization via thermal activa- used to directly bind complexes to the DNA duplex whereas the li- tion of these constructs yields benzannulated product indicative gands may be functionalized for subsequent reactions such as radical- CHEMISTRY of diradical generation in all complexes within 3 h at 37 °C. A sig- induced DNA cleavage (14–19). Complexes using these mechanisms nificant metal dependence on the rate of the reaction is observed often demonstrate inhibition of DNA replication, leading to G2 [Cu(II) > Fe(II) > Zn(II)], which is mirrored in in vitro DNA-damaging arrest to halt progression of the damaged DNA during the cell cycle; outcomes. Whereas in situ chelation of PyED leads to considerable however, many suffer from lengthy reaction times of up to 48 h or degradation in the presence of all metals within 1 h under hyper- inefficient DNA degradation. Thus, development of molecules that thermia conditions, Cu(II) activation produces >50% compromised react on shorter timescales or with higher potency are important to DNA within 5 min. Additionally, Cu(II) chelated PyED outcompetes advance the potential of these DNA-damaging therapeutics. DNA polymerase I to successfully inhibit template strand extension. One of the best-known molecules that produces radical species · = μ BIOCHEMISTRY Exposure of HeLa cells to Cu(PyBD) SO4 (IC50 10 M) results in a G2/M upon interaction with a metal center [i.e., Cu(II), Fe(II)] is arrest compared with untreated samples, indicating significant DNA bleomycin (BLM). Administered as a metal-free ligand, BLM damage. These results demonstrate metal-controlled radical gener- ation for degradation of biopolymers under physiologically relevant Significance temperatures on short timescales. Pharmaceuticals often act within a lock-and-key model whereby metal-mediated radicals | DNA degradation | polymerase inhibition | molecules bind their targets nearly irreversibly, either stalling or enediyne | Bergman cyclization initiating biological processes. Here, the agent itself performs no chemical transformation on its target but rather triggers an pproximately 14.1 million new cancer cases were diagnosed event or cascade. However, unwanted side effects become more Ain 2012 alone (International Agency for Research on Can- likely as the reactivity of these molecules increases. In contrast, cer, WHO) (1), and although extensive research is underway to molecular compounds may irreversibly damage biological tar- combat these statistics additional therapeutic paradigms are still gets using metal-mediated radical chemistry, but controlling the needed. One of the hallmarks of cancerous cells is their high pro- onset and extent of reaction is challenging. Even so, multiple liferation rate due in part to DNA polymerases that are essential for examples of metal-containing or metal-radical paradigms have damage repair and replication (2). Alterations in these repair path- been used clinically for imaging and chemotherapy. Within this ways or inhibition of the polymerases themselves during S phase have framework we report a class of metal-mediated radical genera- been linked with increased treatment response to DNA-damaging tors that attack DNA, outcompete DNA polymerase, and are cytotoxic drugs. Thus, inhibition of DNA polymerases serves as a cytotoxic in short times and modest concentrations. potential chemotherapeutic target for cancer treatment due to their vital role in fundamental cellular processes (3). Author contributions: H.N. and J.M.Z. designed research; M.R.P., S.E.L., A.L., E.M.M., Q.W., At least 15 DNA polymerases have been discovered, each varying and E.H. performed research; C.-H.C. solved the crystallographic structures; and M.R.P., considerably in processivity and repair ability, making the task of S.E.L., E.M.M., H.N., and J.M.Z. wrote the manuscript. designing specific inhibitors to target individual DNA polymerases The authors declare no conflict of interest. an arduous one. Despite being well-developed, currently available This article is a PNAS Direct Submission. drugs, including toxins that reduce dNTP pools (4, 5), nucleotide Data deposition: The crystallography, atomic coordinates, and structure factors have been deposited in the Cambridge Structural Database, Cambridge Crystallographic Data Cen- analogs that directly block chain extension (6, 7), and genotoxins tre, Cambridge CB2 1EZ, United Kingdom (CCDC nos. 1523776 and 1523777). that damage the DNA template and cause replication stalling (8– See Commentary on page 9497. 11), are narrow in their target scope (2). Given the diversity of DNA 1To whom correspondence may be addressed. Email: [email protected] or hniu@ lesions and the pathways repairing them, effort has been spent on indiana.edu. identifying new strategies that can be applied to a broad spectrum This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. of DNA targets. This alternative paradigm focuses on the ability to 1073/pnas.1621349114/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1621349114 PNAS | Published online July 31, 2017 | E7405–E7414 Downloaded by guest on October 1, 2021 2.5 h at room temperature upon chelation of Mg(II) in methanolic solution (36). In aqueous media, hyperthermal (42.5 °C) treatment of HeLa cells with PyED (20 μM) in the presence of divalent metal ions for 1 h leads to a surviving cell fraction of only 0.5 (37). More- over, this diradical-induced degradation approach is also func- tional against peptidic biopolymer frameworks such as Aβ fibrils, which can be disaggregated upon Cu(II) or Zn(II) chelation within 2 h under physiological conditions (38). Thematically, structure-dependent diradical formation and its influence on substrate activation in real time represents an alter- native therapeutic paradigm and has significant potential for influ- encing kinetically dominant events during cell proliferation. To this end, we report the preparation of PyED–metalloenediyne com- plexes containing Cu(II), Fe(II), and Zn(II) in an effort to evaluate the geometric structure/Bergman cyclization relationship under physiological conditions and probe dynamic arrest of DNA extension processes via diradical degradation. Fig. 1. Raman spectra of Fe(PyED)·Cl2 (red) acquired at 77 K and Fe(PyBD)·Cl2 (blue) acquired at room temperature. The spectrum of Fe(PyED)·Cl2 exhibits a diagnostic alkyne vibration (2,176 cm−1) that is not present in the cyclized Results and Discussion · control complex Fe(PyBD) Cl2. Preparation of Pyridine Metalloenediynes and Cyclized Analogs. The tetradentate enediyne ligand, PyED, and cyclized analog, PyBD, were prepared according to published literature procedures and binds Cu(II) to aid in transportation into the cell, where it is characterized by their 1Hand13C NMR and mass signatures (36). – subsequently replaced by Fe(II) (20). Fe(II) BLM abstracts an A series of air-stable metalloenediyne complexes was synthesized by H-atom from the C4′ deoxyribose sugar to produce a radical, the addition of PyED to a solution of MCl2·xH2OorMSO4·xH2O leading to a gapped DNA site in the presence of O2, subsequent [M
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