Direct observation of the transition state of ultrafast electron transfer reaction of a radiosensitizing drug bromodeoxyuridine

Interaction of low-energy electrons with radiosensitizers

We provide an experimentalist's perspective on the present state-of-the-art in the studies of low-energy electron interactions with common radiosensitizers, including compounds used in combined chemo-radiation therapy and their model systems. Low-energy electrons are important secondary species formed during the interaction of ionizing radiation with matter. Their role in the radiation chemistry of living organisms has become an important topic for more than 20 years. With the increasing number of works and reviews in the field, we would like to focus here on a very narrow area of compounds that have been shown to have radio-sensitizing properties on the one hand, and high reactivity towards low-energy electrons on the other hand. Gas phase experiments studying electron attachment to isolated molecules and environmental effects on reaction dynamics are reviewed for modified DNA components, nitroimidazoles, and organometallics. In the end, we provide a perspective on the future directions that may be important for transferring the fundamental knowledge about the processes induced by low-energy electrons into practice in the field of rational design of agents for concomitant chemo-radiation therapy.

Quasi-Free Electron-Mediated Radiation Sensitization by C5-Halopyrimidines

Substitution of the thymidine moiety in DNA by C5-substituted halogenated thymidine analogues causes significant augmentation of radiation damage in living cells. However, the molecular pathway involved in such radiosensitization process has not been clearly elucidated to date in solution at room temperature. So far, low-energy electrons (LEEs; 0-20 eV) under vacuum condition and solvated electrons (esol-) in solution are shown to produce the σ-type C5-centered pyrimidine base radical through dissociative electron attachment involving carbon-halogen bond breakage. Formation of this σ-type radical and its subsequent reactions are proposed to cause cellular radiosensitization. Here, we report time-resolved measurements at room temperature, showing that a radiation-produced quasi-free electron (eqf-) in solution promptly breaks the C5-halogen bond in halopyrimidines forming the σ-type C5 radical via an excited transient anion radical. These results demonstrate the importance of ultrafast reactions of eqf-, which are extremely important in chemistry, physics, and biology, including tumor radiochemotherapy.

Photoinduced electron transfer in 5-bromouracil labeled DNA. A contrathermodynamic mechanism revisited by electron transfer theories

The understanding of the 5-bromouracil (BrU) based photosensitization mechanism of DNA damage is of large interest due to the potential applications in photodynamic therapy. Photoinduced electron transfer (ET) in BrU labeled duplexes comprising the 5'-GBrU or 5'-ABrU sequence showed that a much lower reactivity was found for the 5'-GBrU pattern. Since the ionization potential of G is lower than that of A, this sequence selectivity has been dubbed a contrathermodynamic one. In the current work, we employ the Marcus and Marcus-Levich-Jortner theory of ET in order to shed light on the observed effect. By using a combination of Density Functional Theory (DFT) and solvation continuum models, we calculated the electronic couplings, reorganization energies, and thermodynamic stimuli for electron transfer which enabled the rates of forward and back ET to be estimated for the two considered sequences. The calculated rates show that the photoreaction could not be efficient if the ET process proceeded within the considered dimers. Only after introducing additional adenines between G and BrU, which accelerates the forward and slows down the back ET, is a significant amount of photodamage expected.

Insights into the deactivation of 5-bromouracil after ultraviolet excitation

5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1nOπ* and 3ππ* states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Mechanisms Responsible for High Energy Radiation Induced Damage to Single-Stranded DNA Modified by Radiosensitizing 5-Halogenated Deoxyuridines

Experimental studies showed that high energy radiation induced base release and DNA backbone breaks mainly occur at the neighboring 5' nucleotide when a single-stranded DNA is modified by radiosensitizing 5-halogenated deoxyuridines. However, no mechanism can be used to interpret these experimental observations. To better understand the radiosensitivity of 5-halogenated deoxyuridines, mechanisms involving hydrogen abstraction by the uracil-5-yl radical from the C2' and C3' positions of an adjacent nucleotide separately followed by the C3'-O3' or N-glycosidic bond rupture and the P-O3' bond breakage are investigated in the DNA sequence 5'-TU(•)-3' employing density functional theory calculations in the present study. It is found that hydrogen abstractions from both positions are comparable with the one from the C2' site slightly more favorable. The N-glycosidic bond cleavage in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is estimated to have the lowest activation free energies, indicating that the adjacent 5' base release dominates electron induced damage to single-stranded DNA incorporated by 5-halogenated deoxyuridines. Relative to the P-O3' bond breakage after the internucleotide C3'-H abstraction, the C3'-O3' bond rupture in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is predicted to have a lower activation free energy, implying that single-stranded DNA backbone breaks are prone to occur at the C3'-O3' bond site. The 5'-TU(•)-3' species has substantial electron affinity and can even capture a hydrated electron, forming the 5'-TU(-)-3' anion. However, the electron induced C3'-O3' bond rupture in 5'-TU(-)-3' anion via a pathway of internucleotide proton abstraction is only minor in both the gas phase and aqueous solution. The present theoretical predictions can interpret rationally experimental observations, thereby demonstrating that the mechanisms proposed here are responsible for high energy radiation induced damage to single-stranded DNA incorporated by radiosensitizing 5-halogenated deoxyuridines. By comparing with previous results, our work proves that the radiosensitizing action of 5-bromo-2-deoxyuridine is not weaker but stronger than its isomer 6-bromo-2-deoxyuridine on the basis of the available data.

In Vitro and In Vivo Studies of a New Class of Anticancer Molecules for Targeted Radiotherapy of Cancer

There is a compelling need to develop anticancer therapies that target cancer cells and tissues. Arising from innovative femtomedicine studies, a new class of non-platinum-based halogenated molecules (called FMD molecules) that selectively kill cancer cells and protect normal cells in treatments of multiple cancers has been discovered. This article reports the first observation of the radiosensitizing effects of such compounds in combination with ionizing radiation for targeted radiotherapy of a variety of cancers. We present in vitro and in vivo studies focused on combination with radiotherapy of cervical, ovarian, head and neck, and lung cancers. Our results demonstrate that treatments of various cancer cells in vitro and in vivo mouse xenograft models with such compounds led to enhanced efficiencies in radiotherapy, while the compounds themselves induced no or little radiotoxicity toward normal cells or tissues. These compounds are therefore effective radiosensitizers that can be translated into clinical trials for targeted radiotherapy of multiple types of cancer. This study also shows the potential of femtomedicine to bring breakthroughs in understanding fundamental biologic processes and to accelerate the discovery of novel drugs for effective treatment or prevention of a variety of cancers. Mol Cancer Ther; 15(4); 640-50. ©2016 AACR.

In Vitro and In Vivo Studies of Non-Platinum-Based Halogenated Compounds as Potent Antitumor Agents for Natural Targeted Chemotherapy of Cancers

Based on a molecular-mechanism-based anticancer drug discovery program enabled by an innovative femtomedicine approach, we have found a previously unknown class of non-platinum-based halogenated molecules (called FMD compounds) as potent antitumor agents for effective treatment of cancers. Here, we present in vitro and in vivo studies of the compounds for targeted chemotherapy of cervical, breast, ovarian, and lung cancers. Our results show that these FMD agents led to DNA damage, cell cycle arrest in the S phase, and apoptosis in cancer cells. We also observed that such a FMD compound caused an increase of reduced glutathione (GSH, an endogenous antioxidant) levels in human normal cells, while it largely depleted GSH in cancer cells. We correspondingly found that these FMD agents exhibited no or little toxicity toward normal cells/tissues, while causing significant cytotoxicity against cancer cells, as well as suppression and delay in tumor growth in mouse xenograft models of cervical, ovarian, breast and lung cancers. These compounds are therefore a previously undiscovered class of potent antitumor agents that can be translated into clinical trials for natural targeted chemotherapy of multiple cancers.

•

Femtomedicine may accelerate drug discovery for effective treatment of cancer.

•

A previously undiscovered class of non-platinum-based halogenated compounds is found to have potent antitumor effects.

•

FMD agents can be used for natural targeted chemotherapy of multiple types of cancer while inducing minimal toxicity.

Electron transfer-based combination therapy of cisplatin with tetramethyl-p-phenylenediamine for ovarian, cervical, and lung cancers

The platinum-based chemotherapy is the standard treatment for several types of cancer. However, cancer cells often become refractory with time and most patients with serious cancers die of drug resistance. Recently, we have discovered a unique dissociative electron-transfer mechanism of action of cisplatin, the first and most widely used platinum-based anticancer drug. Here, we show that the combination of cisplatin with an exemplary biological electron donor, N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD), may overcome the resistance of cancer cells to cisplatin. Our steady-state absorption and fluorescence spectroscopic measurements confirm the effective dissociative electron-transfer reaction between TMPD and cisplatin. More significantly, we found that the combination of 100 μM TMPD with cisplatin enhances double-strand breaks of plasmid DNA by a factor of approximately 3.5 and dramatically reduces the viability of cisplatin-sensitive human cervical (HeLa) cancer cells and highly cisplatin-resistant human ovarian (NIH:OVCAR-3) and lung (A549) cancer cells. Furthermore, this combination enhances apoptosis and DNA fragmentation by factors of 2-5 compared with cisplatin alone. These results demonstrate that this combination treatment not only results in a strong synergetic effect, but also makes resistant cancer cells sensitive to cisplatin. Because cisplatin is the cornerstone agent for the treatment of a variety of human cancers (including testicular, ovarian, cervical, bladder, head/neck, and lung cancers), our results show both the potential to improve platinum-based chemotherapy of various human cancers and the promise of femtomedicine as an emerging frontier in advancing cancer therapy.

Electron stimulated desorption of anions from native and brominated single stranded oligonucleotide trimers

We measured the low energy electron stimulated desorption (ESD) of anions from thin films of native (TXT) and bromine monosubstituted (TBrXT) oligonucleotide trimers deposited on a gold surface (T = thymidine, X = T, deoxycytidine (C), deoxyadenosine (A) or deoxyguanosine (G), Br = bromine). The desorption of H(-), CH(3)(-)/NH(-), O(-)/NH(2)(-), OH(-), CN(-), and Br(-) was induced by 0 to 20 eV electrons. Dissociative electron attachment, below 12 eV, and dipolar dissociation, above 12 eV, are responsible for the formation of these anions. The comparison of the results obtained for the native and brominated trimers suggests that the main pathways of TBrXT degradation correspond to the release of the hydride and bromide anions. Significantly, the presence of bromine in oligonucleotide trimers blocks the electron-induced degradation of nuclobases as evidenced by a dramatic decrease in CN(-) desorption. An increase in the yields of OH(-) is also observed. The debromination yield of particular oligonucleotides diminishes in the following order: BrdU > BrdA > BrdG > BrdC. Based on these results, 5-bromo-2(')-deoxyuridine appears to be the best radiosensitizer among the studied bromonucleosides.

Formation mechanism and structure of a guanine-uracil DNA intrastrand cross-link

The formation and structure of the 5'-G[8-5]U-3' intrastrand cross-link are studied using density functional theory and molecular dynamics simulations due to the potential role of this lesion in the activity of 5-halouracils in antitumor therapies. Upon UV irradiation of 5-halouracil-containing DNA, a guanine radical cation reacts with the uracil radical to form the cross-link, which involves phosphorescence or an intersystem crossing and a rate-determining step of bond formation. Following ionizing radiation, guanine and the uracil radical react, with a rate-limiting step involving hydrogen atom removal. Although cross-link formation from UV radiation is favored, comparison of calculated reaction thermokinetics with that for related experimentally observed purine-pyrimidine cross-links suggests this lesion is also likely to form from ionizing radiation. For the first time, the structure of 5'-G[8-5]U-3' within DNA is identified by molecular dynamics simulations. Furthermore, three conformations of cross-linked DNA are revealed, which differ in the configuration of the complementary bases. Distortions, such as unwinding, are localized to the cross-linked dinucleotide and complementary nucleotides, with minimal changes to the flanking bases. Global changes to the helix, such as bending and groove alterations, parallel cisplatin-induced distortions, which indicate 5'-G[8-5]U-3', may contribute to the cytotoxicity of halouracils in tumor cell DNA using similar mechanisms.

Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA

The ability of a dinucleoside monophosphate to mimic the conformation of B-DNA was tested using a combination of different phosphate models (anionic, neutral, counterion), environments (gas, water), and density functionals (B3LYP, MPWB1K, M06-2X) with the 6-31G(d,p) basis set. Three sequences (5'-GX(Py)-3', where X(Py) = T, U or (Br)U) were considered, which vary in the (natural or modified) 3' pyrimidine nucleobase (X(Py)). These bases were selected due to their presence in natural DNA, structural similarity to T and/or applications in radical-initiated anti-tumour therapies. The accuracy of each of the 54 model, method and sequence combinations was judged based on the ability to reproduce key structural features of natural B-DNA, including the stacked base-base orientation and important backbone torsion angles. B3LYP yields distorted or tilted relative base-base orientations, while many computational challenges were encountered for MPWB1K. Despite wide use in computational studies of DNA, the neutral (protonated) phosphate model could not consistently predict a stacked arrangement for all sequences. In contrast, stacked base-base arrangements were obtained for all sequences with M06-2X in conjunction with both the anionic and (sodium) counterion phosphate models. However, comparison of calculated and experimental backbone conformations reveals the charge-neutralized counterion phosphate model best mimics B-DNA. Structures optimized with implicit solvent (water) are comparable to gas-phase structures, which suggests similar results should be obtained in an environment of intermediate polarity. We recommend the use of either gas-phase or water M06-2X optimizations with the counterion phosphate model to study the structure and/or reactivity of natural or modified DNA with a dinucleoside monophosphate.

Direct observation of ultrafast-electron-transfer reactions unravels high effectiveness of reductive DNA damage

Both water and electron-transfer reactions play important roles in chemistry, physics, biology, and the environment. Oxidative DNA damage is a well-known mechanism, whereas the relative role of reductive DNA damage is unknown. The prehydrated electron (e(pre)-), a novel species of electrons in water, is a fascinating species due to its fundamental importance in chemistry, biology, and the environment. e(pre)- is an ideal agent to observe reductive DNA damage. Here, we report both the first in situ femtosecond time-resolved laser spectroscopy measurements of ultrafast-electron-transfer (UET) reactions of e(pre)- with various scavengers (KNO(3), isopropanol, and dimethyl sulfoxide) and the first gel electrophoresis measurements of DNA strand breaks induced by e(pre)- and OH(•) radicals co-produced by two-UV-photon photolysis of water. We strikingly found that the yield of reductive DNA strand breaks induced by each e(pre)- is twice the yield of oxidative DNA strand breaks induced by each OH(•) radical. Our results not only unravel the long-standing mystery about the relative role of radicals in inducing DNA damage under ionizing radiation, but also challenge the conventional notion that oxidative damage is the main pathway for DNA damage. The results also show the potential of femtomedicine as a new transdisciplinary frontier and the broad significance of UET reactions of e(pre)- in many processes in chemistry, physics, biology, and the environment.

Photoelectron spectroscopic studies of 5-halouracil anions

The parent negative ions of 5-chlorouracil, UCl(-) and 5-fluorouracil, UF(-) have been studied using anion photoelectron spectroscopy in order to investigate the electrophilic properties of their corresponding neutral halouracils. The vertical detachment energies (VDE) of these anions and the adiabatic electron affinities (EA) of their neutral molecular counterparts are reported. These results are in good agreement with the results of previously published theoretical calculations. The VDE values for both UCl(-) and UF(-) and the EA values for their neutral molecular counterparts are much greater than the corresponding values for both anionic and neutral forms of canonical uracil and thymine. These results are consistent with the observation that DNA is more sensitive to radiation damage when thymine is replaced by halouracil. While we also attempted to prepare the parent anion of 5-bromouracil, UBr(-), we did not observe it, the mass spectrum exhibiting only Br(-) fragments, i.e., 5-bromouracil apparently underwent dissociative electron attachment. This observation is consistent with a previous assessment, suggesting that 5-bromouracil is the best radio-sensitizer among these three halo-nucleobases.

Bond breaks of nucleotides by dissociative electron transfer of nonequilibrium prehydrated electrons: a new molecular mechanism for reductive DNA damage

DNA damage is a central mechanism in the pathogenesis and treatment of human diseases, notably cancer. Little is known about reductive DNA damage in causing genetic mutations during oncogenesis and killing cancer cells during radiotherapy. The prehydrated electron (e(-)(pre)) has the highest yield among all the radicals generated in cells during ionizing radiation and has subpicosecond lifetimes (10(-13) s) and energies below 0 eV, but its role in DNA damage is unknown. In this work, our real-time measurements by femtosecond time-resolved laser spectroscopy have revealed that while adenine and cytosine can effectively trap an e(-)(pre) to form stable anions, thymidine and especially guanine are highly susceptible to dissociative electron transfer of e(-)(pre), leading to bond dissociation in DNA. Our finding demonstrates a dissociative electron transfer pathway for reductive DNA damage that might be related to various diseases such as cancer and stroke. Moreover, this finding challenges the conventional notion that damage to the genome is mainly induced by the oxidizing OH* radical and might eventually lead to improved radiotherapy of cancer and radioprotection of humans.

Benign decay vs. photolysis in the photophysics and photochemistry of 5-bromouracil. A computational study

The excited state potential energy surface of 5-bromouracil has been studied with ab initio CASPT2//CASSCF calculations to rationalize the competition between the benign decay and the photolysis found experimentally. The surface is characterized by an extended region of degeneracy between S(1) and S(0). The access to this region has been studied with minimum energy path calculations from the FC structure, the seam of intersection has been mapped in detail, and the decay paths from different regions of the seam have been characterized. There are two decay paths with low barriers that are limiting cases for the actual decay dynamics. The first path involves the bromine elimination and leads to a region of near degeneracy between the ground and excited states, and the second one leads back to the reactant through a conical intersection between the two states. The conical intersection for benign decay is part of a seam that lies along the C(5)-Br stretching coordinate, and decay at the region of the seam with a stretched C(5)-Br bond leads to photolysis. Thus, the reactivity depends on the point of the seam at which decay to the ground state takes place. The low experimental photolysis quantum yield suggests that the energetically favored decay is the one that regenerates the reactant, while the low barriers computed to access the region of decay are in agreement with the measured picosecond excited state lifetime.