Which One among the Pt-Containing Anticancer Drugs More Easily Forms Monoadducts with G and A DNA Bases? A Comparative Study among Oxaliplatin, Nedaplatin, and Carboplatin

Density functional theory methods applied to homogeneous and heterogeneous catalysis: a short review and a practical user guide

The application of density functional theory (DFT) methods in catalysis has been growing fast in the last few decades thanks to both the availability of more powerful high computing resources and the development of new efficient approximations and approaches. DFT calculations allow for the understanding of crucial catalytic aspects that are difficult or even impossible to access by experiments, thus contributing to faster development of more efficient and selective catalysts. Depending on the catalytic system and properties under investigation, different approaches should be used. Moreover, the reliability of the obtained results deeply depends on the approximations involved in both the selected method and model. This review addresses chemists, physicists and materials scientists whose interest deals with the application of DFT-based computational tools in both homogeneous catalysis and heterogeneous catalysis. First, a brief introduction to DFT is presented. Then, the main approaches based on atomic centered basis sets and plane waves are discussed, underlining the main differences, advantages and limitations. Eventually, guidance towards the selection of the catalytic model is given, with a final focus on the evaluation of the energy barriers, which represents a crucial step in all catalytic processes. Overall, the review represents a rational and practical guide for both beginners and more experienced users involved in the wide field of catalysis.

Cytotoxic Pt(II) complexes containing alizarin: a selective carrier for DNA metalation

Many efforts have been made in the last few decades to selectively transport antitumor agents to their potential target sites with the aim to improve efficacy and selectivity. Indeed, this aspect could greatly improve the beneficial effects of a specific anticancer agent especially in the case of orphan tumors like the triple negative breast cancer. A possible strategy relies on utilizing a protective leaving group like alizarin as the Pt(II) ligand to reduce the deactivation processes of the pharmacophore enacted by Pt resistant cancer cells. In this study a new series of neutral mixed-ligand Pt(II) complexes bearing alizarin and a variety of diamine ligands were synthesized and spectroscopically characterized by FT-IR, NMR and UV-Vis analyses. Three Pt(II) compounds, i.e., 2b, 6b and 7b, emerging as different both in terms of structural properties and cytotoxic effects (not effective, 10.49 ± 1.21 μM and 24.5 ± 1.5 μM, respectively), were chosen for a deeper investigation of the ability of alizarin to work as a selective carrier. The study comprises the in vitro cytotoxicity evaluation against triple negative breast cancer cell lines and ESI-MS interaction studies relative to the reaction of the selected Pt(II) complexes with model proteins and DNA fragments, mimicking potential biological targets. The results allow us to suggest the use of complex 6b as a prospective anticancer agent worthy of further investigations.

Binding Motifs of Carboplatin and Oxaliplatin with Guanine: A Combined MS/MS, IRMPD, and Theoretical Study

Complexes generated in the gas phase involving the purine nucleobase guanine bound to second and third generation platinum drugs, namely, carboplatin (CarboPt) and oxaliplatin (OxaliPt), were investigated by combining tandem mass spectrometry, collision-induced dissociation (CID), infrared multiple photon dissociation spectroscopy (IRMPD), and density functional theory (DFT) calculations. As the first step, a spectroscopic characterization of the protonated platinum drugs was accomplished. Protonation of both CarboPt and OxaliPt in the gas phase occurs on one of the two carbonyl groups of the cyclobutanedicarboxylate and oxalate ligand, respectively. Such protonation has been postulated by several theoretical studies as a key preliminary step in the hydrolysis of Pt drugs under acidic conditions. Subsequently, the protonated drugs react with guanine in solution to generate a complex of general formula [Pt drug + H + guanine]+, which was then mass-selected. CID experiments provided evidence of the presence of strong binding between guanine and platinum-based drugs within the complexes. The structures of the two complexes have also been examined by comparing the experimental IRMPD spectra recorded in two spectral regions with DFT-computed IR spectra. For each system, the IRMPD spectra agree with the vibrational spectra calculated for the global minimum structures, which present a monodentate complexation of Pt at the N7 position of canonical guanine. This binding scheme is therefore akin to that observed for cisplatin, while other coordination sites yield substantially less stable species. Interestingly, in the case of oxaliplatin, the IRMPD spectra are consistent with the presence of two isomeric forms very close in energy.

Theoretical investigation on hydrolysis mechanism of cis-platin analogous Pt(II)/Pd(II) complex by DFT calculation and molecular docking approach for their interaction with DNA & HSA

The properties to be an active drug candidate of the complex Pt(TEEDA)Cl₂, C1; Pd(TEEDA)Cl₂, C2 and their hydrolysed product [Pt(TEEDA)(OH₂)₂]²⁺, C1' and [Pd(TEEDA)(OH₂)₂]²⁺, C2' were predicted by Lipinski's rule of 5 and PASS (prediction of activity spectra for substances) web tool. Their structural profile, HOMO-LUMO energy and electronic potential surface ware analysed by DFT calculation. Their TD-DFT spectra were compared with experimental UV-Vis spectra. The hydrolysis mechanisms of C1 & C2 to the diaqua form C1' and C2' were extensively investigated by DFT method in different levels of theory and using CPCM/water model and compared with recognised Pt based anticancer drugs. All the stationary states, including the transition state for the reactions were identified by the DFT calculation. The IRC calculation confirmed that the transition states are well connected and corelate with reactants and products. Interaction of the complexes with DNA & HSA was also investigated by molecular docking study.

Cytotoxicity of Alizarine versus Tetrabromocathecol Cyclometalated Pt(II) Theranostic Agents: A Combined Experimental and Computational Investigation

Platinum compounds cytotoxicity is strictly related to their ability to be converted into active mono- and di-aquated species and consequently to the replacement of labile ligands by water molecules. This activation process makes the platinum center prone to nucleophilic substitution by DNA purines. In the present work, quantum mechanical density functional theory (DFT) computations and experimental investigations were carried out in order to shed light on the relationship between the internalization, aquation, and DNA binding of two isostructural anionic theranostic complexes previously reported by our group, NBu₄[(PhPy)Pt(Aliz)], 1 (IC₅₀ 1.9 ± 1.6 μM), and NBu₄[(PhPy)Pt(BrCat)], 2 (IC₅₀ 52.8 ± 3.9 μM). Cisplatin and a neutral compound [(NH₃)₂Pt(Aliz)], 3, were also taken as reference compounds. The computed energy barriers and the endergonicity of the hydrolysis reactions showed that the aquation rates are comparable for 1 and 2, with a slightly higher reactivity of 1. The second hydrolysis process was proved to be the rate-determining step for both 1 and 2, unlike for compound 3. The nucleophilic attack by the N7 site of guanine to both mono- and di-aquated forms of the complexes was computationally investigated as well, allowing to rationalize the observed different cytotoxicity. Computational results were supported by photostability data and biological assays, demonstrating DNA as the main target for compound 1.

An experimental−theoretical approach to study the cytotoxicity of ionic Pt(II) complexes containing (O^O) chelating ancillary ligands.

Synthesis, Characterization, Thermal Analysis, DFT, and Cytotoxicity of Palladium Complexes with Nitrogen-Donor Ligands

Three new palladium complexes ([Pd(DABA)Cl₂], [Pd(CPDA)Cl₂], and [Pd(HZPY)Cl₂]) bearing dinitrogen ligands (DABA: 3,4-diaminobenzoic acid; CPDA: 4-chloro-o-phenylenediamine; HZPY: 2-hydraziniopyridine) were synthesized, characterized, and tested against breast cancer (MCF-7), prostate carcinoma cell line (PC3) and liver carcinoma cell line (HEPG2). [Pd(DABA)Cl₂] complex exhibited the highest inhibition percentage, lying between 68-71%. The hydrolysis mechanism of each palladium complex, the key step preceding the binding to the biological target, as well as their photophysical properties were explored by means of DFT and TDDFT computations. Results indicate a faster hydrolysis process for the Pd(DABA)Cl₂ complex. The computed activation energies for the first and second hydrolysis processes suggest that all the compounds could reach DNA in their monohydrated form.

How can the cisplatin analogs with different amine act on DNA during cancer treatment theoretically?

Cisplatin is a widely used anti-cancer drug which inhibits the replication and polymerization of DNA molecule while showing some side effects and drug resistance. For this reason, to enhance its therapeutic index, researchers have synthesized several thousand analogs and tested their properties. In this project, several cisplatin analogs were designed to theoretically study the biological activity and lipophilicity effects on amine changes. The amines of the cisplatin molecule were substituted with aliphatic amines in different analogs. Computational methods such as molecular dynamics simulation, molecular docking, and molecular mechanics Poisson-Boltzmann surface area analysis were performed to investigate the binding of six cisplatin derivatives with DNA. The binding affinity and potential interactions of these drugs with double-strand DNA were analyzed. The stability effect of these drugs was investigated via root-mean-square deviation and root-mean-square fluctuation analysis, which showed that some analogs can break base-pair interaction at the end of DNA and reduced the stability of DNA. Also, the results revealed that the hydrogen bond is one of the most important factors in the binding of cisplatin's adduct to DNA. Molecular mechanics Poisson-Boltzmann surface area analysis indicated that electrostatic and van der Waals interactions are the most important deriving forces to the binding of cisplatin's drug to DNA. Finally, data revealed that cisplatin and the cis-dichloro-dimethylamine-platin tendency for binding to DNA are greater than that of other analogs.

Nudged Elastic Band Method for Molecular Reactions Using Energy-Weighted Springs Combined with Eigenvector Following

The climbing image nudged elastic band method (CI-NEB) is used to identify reaction coordinates and to find saddle points representing transition states of reactions. It can make efficient use of parallel computing as the calculations of the discretization points, the so-called images, can be carried out simultaneously. In typical implementations, the images are distributed evenly along the path by connecting adjacent images with equally stiff springs. However, for systems with a high degree of flexibility, this can lead to poor resolution near the saddle point. By making the spring constants increase with energy, the resolution near the saddle point is improved. To assess the performance of this energy-weighted CI-NEB method, calculations are carried out for a benchmark set of 121 molecular reactions. The performance of the method is analyzed with respect to the input parameters. Energy-weighted springs are found to greatly improve performance and result in successful location of the saddle points in less than a thousand energy and force evaluations on average (about a hundred per image) using the same set of parameter values for all of the reactions. Even better performance is obtained by stopping the calculation before full convergence and complete the saddle point search using an eigenvector following method starting from the location of the climbing image. This combination of methods, referred to as NEB-TS, turns out to be robust and highly efficient as it reduces the average number of energy and force evaluations down to a third, to 305. An efficient and flexible implementation of these methods has been made available in the ORCA software.

Novel approach to accurately predict bond strength and ligand lability in platinum-based anticancer drugs

Prompted by the antineoplastic properties of cisplatin, a plethora of platinum(ii)-based complexes have been synthesized in the past decades. At present, their rational design is based on a number of structure-activity relationships involving the nature of the ligands initially coordinated to platinum(ii): either non-labile (acting as a carrier) or labile (undergoing substitution). The coordinate bond strength of the labile ligand plays a key role in the first step of the drug mechanism of action, i.e., the hydrolysis process, which is associated to the retention time of the medicine in the body. Therefore, an accurate determination of the metal-ligand bond strength becomes highly relevant as it will help the rational design of novel chemotherapeutic agents. Herein, we challenge the recently developed intrinsic bond strength index (IBSI) as a rapid and practical tool to assess the ligand lability in Pt(ii) complexes. In a first stage, given the importance of the trans-effect in synthetic strategies of cisplatin-based drugs, the effect of eleven trans-directing ligands T is quantified in two sets of complexes [Pt(NH3)2(H2O)T]n+ and [PtCl2(NH3)T]m+ where T = H2O, F-, NH3, Cl-, Br-, I-, SO32-, CH3-, CN-, CO, and H-. An essential outcome of this work is a novel index IBSItrans = IBSIσ + IBSIπ able to rank the directing ligands by their trans-effect according to their σ-donation and π-backbonding electronic contributions. In a second stage, we apply the IBSI score to a panel of eleven case studies, comprising mostly antineoplastic agents, such as cisplatin, carboplatin, lobaplatin etc., in order to quantify the coordinate bond strength of the ligands, providing insights about the hydrolysis process. The obtained results, in good agreement with experimental data and reported theoretical studies, demonstrate that the IBSI score is able to deliver a rapid and reliable picture of the coordinate bond strength, representing a chemically intuitive tool helpful for the development of novel anticancer agents prior to synthetic efforts.

Theoretical exploration of the photophysical properties of two-component RuII-porphyrin dyes as promising assemblies for a combined antitumor effect

Due to the extraordinary success of porphyrins in photodynamic therapy (PDT) and Ru compounds as chemotherapeutics, a series of RuII-porphyrin complexes have recently been synthesized and proposed as promising dual-action therapeutic agents. The results of a careful DFT and TDDFT investigation on four mononuclear pyridyl triphenylporphyrin RuII-arene complexes are herein reported and compared with those obtained for the metal-free derivatives. The investigation aims at shedding light on the modulation of the photophysical properties of the light absorber upon metalation and exploring the hydrolysis process of the RuII-moiety in the presence of the bulky porphyrin unit. Type I and Type II photoreactions were analyzed computing absorption spectra, singlet-triplet energy gaps, spin orbit coupling constants and vertical electron affinity (VEA) along with ionization potentials (VIP) for all the investigated compounds, while the chloride/water exchange reaction kinetics were determined by exploring the first and second aquation reactions of the Ru-moiety. Despite the highly similar photophysical properties displayed by the members of this class of compounds, an analysis of the hydrolysis processes in the dark allows to point out an interesting difference related to the type of pyridylporphyrin isomer and could be a preliminary explanation of the greater phototoxicity experimentally found for 3'-pyridyl substituted compounds.

Computational Approaches Towards Kinases as Attractive Targets for Anticancer Drug Discovery and Development

BACKGROUND

One of the major goals of computational chemists is to determine and develop the pathways for anticancer drug discovery and development. In recent past, high performance computing systems elicited the desired results with little or no side effects. The aim of the current review is to evaluate the role of computational chemistry in ascertaining kinases as attractive targets for anticancer drug discovery and development.

METHODS

Research related to computational studies in the field of anticancer drug development is reviewed. Extensive literature on achievements of theorists in this regard has been compiled and presented with special emphasis on kinases being the attractive anticancer drug targets.

RESULTS

Different approaches to facilitate anticancer drug discovery include determination of actual targets, multi-targeted drug discovery, ligand-protein inverse docking, virtual screening of drug like compounds, formation of di-nuclear analogs of drugs, drug specific nano-carrier design, kinetic and trapping studies in drug design, multi-target QSAR (Quantitative Structure Activity Relationship) model, targeted co-delivery of anticancer drug and siRNA, formation of stable inclusion complex, determination of mechanism of drug resistance, and designing drug like libraries for the prediction of drug-like compounds. Protein kinases have gained enough popularity as attractive targets for anticancer drugs. These kinases are responsible for uncontrolled and deregulated differentiation, proliferation, and cell signaling of the malignant cells which result in cancer.

CONCLUSION

Interest in developing drugs through computational methods is a growing trend, which saves equally the cost and time. Kinases are the most popular targets among the other for anticancer drugs which demand attention. 3D-QSAR modelling, molecular docking, and other computational approaches have not only identified the target-inhibitor binding interactions for better anticancer drug discovery but are also designing and predicting new inhibitors, which serve as lead for the synthetic preparation of drugs. In light of computational studies made so far in this field, the current review highlights the importance of kinases as attractive targets for anticancer drug discovery and development.

The role of arsenic in the hydrolysis and DNA metalation processes in an arsenous acid-platinum(ii) anticancer complex

Platinum(ii)-based molecules are the most commonly used anticancer drugs in the chemotherapeutic treatment of tumours but possess serious side effects and some cancer types exhibit resistance with respect to these compounds (e.g. cisplatin). For these reasons, the research of new compounds that can bypass this limitation is in continuous development. Recently, mixed Pt(ii)-As(iii) systems have been synthesized and tested as potential anticancer agents. The mechanism of action of these kinds of drugs is unclear. Since in other platinum(ii) containing drugs, hydrolysis plays an important role in the activation of the compound before it reaches DNA, we have explored the aquation process using density functional theory (DFT), focusing our attention on the arsenoplatin complex, [Pt(μ-NHC(CH₃)O)₂ClAs(OH)₂]. As DNA is believed to be the cellular target for Pt anticancer drugs, the metalation mechanism of DNA purine bases has been also investigated. Also for this new drug it appears that guanine is the preferred site with respect to adenine as with other platinum-containing compounds. A comparison with cisplatin is performed in order to highlight the contribution of arsenic in the anticancer activity of this new proposed anticancer agent.

Bis(dimethylsulfoxide)carbonateplatinum(ii), a new synthon for a low-impact, versatile synthetic route to anticancer Pt carboxylates

The work describes a new low-impact synthetic route to Pt(ii)-carboxylate complexes, a class of compounds provided with established anticancer activity. The process is based on the ligand substitution on [PtCO3(Me2SO-S)2] (), a new synthon that can be easily prepared in water with high yield, is stable as a solid, and is reactive in solution where all its ligands can be easily replaced. It reacts with acidic O-donors releasing CO2 as the only side-product, whose development also supplies a driving force toward the products. The substitution of carbonate led to new Pt-DMSO carboxylate complexes , while the total substitution of the ligands of complex gave new Pt-phosphino carboxylates in high yields. The X-ray crystal structures of complexes [Pt(d(-)-quinate-O,O')(Me2SO-S)2] (), [Pt(salicylate)(Me2SO-S)2] () and [Pt(salicylate)(PPh3)2] () were determined. The tests of the antiproliferative activity of complexes on two human tumoral cell lines, A2780 (cisplatin-sensitive) and SKOV-3 (cisplatin-resistant), showed that the PTA (PTA = 1,3,5-triaza-7-phosphaadamantane) complexes were the most active on both cell lines.

VP, Misini B, Das P, Dasgupta S, Linert W, Moi SC. Synthesis, biological evaluation, substitution behaviour and DFT study of Pd(ii) complexes incorporating benzimidazole derivative

Pd(ii) complexes with good DNA/BSA binding ability exhibit cytotoxicity comparable to cisplatin on different cancer cells along with reduced toxicity towards normal cells.

Synergistic Effects in PtII -Porphyrinoid Dyes as Candidates for a Dual-Action Anticancer Therapy: A Theoretical Exploration

The combination of a photosensitizer (PS) with a cisplatin-like unit represents a challenging strategy to increase the effectiveness of photodynamic therapy and to afford a dual-action anticancer treatment. Recently, new tetra-Pt^II -porphyrin conjugates have been proposed as promising multitarget agents. To reveal the effect of the Pt^II center on the chemical and physical properties of the PS and to explore the effect of the PS on the activation mechanism of Pt^II ligand before reaching its biological target, we carried out a first-principle investigation on these tetra-Pt^II -porphyrin conjugates. To propose a further advance in this novel field and to gain useful insights for the design of new, more efficient Pt^II -PS conjugates, we introduced structural modifications into the porphyrin dye, which involved the synthesis of the tetra-Pt^II -chlorin and tetra-Pt^II -bacteriochlorin derivatives. Results showed that the designed dyes better met the criteria to be successful in a dual-action therapy, as they displayed improved optical properties and reduced the hydrolysis rate of the Pt^II moiety, the latter being a desirable feature to avoid many side reactions of the conjugate during their transport to the biological target.

Molecular dynamics simulation and free energy analysis of the interaction of platinum-based anti-cancer drugs with DNA

Cisplatin and oxaliplatin are two widely-used anti-cancer drugs which covalently bind to a same location in DNA strands. Platinum agents make intrastrand and interstrand cross-links with the N7 atoms of guanine nucleotides which prevent DNA from polymerization by causing a distortion in the double helix. Molecular dynamics simulations and free energy calculations were carried out to investigate the binding of two platinum-based anti-cancer drugs with DNA. We compared the binding of these drugs which differ in their carrier ligands, and hence their potential interactions with DNA. When a platinum agent binds to nucleotides, it causes a high amount of deformation in DNA structure. To find the extent of deformation, torsion angles and base pair and groove parameters of DNA were considered. These parameters were compared with normal B-DNA which was considered as the undamaged DNA. The formation of hydrogen bonds between drugs and DNA nucleotides was examined in solution. It was shown that oxaliplatin forms more hydrogen bonds than cisplatin. Our results confirm that the structure of the platinated DNA rearranges significantly and cisplatin tries to deform DNA more than oxaliplatin. The binding free energies were also investigated to understand the affinities, types and the contributions of interactions between drugs and DNA. It was concluded that oxaliplatin tendency for binding to DNA is more than cisplatin in solvent environment. The binding free energy was calculated based on the MM/PBSA and MM/GBSA methods and the results of QM/MM calculations verified them.

Comparisons of the survival time of patients with ovarian cancer adopting post-operative chemotherapy by use of paclitaxel combined with carboplatin or nedaplatin

BACKGROUND

The current study aims to evaluate and compare the efficacy of post-operative chemotherapy using paclitaxel plus carboplatin or nedaplatin in patients with ovarian cancer, as well as the effects of different combinational therapies on the survival times of patients.

METHODS

Ninety-four patients were recruited for the study. These ovarian cancer patients were admitted into the Cancer Hospital Affiliated with Harbin Medical University for surgery from January 2008 to October 2009. They were divided into different groups according to their post-operative chemotherapy schemes: paclitaxel plus carboplatin (CBP group, n = 48) and paclitaxel plus nedaplatin (NDP group, n = 46). Variance analysis was used to compare the effects of different chemotherapy schemes and pathological types of ovarian cancer on the level of CA125 in serum at different treatment time points. Univariate and multivariate analyses were employed to evaluate the survival times of patients in different groups and pathological types and ages.

RESULTS

No significant differences were observed regarding the effects of various chemotherapy schemes (P = 0.561) and pathological types (P = 0.903) on the level of CA125 in serum of patients with ovarian cancer. However, the duration of chemotherapy had a profound impact on the level of CA125 in serum (P < 0.001). The survival times of patients was not affected by age (P = 0.101) and pathological type of ovarian cancer (P = 0.94) significantly. However, it was significantly affected by the chemotherapy scheme.

CONCLUSIONS

Combined chemotherapy using carboplatin plus paclitaxel should be considered as the preferred treatment scheme for the initial treatment of ovarian cancer.

Synergistic Effects of Metals in a Promising Ru(II) -Pt(II) Assembly for a Combined Anticancer Approach: Theoretical Exploration of the Photophysical Properties

Ru(II) -Pt(II) complexes are a class of bioactive molecules of interest as anticancer agents that combine a light-absorbing chromophore with a cisplatin-like unit. The results of a DFT and TDDFT investigation of a Ru(II) complex and its conjugate with a cis-PtCl2 moiety reveal that a synergistic effect of the metals makes the assembly a promising multitarget anticancer drug. Inspection of type I and type II photoreactions and spin-orbit coupling computations reveals that the cis-PtCl2 moiety improves the photophysical properties of the Ru(II) chromophore, ensuring efficient singlet oxygen generation and making the assembly suitable for photodynamic therapy. At the same time, the Ru(II) chromophore promotes a new alternative activation mechanism of the Pt(II) ligand via a triplet metal-to-ligand charge transfer ((3) MLCT) state, before reaching the biological target. The importance of the supramolecular architecture is accurately derived, opening interesting new perspectives on the use of bimetallic Ru(II) -Pt(II) assemblies in a combined anticancer approach.

Activation and Reactivity of a Bispidine Analogue of Cisplatin: A Theoretical Investigation

The reactivity of a bispidine, 3,7-diazabicyclo[3.3.1]nonane, analogue of cisplatin, a new anticancer drug with promising properties, is theoretically investigated to clarify the in vitro reactivity and in vivo mechanism of action of this compound. Thermodynamics and kinetics of the first and second aquation steps and of the reaction of the generated mono- and diaqua species with guanine, the main target of the platinum based antitumor compounds, have been studied. In agreement with the experimental evidence, the bispidine analogue is significantly less reactive than cisplatin toward aquation but the formed aquaspecies show a good reactivity with guanine, consistently with the promising anticancer properties of these new compounds.

Alternative role of cisplatin in DNA damage – theoretical studies on the influence of excess electrons on the cisplatin–DNA complex

Interaction of excess electrons with cisplatin–DNA generates highly reactive Pt-containing species towards C–H abstraction, which strongly contributes to DNA damage.

Atomic level rendering of DNA-drug encounter

Computer simulations have been demonstrated to be important for unraveling atomic mechanisms in biological systems. In this study, we show how combining unbiased molecular dynamic simulations with appropriate analysis tools can successfully describe metal-based drug interactions with DNA. To elucidate the noncovalent affinity of cisplatin's family to DNA, we performed extensive all-atom molecular dynamics simulations (3.7 μs total simulation length). The results show that the parent drug, cisplatin, has less affinity to form noncovalent adducts in the major groove than its aquo complexes. Furthermore, the relative position in which the drugs enter the major groove is dependent on the compound's net charge. Based on the simulations, we estimated noncovalent binding free energies through the use of Markov state models. In addition, and to overcome the lack of experimental information, we employed two additional methods: Molecular Mechanics Poisson-Boltzmann Surface Area (MMPB-SA) and steered molecular dynamics with the Jarzynski estimator, with an overall good agreement between the three methods. All complexes show interaction energies below 3 kcal/mol with DNA but the charged hydrolysis products have slightly more favorable binding free energies than the parent drug. Moreover, this study sets the precedent for future unbiased DNA-ligand simulations of more complex binders.

XRCC1 and XPD genetic polymorphisms and clinical outcomes of gastric cancer patients treated with oxaliplatin-based chemotherapy: a meta-analysis

This meta-analysis aimed to obtain a comprehensive and reliable assessment of the relationships between XRCC1 Arg399Gln and XPD Lys751Gln polymorphisms and the clinical outcomes of gastric cancer (GC) patients treated with oxaliplatin-based chemotherapy. The PubMed, CINAHL, Web of Science, CISCOM, EBSCO, Google Scholar, Cochrane Library, and CBM databases were searched for relevant articles published before September 1, 2013 without language restrictions. Crude odd ratios (ORs) or hazard risk (HR) [95 % confidence intervals (CI)] were calculated. Twelve clinical cohort studies were assessed with a total 1,024 GC patients treated with oxaliplatin-based chemotherapy. Our meta-analysis findings revealed that GC patients with the GA+AA (A carrier) genotypes of XRCC1 Arg399Gln showed a lower effective clinical response (CR+PR) than those with the GG (A non-carrier) genotype (OR=0.41, 95 % CI 0.20∼0.82, P=0.012). However, there was no statistically significant difference in effective clinical response between those with XPD AC+CC (C carrier) genotypes and CC (C non-carrier) genotype (OR=0.55, 95 % CI 0.28∼1.07, P=0.076). Furthermore, the GA+AA genotypes of XRCC1 Arg399Gln was associated with a worse progression-free survival (PFS) and overall survival (OS) compared with the CC genotype (PFS, HR=1.90, 95 % CI 1.12∼2.69, P<0.001; OS, HR=2.13, 95 % CI 0.79∼3.47, P=0.002, respectively). No relationships were found between XPD Lys751Gln polymorphism and both PFS and OS (all P>0.05). No publication bias was detected in this meta-analysis. Results from the current meta-analysis indicate that XRCC1 Arg399Gln polymorphism may be associated with poor clinical outcomes in GC patients treated with oxaliplatin-based chemotherapy.

Experimental and theoretical investigations of the self-association of oxaliplatin

The issue of self-aggregation of oxaliplatin in water as well as in the gas phase is investigated analytically and analyzed by state-of-the-art DFT-D methods.

Mechanism of the cis-[Pt(1R,2R-DACH)(H2O)2]2+ intrastrand binding to the double-stranded (pGpG)·(CpC) dinucleotide in aqueous solution: a computational DFT study

A mechanism of the intrastrand 1,2-cross-link formation between the double-stranded pGpG·CpC dinucleotide (ds(pGpG)) and fully aquated oxaliplatin cis-[Pt(DACH)(H2O)2](2+) (DACH = cyclohexane-1R,2R-diamine) is presented. All structures of the reaction pathways including the transition states (TSs) were fully optimized in water solvent using DFT methodology with dispersion corrections. Both 5' → 3' and 3' → 5' binding directions were considered. In the first step there is a slight kinetic preference for 5'-guanine (5'G) monoadduct formation with an activation Gibbs free energy of 18.7 kcal/mol since the N7 center of the 5'G base is fully exposed to the solvent. On the other hand, the N7 atom of 3'-guanine (3'G) is sterically shielded by 5'G. The lowest energy path for formation of the 3'G monoadduct with an activation barrier of 19.3 kcal/mol is connected with a disruption of the 'DNA-like' structure of ds(pGpG). Monoadduct formation is the rate-determining process. The second step, chelate formation, is kinetically preferred in the 3' → 5' direction. The whole process of the platination is exergonic by up to -18.8 kcal/mol. Structural changes of ds(pGpG), charge transfer effects, and the influence of platination on the G·C base pair interaction strengths are also discussed in detail.