Bioactivity, molecular docking and anticancer behavior of pyrrolidine based Pt(II) complexes: Their kinetics, DNA and BSA binding study by spectroscopic methods

The complex [Pt(AEP)Cl₂]; C-1 (where, AEP = 1-(2-Aminoethyl) pyrrolidine) and its hydrolyzed diaqua form cis-[Pt(AEP)(H₂O)₂]²⁺; C-2 were synthesized for their bioactivity and in vitro kinetic study with bioactive thiol group (-SH) containing ligands (like; L- cysteine and N-ac-L- cysteine) for their biological importance for 'drug reservoir' activity. The Thermal Gravimetric Analysis (TGA) was executed to confirm about the weight loss due to coordinated water molecules at high temperature range. At pH 4.0, the substitution behavior of C-2 with the thiols was studied in pseudo-first order reaction condition. The interaction mechanism of thiols with complex C-2 to their corresponding thiol substituted C-3 [Pt(AEP)(L-cys)] and C-4 [Pt(AEP)(N-ac-L-cys)] (where L-cys = L-cysteine and N-ac-L-cys = N-ac-L- cysteine) were proposed from their thermodynamical activation parameters (ΔH^≠ and ΔS^≠), which were obtained from Eyring equation. DNA and BSA binding activity of the complexes C-1 to C-4 were investigated by gel electrophoresis technique, spectroscopic titration and viscosity methods. The binding activity of the complexes with DNA and BSA was evaluated using a theoretical approach molecular docking study. The drug-like nature of the complexes is supported by the prediction of activity spectra for substance (PASS) from 2D structure of the Pt(II) complexes. Structural optimization, HOMO-LUMO energy calculation, Molecular electrostatic potential surface, NBO and TD-DFT calculation were executed by using density functional theory (DFT) with Gaussian 09 software package to pre-assessment of biological activity of the complexes. DFT-based descriptors were determined from the HOMO-LUMA energy to be related with the ability of binding affinity of Pt(II) complexes towards DNA and BSA to the formation of their corresponding adducts. The anticancer property of the design complexes were examined on HCT116 (colorectal carcinoma) cancer cell lines and as well as human normal cell NKE (Normal Kidney Epithelial) and compared with the recognised anticancer drug cisplatin. The Reactive Oxygen Species (ROS) production was assessed by DCFDA assay in presence of the Pt(II) complexes.

Electromagnetic bioeffects: a multiscale molecular simulation perspective

Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.

Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action

Phenanthriplatin (PtPPH) is a monovalent platinum(II)-based complex with a large cytotoxicity against cancer cells. Although the aqua-activated drug has been assumed to be the precursor for DNA damage, it is still under debate whether the way in which that metallodrug attacks to DNA is dominated by a direct binding to a guanine base or rather by an intercalated intermediate product. Aiming to capture the mechanism of action of PtPPH, the present contribution used theoretical tools to systematically assess the sequence of all possible mechanisms on drug activation and reactivity, for example, hydrolysis, intercalation, and covalent damage to DNA. Ab initio quantum mechanical (QM) methods, hybrid QM/QM′ schemes, and independent gradient model approaches are implemented in an unbiased protocol. The performed simulations show that the cascade of reactions is articulated in three well-defined stages: (i) an early and fast intercalation of the complex between the DNA bases, (ii) a subsequent hydrolysis reaction that leads to the aqua-activated form, and (iii) a final formation of the covalent bond between PtPPH and DNA at a guanine site. The permanent damage to DNA is consequently driven by that latter bond to DNA but with a simultaneous π–π intercalation of the phenanthridine into nucleobases. The impact of the DNA sequence and the lateral backbone was also discussed to provide a more complete picture of the forces that anchor the drug into the double helix.

The influence of external electric fields on proton transfer tautomerism in the guanine-cytosine base pair

The Watson-Crick base pair proton transfer tautomers would be widely considered as a source of spontaneous mutations in DNA replication if not for their short lifetimes and thermodynamic instability. This work investigates the effects external electric fields have on the stability of the guanine-cytosine proton transfer tautomers within a realistic strand of aqueous DNA using a combination of ensemble-based classical molecular dynamics (MD) coupled to quantum mechanics/molecular mechanics (QM/MM). Performing an ensemble of calculations accounts for the stochastic aspects of the simulations while allowing for easier identification of systematic errors. The methodology applied in this work has previously been shown to estimate base pair proton transfer rate coefficients that are in good agreement with recent experimental data. A range of electric fields in the order of 104 to 109 V m-1 is investigated based on their real-life medicinal applications which include gene therapy and cancer treatments. The MD trajectories confirm that electric fields up to 1.00 × 109 V m-1 have a negligible influence on the structure of the base pairs within DNA. The QM/MM results show that the application of large external electric fields (1.00 × 109 V m-1) parallel to the hydrogen bonds increases the thermodynamic population of the tautomers by up to one order of magnitude; moreover, the lifetimes of the tautomers remain insignificant when compared to the timescale of DNA replication.

A vibrational spectroscopic and computational study of gaseous protonated and alkali metal cationized G-C base pairs

The structures and properties of metal cationized complexes of 9-ethylguanine (9eG) and 1-methylcytosine (1mC), (9eG:1mC)M⁺, where M⁺ = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ as well as the protonated complex, (9eG:1mC)H⁺, have been studied using a combination of IRMPD spectroscopy and computational methods. For (9eG:1mC)H⁺, the dominant structure is a Hoogsteen type complex with the proton covalently bound to N3 of 1mC despite this being the third best protonation site of the two bases; based on proton affinities N7 of 9eG should be protonated. However, this structural oddity can be explained considering both the number of hydrogen bonds that can be formed when N3 of 1mC is protonated as well as the strong ion-induced dipole interaction that exists between an N3 protonated 1mC and 9eG due to the higher polarizability of 9eG. The anomalous dissociation of (9eG:1mC)H⁺, forming much more (1mC)H⁺ than would be predicted based on the computed thermochemistry, can be explained as being due to the structural oddity of the protonation site and that the barrier to proton transfer from N3 of 1mC to N7 of 9eG grows dramatically as the base pair begins to dissociate. For the (9eG:1mC)M⁺; M = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ complexes, single unique structures could not be assigned. However, the experimental spectra were consistent with the computed spectra. For (9eG:1mC)Li⁺, the lowest energy structure is one in which Li⁺ is bound to O6 of 9eG and both O2 and N3 of 1mC; there is also an interbase hydrogen bond from the amine of 1mC to N7 of 9eG. For Na⁺, K⁺, and Rb⁺, similar binding of the metal cation to 1mC is calculated but, unlike Li⁺, the lowest energy structure is one in which the metal cation is bound to N7 of 9eG; there is also an interbase hydrogen bond between the amine of 1mC and the carbonyl of 9eG. The lowest energy structure for the Cs complex is the Watson-Crick type base pairing with Cs⁺ binding only to 9eG through O6 and N7 and with three hydrogen bonds between 9eG and 1mC. It also interesting to note that the Watson-Crick base pairing structure gets lower in Gibbs energy relative to the lowest energy complexes as the metal gets larger. This indicates that the smaller, more densely charged cations have a greater propensity to interfere with Watson-Crick base pairing than do the larger, less densely charged metal cations.

Tuning the Optical Properties of Novel Antitumoral Drugs Based on Cyclometalated Iridium(III) Complexes

Most of the current efforts in drug discovery are devoted to the design of molecules able to mitigate side effects by concentrating the biological action in the targeted tissue. One promising strategy is photodynamic therapy, which is based on the in situ generation of reactive singlet oxygen upon radiation exposure. However, such an approach requires the use of an efficient photosensitizer. This contribution deals with the optical properties of an Ir(III) complex, [Ir(pbz)₂(N^N)] (pbz = 2-phenylbenzimidazole; N^N = methyl 1-butyl-2-pyridyl-benzimidazole-5-carboxylate), which has recently been shown to exhort a strong photoactivity, but still needs further improvements to reach clinical applications. We performed density functional theory calculations at the M06, PBE0, ωB97xD, and CAM-B3LYP levels to predict the impact of introducing electron donor-acceptor groups into the nature of the lowest excited states. The simulations performed demonstrate that the presence of a NH₂ at the pbz ligand and a NO₂ group at the N^N ligand yield a bathochromic shift of absorption spectrum. We report the most sensitive positions to tune the optical signatures of this family of complexes.

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.

Possible use of BN-modified fullerene as a nano-biosensor to detect adenine–thymine Watson–Crick base pair in mutagenic tautomeric form: Theoretical approach

The present work deals with the theoretical investigation of electronic structure features and stability of adenine–thymine (AT) and rare tautomer of adenine–thymine (rAT) base pairs along with their complexes with Cu 2+ cation and their interactions with BN doped fullerene ( C 58 BN ). All the calculations have been performed with density functional theory using B3LYP functional. Electronic structures of the two base pairs are almost identical. Hence, it is rather difficult to distinguish between the two base pairs on the basis of their electronic properties. As per our theoretical calculations, we have observed that, BN modified fullerene could act as a nano-biosensor for detection of mispairing between these two complementary bases as well as their Cu 2+ complexes.

Assessing the importance of proton transfer reactions in DNA

Although engineered by millions of years of evolution, the cellular machinery is not flawless, and errors regularly appear during DNA replication. The subsequent alteration of the stored genetic message results in a mutation and might be the starting point of important health disorders. The question therefore is what causes DNA mutations? All living organisms are constantly exposed to a number of external agents such as free radicals and to radiation, which may lead to induced mutations. There are also mutations happening without invoking the action of any exogenous element, the so-called spontaneous mutations. The former can be partially controlled by avoiding exposure to high-risk environments, while the latter are more intriguing because their origin is unclear and difficult to determine. As noted by Watson and Crick when they first discovered the DNA structure, the correct replication of DNA rests on the assumption that the base pairs remain in their most stable, canonical form. However, protons along the interbase hydrogen-bond network are not static entities. They can in fact interchange their positions in DNA bases through proton transfer (PT) reactions before strands unwind, giving rise to noncanonical structures defined as rare tautomers. The importance of these rare tautomers was also cleverly anticipated by Watson and Crick and some years later claimed by Löwdin to be a source of spontaneous mutations. In Watson and Crick's words: "It would be of interest to know the precise difference in free energy between the various tautomeric forms under physiological conditions." Unfortunately, rare tautomeric forms are very difficult to detect, so no direct and accurate free energy measure has been discerned. In contrast, theoretical chemistry is making good progress toward the quantification of PT reactions in DNA and their biological consequences. This Account touches upon the theoretical studies devoted to appraising the importance of rare tautomers as promoters of spontaneous mutations. We focus in particular on the crucial role played by the biological environment on DNA stability. It has now been demonstrated that valuable macroscopic predictions require not only highly accurate theories but also refined chemical models. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations performed on short but complete DNA sequence fragments emerge in this context as the most adequate tools. In addition, these methods can be used to quantify the effect of different external agents on the PT tautomeric equilibria and, eventually, to conveniently handle them. This is the case for the possible alteration of the naturally observed mutation rate by exposure to intense electric fields. Theoretical predictions envision in this respect promising applications of ultrashort electric pulses in medicine to selectively modify the mutated/canonical ratio in DNA.

Coupling between hydrogen atoms transfer and stacking interaction in adenine-thymine/guanine-cytosine complexes: a theoretical study

Four different complexes of two base pairs, an adenine-thymine and a guanine-cytosine one, have been studied in order to understand the modifications induced by the staking interaction between the two base pairs on the hydrogen atoms transfers between the bases in either base pair. The inclusion of these two kinds of interactions allows us to clarify if some properties, as the mechanism of hydrogen transfer, is exclusively a local effect of a base pair or can be modified by a more long-range interaction between the base pairs. The results on these four complexes are compared with those of the monomeric systems, the A-T and G-C base pair, and with those of the A-T and G-C dimers. The specificity of each complex and of each hydrogen bond has been analyzed.

Tumour repopulation and the role of abortive division in squamous cell carcinomas during chemotherapy

OBJECTIVES

In head and neck cancers, tumour cell repopulation during chemotherapy is one reason for treatment failure. Some of the mechanisms responsible for this repopulation are cell recruitment and abortive division. Due to lack of quantitative data in the literature regarding these mechanisms, the aim of this study was to investigate the interplay between recruitment and abortive division during cisplatin chemotherapy and to quantify the impact of these mechanisms on tumour control.

MATERIALS AND METHODS

An in silico Monte Carlo tumour model was developed to simulate tumour behaviour during chemotherapy. The virtual tumour had the composition and kinetic properties of a biological tumour. Effect of cisplatin on cell cycle and repopulation mechanisms were simulated and interpreted.

RESULTS

Abortive division contributed to cell production within the tumour during chemotherapy. There was a strong relationship between recruitment and tumour growth due to abortive division. This observation was supported by the value of proliferative/stem ratio, which increased from 1.3 to 36, even when using small recruitment parameters.

CONCLUSIONS

While abortive division contributed towards tumour repopulation during chemotherapy, this mechanism could be controlled by daily doses of cisplatin. On the other hand, stem cells require an additional cytotoxic agent to overcome repopulation due to cell recruitment. Consequently, repopulation via abortive division during chemotherapy did not entail alterations in treatment schedule, nor dose escalation, to control the tumour.

Theoretical investigation of the coupling between hydrogen-atom transfer and stacking interaction in adenine-thymine dimers

Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.