Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations

The electric regulation mechanism of drug molecules intercalating with DNA

The insertion of small drug molecules into DNA can change its electrical properties, thereby controlling the probability of its electrical transmission. This characteristic has enabled its widespread application in molecular electronics. However, the current understanding of the intercalation properties and electronic transmission mechanisms is still not deep enough, which severely restricts its practical application. In this paper, the density functional theory and the non-equilibrium Green's function formula are combined to bind three different small drug molecules to the same sequence of DNA through intercalation, in order to discuss the impact of intercalation and molecular structure on the electrical properties of DNA. After inserting two MAR70 molecules, the conductivity decreased from 2.38×10-5 G0 to 3.37×10-7 G0 . Upon the insertion of Nogalamycin, the conductivity dropped to 2.01×10-5 G0, only slightly lower than that of bare B-DNA. However, when cyanomorpholinodoxorubicin was inserted, the conductivity was 2.65×10-6 G0. In our study, we observed some common characteristics. After intercalating with drug molecules, new energy levels were induced, altering the positions of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energy levels, resulting in a narrowed bandgap and consequently reduced conductivity of the complex. Furthermore, the conductivity was also related to the number of inserted drug molecules, fewer inserted molecules led to a decrease in conductivity. The results of this study indicate that embedding drug molecules can reduce or regulate the conductivity of DNA, providing new insights for its application in the field of nanoelectronics.

Interactions of a Novel Anthracycline with Oligonucleotide DNA and Cyclodextrins in an Aqueous Environment

Berubicin, a chemotherapy medication belonging to the class of anthracyclines, is simulated in double-stranded DNA sequences and cyclodextrins in an aqueous environment via full-atom molecular dynamics simulations on the time scale of microseconds. The drug is studied in both the neutral and protonated states so as to better comprehend the role of its charge in the formed complexes. The noncovalent berubicin-DNA and berubicin-cyclodextrin complexes are investigated in detail, paying special attention to their thermodynamic description by employing the double decoupling method, the solvent balance method, the weighted solvent accessible surface model, and the linear interaction energy method. A novel approach for extracting the desolvation thermodynamics of the binding process is also presented. Both the binding and desolvation Gibbs energies are decomposed into entropic and enthalpic contributions so as to elucidate the nature of complexation and its driving forces. Selected structural and geometrical properties of all the complexes, which are all stable, are analyzed. Both cyclodextrins under consideration are widely utilized for drug delivery purposes, and a comparative investigation between their bound states with berubicin is carried out.

Insights into the Degradation of Polymer-Drug Conjugates by an Overexpressed Enzyme in Cancer Cells

Intensive efforts have been made to provide better treatments to cancer patients. Currently, nanoparticle-based drug delivery systems have gained propulsion, as they can overcome the drawbacks of free drugs. However, drug stability inside the nanocapsule must be ensured to prevent burst release. To overcome this, drugs conjugated to amphiphilic copolymers, assembled into nanoparticles, can provide a sustained release if endogenously degraded. Thus, we have designed and assessed the drug release viability of polymer-drug conjugates by the human Carboxylesterase 2, for a targeted drug activation. We performed molecular dynamics simulations applying a quantum mechanics/molecular mechanics potential to study the degradation profiles of 30 designed conjugates, where six were predicted to be hydrolyzed by this enzyme. We further analyzed the enzyme-substrate environment to delve into what structural features may lead to successful hydrolysis. These findings contribute to the development of new medicines ensuring effective cancer treatments with fewer side effects.

UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA

UV-Resonance Raman (RR) spectroscopy is a valuable tool to study the binding of drugs to biomolecular receptors. The extraction of information at the molecular level from experimental RR spectra is made much easier and more complete thanks to the use of computational approaches, specifically tuned to deal with the complexity of the supramolecular system. In this paper, we propose a protocol to simulate RR spectra of complex systems at different levels of sophistication, by exploiting a quantum mechanics/molecular mechanics (QM/MM) approach. The approach is challenged to investigate RR spectra of a widely used chemotherapy drug, doxorubicin (DOX) intercalated into a DNA double strand. The computed results show good agreement with experimental data, thus confirming the reliability of the computational protocol.

Novel ABA block copolymers: preparation, temperature sensitivity, and drug release

A new PEGylated macroiniferter was prepared based on the polycondensation reaction of polyethylene oxide (PEO), methylene diphenyl diisocyanate (MDI), and 1,1,2,2-tetraphenyl-1,2-ethanediol (TPED). The macroiniferter consists of PEO end groups and readily reacts with acrylamides (such as N-isopropylacrylamide, NIPAM) and forms ABA block copolymers (PEO-PNIPAM-PEO). This approach of making amphiphilic ABA block copolymers is robust, versatile, and useful, particularly for the development of polymers for biomedical applications. The resulting amphiphilic PEO-PNIPAM-PEO block copolymers are also temperature sensitive, and their phase transition temperatures are close to human body temperature and therefore they have been applied as drug carriers for cancer treatment. Two PEO-PNIPAM-PEO polymers with different molecular weights were prepared and selected to make temperature-sensitive micelles. As a result of the biocompatibility of these micelles, cell viability tests proved that these micelles have low toxicity toward cancer cells. The resultant polymer micelles were then used as drug carriers to deliver the hydrophobic anticancer drug doxorubicin (DOX), and the results showed that they exhibit significantly higher cumulative drug release efficiency at higher temperatures. Moreover, after loading DOX into the micelles, cellular uptake experiments showed easy uptake and cell viability tests showed that DOX-loaded micelles possess a better therapeutic effect than free DOX at the same dose.

Molecular Dynamics Simulation of the Interaction between Graphene Oxide Quantum Dots and DNA Fragment

Due to their excellent physical properties, graphene oxide quantum dots (GOQDs) are widely used in various fields, especially biomedicine. However, due to the short study period, their biosafety and potential genotoxicity to human and animal cells are not well elucidated. In this study, the adsorption of GOQDs with different concentrations and oxidation degrees on DNA was investigated using a molecular dynamics simulation method. The toxicity to DNA depended on the interaction mechanism that GOQDs adsorbed on DNA fragments, especially in the minor groove of DNA. When the number of the adsorbed GOQDs in the minor groove of DNA is small, the GOQD inserts into the interior of the base pair. When there are more GOQDs in the minor groove of DNA, the base pairs at the adsorption sites of DNA unwind directly. This interaction way damaged the double helix structure of DNA seriously. We also compare the different functional groups of -1COOH. The results show that the interaction energy between 1COOH-GQD and DNA is stronger than that between 1OH-GQD and DNA. However, the damage to DNA is the opposite. These findings deepen our understanding of graphene nanotoxicity in general.

Molecular spectroscopic and molecular simulation studies on the interaction of oral contraceptive drug Ormeloxifene with CT-DNA

The interaction between oral contraceptive drug Ormeloxifene (ORM) and calf thymus DNA (CT-DNA) was studied using UV-Vis, fluorescence, circular dichroism (CD) and ¹H NMR spectral techniques under physiological buffer (pH 7.4). Competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, KI quenching studies, molecular docking and metadynamics simulation studies were also substantiated the spectroscopic results. ORM is found to binds in the minor groove of CT-DNA as evidenced by: (1) non-displacement of EB from EB/CT-DNA complex; (2) appreciable displacement of Hoechst 33258 from its CT-DNA complex; (3) slight alteration in the CD signal; (4) small shifts (Δδ < 0.033 ppm) without broadening in ¹H NMR signals and (5) the nearly equal extent of quenching of fluorescence of ORM by KI in the absence and presence of CT-DNA. Negative values of both enthalpy and entropy changes pointed out that the interaction between ORM and CT-DNA is governed mainly by H-bonding and van der Waals forces. Negative free energy change suggested a spontaneous interaction between ORM and CT-DNA. The free energy landscape of the binding process was computed using metadynamics simulation. The simulation study results disclosed that ORM binds to the minor groove of DNA through H-bonding and π-π stacking interactions. The results of molecular docking and simulation studies corroborate the available experimental data.

Evaluation of the Interaction of Cinacalcet with Calf Thymus dsDNA: Use of Electrochemical, Spectrofluorimetric, and Molecular Docking Methods

The binding of drugs to DNA plays a critical role in new drug discovery and is important for designing better drugs. In this study, the interaction and binding mode of calf-thymus double-stranded deoxyribonucleic acid (ct-dsDNA) with cinacalcet (CIN) from the calcimimetic drug that mimics the action of calcium on tissues group were investigated. The interaction of CIN with ct-dsDNA was observed by the differential pulse voltammetry (DPV) technique by following the decrease in electrochemical oxidation signals to deoxyguanosine and adenosine. A competitive study was performed on an indicator, methylene blue, to investigate the interaction of the drug with ct-dsDNA by fluorescence spectroscopy. Interaction studies have shown that the binding mode for the interaction of CIN with ct-dsDNA could be groove-binding. According to the results obtained, the binding constant values were found to be 6.30 × 10⁴ M⁻¹ and 3.16 × 10⁵ M⁻¹, respectively, at 25 °C as obtained from the cyclic voltammetry (CV) and spectroscopic techniques. Possible molecular interactions of CIN with dsDNA were explored via molecular docking experiments. The docked structure indicated that CIN could fit well into the minor groove of the DNA through H-bonding and π-π stacking contact with CIN.

Loading of DOX into a tetrahedral DNA nanostructure: the corner does matter

With the rapid development of nanotechnology, various DNA nanostructures have been synthesized and widely used in drug delivery. However, the underlying mechanisms of drug molecule loading into the DNA nanostructure are still elusive. In this work, we systematically investigate the interactions of a tetrahedral DNA nanostructure (TDN) with the anti-cancer drug doxorubicin (DOX) by combining molecular docking and all-atom molecular dynamics simulations. It is found that there are five possible binding modes in the single TDN-DOX interactions, namely the outside-corner mode, the inside-corner mode, the major-groove mode, the minor-groove mode, and the intercalation mode, where the van der Waals (VDW) interaction and the electrostatic (ELE) interaction dominate in the case of unionized DOX and ionized DOX, respectively. Moreover, with the increase of the DOX number, some of the interaction modes may disappear and the inside-corner mode is the most energy-favorable mode. The present study enhances the molecular understanding of the role of TDN as the drug carrier, which may provide a useful guideline for the future design of DNA nanostructures.

Role of intercalation in the electrical properties of nucleic acids for use in molecular electronics

Intercalating ds-DNA/RNA with small molecules can play an essential role in controlling the electron transmission probability for molecular electronics applications such as biosensors, single-molecule transistors, and data storage. However, its applications are limited due to a lack of understanding of the nature of intercalation and electron transport mechanisms. We addressed this long-standing problem by studying the effect of intercalation on both the molecular structure and charge transport along the nucleic acids using molecular dynamics simulations and first-principles calculations coupled with the Green's function method, respectively. The study on anthraquinone and anthraquinone-neomycin conjugate intercalation into short nucleic acids reveals some universal features: (1) the intercalation affects the transmission by two mechanisms: (a) inducing energy levels within the bandgap and (b) shifting the location of the Fermi energy with respect to the molecular orbitals of the nucleic acid, (2) the effect of intercalation was found to be dependent on the redox state of the intercalator: while oxidized anthraquinone decreases, reduced anthraquinone increases the conductance, and (3) the sequence of the intercalated nucleic acid further affects the transmission: lowering the AT-region length was found to enhance the electronic coupling of the intercalator with GC bases, hence yielding an increase of more than four times in conductance. We anticipate our study to inspire designing intercalator-nucleic acid complexes for potential use in molecular electronics via creating a multi-level gating effect.

Current research on circular RNAs and their potential clinical implications in breast cancer

Breast cancer (BC) is one of the most common cancers and the leading causes of death among women worldwide, and its morbidity rate is growing. Discovery of novel biomarkers is necessary for early BC detection, treatment, and prognostication. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs with covalently closed continuous loops, have been found to have a crucial role in tumorigenesis. Studies have demonstrated that circRNAs are aberrantly expressed in the tumor tissues and plasma of patients with BC, and they modulate gene expression affecting the proliferation, metastasis, and chemoresistance of BC by specifically binding and regulating the expression of microRNAs (miRNAs). Therefore, circRNAs can be used as novel potential diagnostic and prognostic markers, and therapeutic targets for BC. This article summarizes the properties, functions, and regulatory mechanisms of circRNAs, particularly current research on their association with BC proliferation, metastasis, and chemoresistance.

Unraveling the interaction between doxorubicin and DNA origami nanostructures for customizable chemotherapeutic drug release

Doxorubicin (DOX) is a common drug in cancer chemotherapy, and its high DNA-binding affinity can be harnessed in preparing DOX-loaded DNA nanostructures for targeted delivery and therapeutics. Although DOX has been widely studied, the existing literature of DOX-loaded DNA-carriers remains limited and incoherent. Here, based on an in-depth spectroscopic analysis, we characterize and optimize the DOX loading into different 2D and 3D scaffolded DNA origami nanostructures (DONs). In our experimental conditions, all DONs show similar DOX binding capacities (one DOX molecule per two to three base pairs), and the binding equilibrium is reached within seconds, remarkably faster than previously acknowledged. To characterize drug release profiles, DON degradation and DOX release from the complexes upon DNase I digestion was studied. For the employed DONs, the relative doses (DOX molecules released per unit time) may vary by two orders of magnitude depending on the DON superstructure. In addition, we identify DOX aggregation mechanisms and spectral changes linked to pH, magnesium, and DOX concentration. These features have been largely ignored in experimenting with DNA nanostructures, but are probably the major sources of the incoherence of the experimental results so far. Therefore, we believe this work can act as a guide to tailoring the release profiles and developing better drug delivery systems based on DNA-carriers.

LRP1-mediated pH-sensitive polymersomes facilitate combination therapy of glioblastoma in vitro and in vivo

BACKGROUND

Glioblastoma (GBM) is the most invasive primary intracranial tumor, and its effective treatment is one of the most daunting challenges in oncology. The blood-brain barrier (BBB) is the main obstacle that prevents the delivery of potentially active therapeutic compounds. In this study, a new type of pH-sensitive polymersomes has been designed for glioblastoma therapy to achieve a combination of radiotherapy and chemotherapy for U87-MG human glioblastoma xenografts in nude mice and significantly increased survival time.

RESULTS

The Au-DOX@PO-ANG has a good ability to cross the blood-brain barrier and target tumors. This delivery system has pH-sensitivity and the ability to respond to the tumor microenvironment. Gold nanoparticles and doxorubicin are designed as a complex drug. This type of complex drug improve the radiotherapy (RT) effect of glioblastoma. The mice treated with Au-DOX@PO-ANG NPs have a significant reduction in tumor volume.

CONCLUSION

In summary, a new pH-sensitive drug delivery system was fabricated for the treatment of glioblastoma. The new BBB-traversing drug delivery system potentially represents a novel approach to improve the effects of the treatment of intracranial tumors and provides hope for glioblastoma treatment.

Molecular Dynamics Study on the Binding of an Anticancer DNA G-Quadruplex Stabilizer, CX-5461, to Human Telomeric, c-KIT1, and c-Myc G-Quadruplexes and a DNA Duplex

DNA G-quadruplex (G4) stabilizer, CX-5461, is in phase I/II clinical trials for advanced cancers with BRCA1/2 deficiencies. A FRET-melting temperature increase assay measured the stabilizing effects of CX-5461 to a DNA duplex (∼10 K), and three G4 forming sequences negatively implicated in the cancers upon its binding: human telomeric (∼30 K), c-KIT1 (∼27 K), and c-Myc (∼25 K). Without experimentally solved structures of these CX-5461-G4 complexes, CX-5461's interactions remain elusive. In this study, we performed a total of 73.5 μs free ligand molecular dynamics binding simulations of CX-5461 to the DNA duplex and three G4s. Three binding modes (top, bottom, and side) were identified for each system and their thermodynamic, kinetic, and structural nature were deciphered. The molecular mechanics/Poisson Boltzmann surface area binding energies of CX-5461 were calculated for the human telomeric (-28.6 kcal/mol), c-KIT1 (-23.9 kcal/mol), c-Myc (-22.0 kcal/mol) G4s, and DNA duplex (-15.0 kcal/mol) systems. These energetic differences coupled with structural differences at the 3' site explained the different melting temperatures between the G4s, while CX-5461's lack of intercalation to the duplex explained the difference between the G4s and duplex. Based on the interaction insight, CX-5461 derivatives were designed and docked, showing higher selectivity to the G4s over the duplex.

Thermodynamic Dissection of the Intercalation Binding Process of Doxorubicin to dsDNA with Implications of Ionic and Solvent Effects

Doxorubicin (DOX) is a cancer drug that binds to dsDNA through intercalation. A comprehensive microsecond timescale molecular dynamics study is performed for DOX with 16 tetradecamer dsDNA sequences in explicit aqueous solvent, in order to investigate the intercalation process at both binding stages (conformational change and insertion binding stages). The molecular mechanics generalized Born surface area (MM-GBSA) method is adapted to quantify and break down the binding free energy (BFE) into its thermodynamic components, for a variety of different solution conditions as well as different DNA sequences. Our results show that the van der Waals interaction provides the largest contribution to the BFE at each stage of binding. The sequence selectivity depends mainly on the base pairs located downstream from the DOX intercalation site, with a preference for (AT)₂ or (TA)₂ driven by the favorable electrostatic and/or van der Waals interactions. Invoking the quartet sequence model proved to be most successful to predict the sequence selectivity. Our findings also indicate that the aqueous bathing solution (i.e., water and ions) opposes the formation of the DOX-DNA complex at every binding stage, thus implying that the complexation process preferably occurs at low ionic strength and is crucially dependent on solvent effects.

(2S,4R)-4-[18F]Fluoroglutamine as a PET Indicator for Bone Marrow Metabolism Dysfunctional: from Animal Experiments to Clinical Application

PURPOSE

Previous reports confirmed that (2S,4R)-4-[¹⁸F]Fluoroglutamine ([¹⁸F]GLN) accumulated in bone and bone marrow. This study investigates the potential of using [¹⁸F]GLN positron emission tomography (PET) to monitor changes of bone marrow activity after chemotherapy (myelosuppression).

PROCEDURES

Bone marrow inhibition model in mice was induced by an intravenous injection of chemotherapy drug (doxorubicin or rituximab) and the inhibition was confirmed by routine blood cell counts. Bone uptakes of these four radiotracers (2-deoxy-2-[¹⁸F]fluoro-D-glucose, [¹⁸F]GLN, 3'-dexoy-3'-[¹⁸F]fluorothymidine ([¹⁸F]FLT), and sodium [¹⁸F]fluoride) in the mice were measured after i.v. injection and dissection of femur and tibia, and the uptakes in bone-only (BO) and bone marrow (BM) were obtained after separating bone from bone marrow. Additionally, six volunteers were recruited and evaluated with [¹⁸F]GLN. The PET-/CT-guided volumes of interests (VOI) in cervical, thoracic, lumbar vertebra, and skull cortical bone were defined as bone marrow or bone for evaluation, respectively.

RESULTS

[¹⁸F]GLN showed a relatively high bone marrow uptake in mice (up to 9.5 ± 1.3 % ID/g) at 1 h after injection, which was 2.1 times that of [¹⁸F]FLT. The [¹⁸F]GLN uptakes in the bone marrow were substantially inhibited by chemotherapy drug. The decrease of [¹⁸F]GLN's bone marrow uptake was consistent with the reduction of white blood cells (myelosuppression). For [¹⁸F]GLN/PET imaging in humans, the SUV_mean value of bone marrow (1 h after i.v. injection) was between 3.1 and 3.6 in the healthy volunteers (n = 3), and between 1.8 and 2.2 (n = 3) (P < 0.001) in myelosuppression patients, showing a clear reduction of bone marrow uptake.

CONCLUSIONS

Dissection experiments in mice showed that [¹⁸F]GLN displayed relatively high bone marrow uptake, and the uptake was sensitive to bone marrow inhibition induced by doxorubicin/rituximab. The same conclusion was confirmed [¹⁸F]GLN/PET imaging in humans. Therefore, [¹⁸F]GLN/PET imaging may be a useful tool to assess reduction of bone marrow activity in cancer patients, who may be at risk of myelosuppression after chemotherapy.

TRIAL REGISTRATION

Approved by Institutional Review Board of Peking University Cancer Hospital (No. 2017KT38). Registered 18 August 2017.

Monitoring the Cellular Delivery of Doxorubicin-Cu Complexes in Cells by Fluorescence Lifetime Imaging Microscopy

In the prodrug research field, information obtained from traditional end point biochemical assays in drug effect studies could provide neither the dynamic processes nor heterogeneous responses of individual cells. In situ imaging microscopy techniques, especially fluorescence lifetime imaging microscopy (FLIM), could fulfill these requirements. In this work, we used FLIM techniques to observe the entry and release of doxorubicin (Dox)-Cu complexes in live KYSE150 cells. The Dox-Cu complex has weaker fluorescence signals but similar lifetime values as compared to the raw Dox, whose fluorescence could be released by the addition of biothiol compound (such as glutathione). The cell viability results indicated that the Dox-Cu compound has a satisfactory killing effect on KYSE150 cells. The FLIM data showed that free doxorubicin was released from Dox-Cu complexes in cytoplasm of KYSE150 cells and then accumulated in the nucleus. After 90 min administration, the fluorescence lifetime signals reached 1.21 and 1.46 ns in the cytoplasm and nucleus, respectively, reflecting the transformation and transportation of Dox-Cu complexes. In conclusion, this work provides a satisfactory example for the research of prodrug monitored by FLIM techniques, expanding the useful applications of FLIM technique in drug development.

Modified gaphene oxide (GO) particles in peptide hydrogels: a hybrid system enabling scheduled delivery of synergistic combinations of chemotherapeutics

The scheduled delivery of synergistic drug combinations is increasingly recognized as highly effective against advanced solid tumors. Of particular interest are composite systems that release a sequence of drugs with defined kinetics and molar ratios to enhance therapeutic effect, while minimizing the dose to patients. In this work, we developed a homogeneous composite comprising modified graphene oxide (GO) nanoparticles embedded in a Max8 peptide hydrogel, which provides controlled kinetics and molar ratios of release of doxorubicin (DOX) and gemcitabine (GEM). First, modified GO nanoparticles (tGO) were designed to afford high DOX loading and sustained release (18.9% over 72 h and 31.4% over 4 weeks). Molecular dynamics simulations were utilized to model the mechanism of DOX loading as a function of surface modification. In parallel, a Max8 hydrogel was developed to release GEM with faster kinetics and achieve a 10-fold molar ratio to DOX. The selected DOX/tGO nanoparticles were suspended in a GEM/Max8 hydrogel matrix, and the resulting composite was tested against a triple negative breast cancer cell line, MDA-MB-231. Notably, the composite formulation afforded a combination index of 0.093 ± 0.001, indicating a much stronger synergism compared to the DOX-GEM combination co-administered in solution (CI = 0.396 ± 0.034).

Binding of BRACO19 to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

Although BRACO19 is a potent G-quadruplex binder, its potential for clinical usage is hindered by its low selectivity towards DNA G-quadruplex over duplex. High-resolution structures of BRACO19 in complex with neither single-stranded telomeric DNA G-quadruplexes nor B-DNA duplex are available. In this study, the binding pathway of BRACO19 was probed by 27.5 µs molecular dynamics binding simulations with a free ligand (BRACO19) to a DNA duplex and three different topological folds of the human telomeric DNA G-quadruplex (parallel, anti-parallel and hybrid). The most stable binding modes were identified as end stacking and groove binding for the DNA G-quadruplexes and duplex, respectively. Among the three G-quadruplex topologies, the MM-GBSA binding energy analysis suggested that BRACO19′s binding to the parallel scaffold was most energetically favorable. The two lines of conflicting evidence plus our binding energy data suggest conformation-selection mechanism: the relative population shift of three scaffolds upon BRACO19 binding (i.e., an increase of population of parallel scaffold, a decrease of populations of antiparallel and/or hybrid scaffold). This hypothesis appears to be consistent with the fact that BRACO19 was specifically designed based on the structural requirements of the parallel scaffold and has since proven effective against a variety of cancer cell lines as well as toward a number of scaffolds. In addition, this binding mode is only slightly more favorable than BRACO19s binding to the duplex, explaining the low binding selectivity of BRACO19 to G-quadruplexes over duplex DNA. Our detailed analysis suggests that BRACO19′s groove binding mode may not be stable enough to maintain a prolonged binding event and that the groove binding mode may function as an intermediate state preceding a more energetically favorable end stacking pose; base flipping played an important role in enhancing binding interactions, an integral feature of an induced fit binding mechanism.

Molecular mechanism and binding free energy of doxorubicin intercalation in DNA

The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive MD simulations. Many molecular factors that control the binding affinity of DOX to DNA to form a stable complex are inspected and quantified by employing continuum solvation models for estimating the binding free energy. The modified MM-PB(GB)SA methodology provides a complete energetic profile of ΔGele, ΔGvDW, ΔGpolar, ΔGnon-polar, TΔStotal, ΔGdeform, ΔGcon, and ΔGion. To identify the sequence specificity of DOX, two different DNA sequences, d(CGATCG) or DNA1 and d(CGTACG) or DNA2, with one molecule (1 : 1 complex) or two molecule (2 : 1 complex) configurations of DOX were selected in this study. Our results show that the DNA deformation energy (ΔGdeform), the energy cost from translational and rotational entropic contributions (TΔStran+rot), the total electrostatic interactions (ΔGpolar-PB/GB + ΔGele) of incorporation, the intramolecular electrostatic interactions (ΔGele) and electrostatic polar solvation interactions (ΔGpolar-PB/GB) are all unfavorable to the binding of DOX to DNA. However, they are overcome by at least five favorable interactions: the van der Waals interactions (ΔGvDW), the non-polar solvation interaction (ΔGnon-polar), the vibrational entropic contribution (TΔSvib), and the standard concentration dependent free energies of DOX (ΔGcon) and the ionic solution (ΔGion). Specifically, the van der Waals interaction appears to be the major driving force to form a stable DOX-DNA complex. We also predict that DOX has stronger binding to DNA1 than DNA2. The DNA deformation penalty and entropy cost in the 2 : 1 complex are less than those in the 1 : 1 complex, thus they indicate that the 2 : 1 complex is more stable than the 1 : 1 complex. We have calculated the total binding free energy (BFE) (ΔGt-sim) using both MM-PBSA and MM-GBSA methods, which suggests a more stable DOX-DNA complex at lower ionic concentration. The calculated BFE from the modified MM-GBSA method for DOX-DNA1 and DOX-DNA2 in the 1 : 1 complex is -9.1 and -5.1 kcal mol-1 respectively. The same quantities from the modified MM-PBSA method are -12.74 and -8.35 kcal mol-1 respectively. The value of the total BFE ΔGt-sim in the 1 : 1 complex is in reasonable agreement with the experimental value of -7.7 ± 0.3 kcal mol-1.

Fluorescence correlation spectroscopy for multiple-site equilibrium binding: a case of doxorubicin–DNA interaction

Quantification of multiple equilibrium binding on the example of doxorubicin–DNA interaction using fluorescence correlation spectroscopy.

2-Bromopalmitate sensitizes osteosarcoma cells to adriamycin-induced apoptosis via the modulation of CHOP

Osteosarcoma is the most common primary malignant bone tumour, but the survival rate of patients has plateaued since the mid-1980s. Adriamycin is an integral component of the current first-line chemotherapies used for osteosarcoma, but dose-dependent severe side effects often limit its clinical application. Here, we propose a potential combination regimen in which adriamycin plus 2-bromopalmitate, a palmitoylation inhibitor, exhibited powerful therapeutic effects on osteosarcoma. First, 2-bromopalmitate strongly increased the proliferation inhibition of adriamycin in both human osteosarcoma cell lines and primary osteosarcoma cells. Adriamycin-induced apoptosis in osteosarcoma cells was enhanced when synergized with 2-bromopalmitate. Our study indicated that the reactive oxygen species scavenger NAC and GSH could largely reverse the apoptosis induced by adriamycin combined with 2-bromopalmitate, demonstrating that reactive oxygen species played an essential role in this combination therapy. Moreover, CHOP was remarkably elevated in the combination group, and silencing of CHOP almost completely blocked the apoptosis induced by the combination of 2-bromopalmitate and adriamycin. Taken together, our study provides a prospective therapeutic strategy to eliminate osteosarcoma, which is propitious to clinical combination therapy development.

Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex-Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

A promising anticancer therapeutic strategy is the stabilization of telomeric G-quadruplexes using G-quadruplex-binding small molecules. Although many G-quadruplex-specific ligands have been developed, their low potency and selectivity to G-quadruplexes over duplex remains unsolved. Recently, a crystal structure of a telomeric 3' quadruplex-duplex hybrid was reported and the quadruplex-duplex interface was suggested to a good target to address the issues. However, there are no high-resolution complex structures reported for G-quadruplex ligands except for a docked BSU6037. In this study, molecular dynamic (MD) binding simulations with a free ligand were used to study binding poses and dynamics of four representative ligands: telomestatin, TMPyP4, BSU6037, and BRACO19. The MD data showed that BSU6037 was able to fully intercalate into the interface whereas TMPyP4 and BRACO19 could only maintain partial intercalation into the interface and telomestatin only binds at the quadruplex and duplex ends. Both linear ligands, BSU6037 and BRACO19, were able to interact with the interface, yet they were not selective over duplex DNA. The DNA geometry, binding modes, and binding pathways were systematically characterized, and the binding energy was calculated and compared for each system. The interaction of the ligands to the interface was by the means of an induced-fit binding mechanism rather than a lock-key mechanism, consisting of the DNA unfolding at the interface to allow entrance of the drug and then the refolding and repacking of the DNA and the ligand to further stabilize the G-quadruplex. On the basis of the findings in this study, modifications were suggested to optimize the interface binding for TMPyp4 and telomestatin.

Nanomaterial-Based Organelles Protect Normal Cells against Chemotherapy-Induced Cytotoxicity

Chemotherapy-induced cytotoxicity in normal cells and organs triggers undesired lesions. Although targeted delivery is used extensively, more than half of the chemotherapy dose still concentrates in normal tissues, especially in the liver. Enabling normal cells or organs to defend against cytotoxicity represents an alternative method for improving chemotherapy. Herein, rationally designed nanomaterials are used as artificial organelles to remove unexpected cytotoxicity in normal cells. Nanocomposites of gold-oligonucleotides (Au-ODN) can capture intracytoplasmic doxorubicin (DOX), a standard chemotherapy drug, blocking the drug's access into the cell nucleus. Cells with implanted Au-ODN are more robust since their viability is maintained during DOX treatment. In vivo experiments confirm that the Au-ODN nanomaterials selectively concentrate in hepatocytes and eliminate DOX-induced hepatotoxicity, increasing the cell's capacity to resist the threatening chemotherapeutic milieu. The finding suggests that introducing functional materials as biological devices into living systems may be a new strategy for improving the regulation of cell fate in more complex conditions and for manufacturing super cells.

Thermosensitive Injectable Hydrogel for Simultaneous Intraperitoneal Delivery of Doxorubicin and Prevention of Peritoneal Adhesion

To improve intraperitoneal chemotherapy and to prevent postsurgical peritoneal adhesion, we aimed to develop a drug delivery strategy for controlled release of a chemotherapeutic drug from the intraperitoneally injected thermosensitive poly(N-isopropylacrylamide)-based hydrogel (HACPN), which is also endowed with peritoneal anti-adhesion properties. Anticancer drug doxorubicin (DOX) was loaded into the hydrogel (HACPN-DOX) to investigate the chemotherapeutic and adhesion barrier effects in vivo. A burst release followed by sustained release of DOX from HACPN-DOX was found due to gradual degradation of the hydrogel. Cell culture studies demonstrated the cytotoxicity of released DOX toward CT-26 mouse colon carcinoma cells in vitro. Using peritoneal carcinomatosis animal model in BALB/c mice with intraperitoneally injected CT-26 cells, animals treated with HACPN-DOX revealed the best antitumor efficacy judging from tumor weight and volume, survival rate, and bioluminescence signal intensity when compared with treatment with free DOX at the same drug dosage. HACPN (or HACPN-DOX) also significantly reduced the risk of postoperative peritoneal adhesion, which was generated by sidewall defect-cecum abrasion in tumor-bearing BALB/c mice, from gross and histology analyses. This study could create a paradigm to combine controlled drug release with barrier function in a single drug-loaded injectable hydrogel to enhance the intraperitoneal chemotherapeutic efficacy while simultaneously preventing postsurgical adhesion.

Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent

RHPS4, a potent binder to human telomeric DNA G-quadruplex, shows high efficacy in tumor cell growth inhibition. However, it's preferential binding to DNA G-quadruplex over DNA duplex (about 10 fold) remains to be improved toward its clinical application. A high resolution structure of the single-stranded telomeric DNA G-quadruplexes, or B-DNA duplex, in complex with RHPS4 is not available yet, and the binding nature of this ligand to these DNA forms remains to be elusive. In this study, we carried out 40 μs molecular dynamics binding simulations with a free ligand to decipher the binding pathway of RHPS4 to a DNA duplex and three G-quadruplex folders (parallel, antiparallel and hybrid) of the human telomeric DNA sequence. The most stable binding mode identified for the duplex, parallel, antiparallel and hybrid G-quadruplexes is an intercalation, bottom stacking, top intercalation and bottom intercalation mode, respectively. The intercalation mode with similar binding strength to both the duplex and the G-quadruplexes, explains the lack of binding selectivity of RHPS4 to the G-quadruplex form. Therefore, a ligand modification that destabilizes the duplex intercalation mode but stabilizes the G-quadruplex intercalation mode will improve the binding selectivity toward G-quadruplex. The intercalation mode of RHPS4 to both the duplex and the antiparallel and the hybrid G-quadruplex follows a base flipping-insertion mechanism rather than an open-insertion mechanism. The groove binding, the side binding and the intercalation with flipping out of base were observed to be intermediate states before the full intercalation state with paired bases.

Probing the Binding Pathway of BRACO19 to a Parallel-Stranded Human Telomeric G-Quadruplex Using Molecular Dynamics Binding Simulation with AMBER DNA OL15 and Ligand GAFF2 Force Fields

Human telomeric DNA G-quadruplex has been identified as a good therapeutic target in cancer treatment. G-quadruplex-specific ligands that stabilize the G-quadruplex have great potential to be developed as anticancer agents. Two crystal structures (an apo form of parallel stranded human telomeric G-quadruplex and its holo form in complex with BRACO19, a potent G-quadruplex ligand) have been solved, yet the binding mechanism and pathway remain elusive. In this study, we simulated the binding of a free BRACO19 molecule to the apo form of the G-quadruplex using the latest AMBER DNA (OL15) and ligand (GAFF2) force fields. Three binding modes have been identified: top stacking, bottom intercalation, and groove binding. Bottom intercalation (51% of the population) resembles the bottom binding pose in the complex crystal structure very well. The groove binding mode is less stable than the bottom binding mode and is likely to be an intermediate state leading to the bottom binding mode. A flip-insertion mechanism was observed in the bottom intercalation mode, during which flipping of the bases outward makes space for ligand insertion, after which the bases flip back to increase the stability of the complex. In addition to reproducing the base-flipping behavior for some loop residues upon ligand binding, the direct alignment type of the ATAT-tetrad was observed in our simulations for the first time. These successes provide initial support for using this combination of the OL15 and GAFF2 force fields to study quadruplex-ligand interactions.

Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands

DNA G-quadruplex structures are emerging cancer-specific targets for chemotherapeutics. Ligands that bind to and stabilize DNA G-quadruplexes have the potential to be anti-cancer drugs. Lack of binding selectivity to DNA G-quadruplex over DNA duplex remains a major challenge when attempting to develop G-quadruplex ligands into successful anti-cancer drugs. Thorough understanding of the binding nature of existing non-selective ligands that bind to both DNA quadruplex and DNA duplex will help to address this challenge. Daunomycin and doxorubicin, two commonly used anticancer drugs, are examples of non-selective DNA ligands. In this study, we extended our early all-atom binding simulation studies between doxorubicin and a DNA duplex (d(CGATCG)₂) to probe the binding between daunomycin and a parallel DNA quadruplex (d(TGGGGT)₄) and DNA duplex. In addition to the end stacking mode, which mimics the mode in the crystal structure, a pure groove binding mode was observed in our free binding simulations. The dynamic and energetic properties of these two binding modes are thoroughly examined, and a detailed comparison is made between DNA quadruplex binding modes and DNA duplex binding modes. Implications on the design of more selective DNA quadruplex ligands are also discussed. Graphical abstract Top stacking and groov binding modes from the MD simulations.

The Role of the DNA Backbone in Minor-Groove Ligand Binding

Molecular recognition between ligands and nucleic acids plays a key role in therapeutic activity. Some molecules interact with DNA in a nonbonded manner through intercalation or through the DNA grooves. The recognition of minor-groove binders is attributed to a set of hydrogen-bonding interactions between the binders and the hydrogen-bond-acceptor groups on the groove floor and walls. It is commonly considered that interactions with the sugar groups of the DNA backbone are insignificant and do not contribute to the binding affinity or the specificity. However, our group has found that the deoxyribose rings have a central function in the recognition and the intercalation of metal complexes into DNA. Herein, we determined the specific interactions between the binder CGP 40215A and the minor-groove atoms, based on the local properties of electron density. We found that specific interactions between the deoxyribose moiety within the backbone of DNA and the binder are essential for molecular recognition, and they are responsible for one third of the interaction energy.

Angiopep-2-conjugated poly(ethylene glycol)-co- poly(ε-caprolactone) polymersomes for dual-targeting drug delivery to glioma in rats

The blood–brain barrier is a formidable obstacle for glioma chemotherapy due to its compact structure and drug efflux ability. In this study, a dual-targeting drug delivery system involving Angiopep-2-conjugated biodegradable polymersomes loaded with doxorubicin (Ang-PS-DOX) was developed to exploit transport by the low-density lipoprotein receptor-related protein 1 (LRP1), which is overexpressed in both blood–brain barrier and glioma cells. The polymersomes (PS) were prepared using a thin-film hydration method. The PS were loaded with doxorubicin using the pH gradient method (Ang-PS-DOX). The resulting PS were uniformly spherical, with diameters of ~135 nm and with ~159.9 Angiopep-2 molecules on the surface of each PS. The drug-loading capacity and the encapsulation efficiency for doxorubicin were 7.94%±0.17% and 95.0%±1.6%, respectively. Permeability tests demonstrated that the proton diffusion coefficient across the PS membrane was far slower than that across the liposome membrane, and the common logarithm value was linearly dependent on the dioxane content in the external phase. Compared with PS-DOX, Ang-PS-DOX demonstrated significantly higher cellular uptake and stronger cytotoxicity in C6 cells. In vivo pharmacokinetics and brain distribution experiments revealed that Ang-PS-DOX achieved a more extensive distribution and more abundant accumulation in glioma cells than PS-DOX. Moreover, the survival time of glioma-bearing rats treated with Ang-PS-DOX was significantly prolonged compared with those treated with PS-DOX or a solution of free doxorubicin. These results suggested that Ang-PS-DOX can target glioma cells and enhance chemotherapeutic efficacy.

DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes

Extensive molecular-dynamics (MD) simulations have been used to investigate DNA-dye and DNA-photosensitizer conjugates, which act as reactants in templated reactions leading to the generation of fluorescent products in the presence of specific desoxyribonucleic acid sequences (targets). Such reactions are potentially suitable for detecting target nucleic acids in live cells by fluorescence microscopy or flow cytometry. The simulations show how the attached dyes/photosensitizers influence DNA structure and reveal the relative orientations of the chromophores with respect to each other. Our results will help to optimize the reactants for the templated reactions, especially length and structure of the spacers used to link reporter dyes or photosensitizers to the oligonucleotides responsible for target recognition. Furthermore, we demonstrate that the structural ensembles obtained from the simulations can be used to calculate steady-state UV-vis absorption and emission spectra. We also show how important quantities describing the quenching of the reporter dye via fluorescence resonance energy transfer (FRET) can be calculated from the simulation data, and we compare these for different relative chromophore geometries.

Investigating the impacts of DNA binding mode and sequence on thermodynamic quantities and water exchange values for two small molecule drugs

Doxorubicin and nogalamycin are antitumor antibiotics that interact with DNA via intercalation and threading mechanisms, respectively. Because the importance of water, particularly its impact on entropy changes, has been established in other biological processes, we investigated the role of water in these two drug-DNA binding events. We used the osmotic stress method to calculate the number of water molecules exchanged (Δnwater), and isothermal titration calorimetry to measure Kbinding, ΔH, and ΔS for two synthetic DNAs, poly(dA·dT) and poly(dG·dC), and calf thymus DNA (CT DNA). For nogalamycin, Δnwater<0 for CT DNA and poly(dG·dC). For doxorubicin, Δnwater>0 for CT DNA and Δnwater<0 for poly(dG·dC). For poly(dA·dT), Δnwater~0 with both drugs. Net enthalpy changes were always negative, but net entropy changes depended on the drug. The effect of water exchange on the overall sign of entropy change appears to be smaller than other contributions.

Chemo/Photoacoustic Dual Therapy with mRNA-Triggered DOX Release and Photoinduced Shockwave Based on a DNA-Gold Nanoplatform

A multifunctional nanoparticle based on gold nanorod (GNR), utilizing mRNA triggered chemo-drug release and near-infrared photoacoustic effect, is developed for a combined chemo-photoacoustic therapy. The constructed nanoparticle (GNR-DNA/FA:DOX) comprises three functional components: (i) GNR as the drug delivery platform and photoacoustic effect enhancer; (ii) toehold-possessed DNA dressed on the GNR to load doxorubicin (DOX) to implement a tumor cell specific chemotherapy; and (iii) folate acid (FA) modified on GNR to guide the nanoparticle to target tumor cells. The results show that, upon an effective and specific delivery of the nanoparticles to the tumor cells with overexpressed folate receptors, the cytotoxic DOX loaded on the GNR-DNA nanoplatform can be released through DNA displacement reaction in melanoma-associated antigen gene mRNA expressed cells. With 808 nm pulse laser irradiation, the photoacoustic effect of the GNR leads to a direct physical damage to the cells. The combined treatment of the two modalities can effectively destroy tumor cells and eradicate the tumors with two distinctively different and supplementing mechanisms. With the nanoparticle, photoacoustic imaging is successfully performed in situ to monitor the drug distribution and tumor morphology for therapeutical guidance. With further in-depth investigation, the proposed nanoparticle may provide an effective and safe alternative cancer treatment modality.

On-demand drug delivery from local depots

Stimuli-responsive polymeric depots capable of on-demand release of therapeutics promise a substantial improvement in the treatment of many local diseases. These systems have the advantage of controlling local dosing so that payload is released at a time and with a dose chosen by a physician or patient, and the dose can be varied as disease progresses or healing occurs. Macroscale drug depot can be induced to release therapeutics through the action of physical stimuli such as ultrasound, electric and magnetic fields and light as well as through the addition of pharmacological stimuli such as nucleic acids and small molecules. In this review, we highlight recent advances in the development of polymeric systems engineered for releasing therapeutic molecules through physical and pharmacological stimulation.

Drug-carrier interaction analysis in the cell penetrating peptide-modified liposomes for doxorubicin loading

Doxorubicin (DOX) is widely used as an antitumor model drug in liposomes because of its high encapsulation efficiency. The cell-penetrating peptide (CPP) has potential applications in drug delivery systems. However, we discovered that the encapsulation efficiency of DOX decreased with increasing modification density of CPP on liposomes. To explore the interaction mechanisms of CPP-modified liposomes (CPPL) for DOX loading, X-ray diffraction, Fourier transform infrared spectroscopy and Raman spectroscopy were utilised, and theoretical calculations based on molecular dynamics simulation were performed. Results showed that the monomeric intermolecular interaction between CPP and DOX, in which the guanidinium group of CPP was parallel to the planar aromatic chromophore of DOX, depending on the cation-pi interaction and hydrogen bonds, weakened the tendency of DOX transporting into the internal medium from the liposomal external medium. Analysis of the interaction between CPP and DOX at the molecular level provided theoretical guidance for the further development of CPPL.

Intercalation processes of copper complexes in DNA

The family of anticancer complexes that include the transition metal copper known as Casiopeínas® shows promising results. Two of these complexes are currently in clinical trials. The interaction of these compounds with DNA has been observed experimentally and several hypotheses regarding the mechanism of action have been developed, and these include the generation of reactive oxygen species, phosphate hydrolysis and/or base-pair intercalation. To advance in the understanding on how these ligands interact with DNA, we present a molecular dynamics study of 21 Casiopeínas with a DNA dodecamer using 10 μs of simulation time for each compound. All the complexes were manually inserted into the minor groove as the starting point of the simulations. The binding energy of each complex and the observed representative type of interaction between the ligand and the DNA is reported. With this extended sampling time, we found that four of the compounds spontaneously flipped open a base pair and moved inside the resulting cavity and four compounds formed stacking interactions with the terminal base pairs. The complexes that formed the intercalation pocket led to more stable interactions.

Probing the relationship between anti-Pneumocystis carinii activity and DNA binding of bisamidines by molecular dynamics simulations

The anti-Pneumocystis carinii activity of 13 synthetic pentamidine analogs was analyzed. The experimental differences in melting points of DNA dodecamer 5'-(CGCGAATTCGCG)₂-3' complexes (ΔT_m), and in the biological activity measured using ATP bioluminescence assay (IC₅₀) together with the theoretical free energy of DNA-ligand binding estimated by the proposed computational protocol, showed that the experimental activity of the tested pentamidines appeared to be due to the binding to the DNA minor groove with extended AT sequences. The effect of heteroatoms in the aliphatic linker, and the sulfonamide or methoxy substituents on the compound inducing changes in the interactions with the DNA minor groove was examined and was correlated with biological activity. In computational analysis, the explicit solvent approximation with the discrete water molecules was taken into account, and the role of water molecules in the DNA-ligand complexes was defined.

The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes

Among all tools available to design new drugs, molecular dynamics (MD) simulations have become an essential technique. Initially developed to investigate molecular models with a limited number of atoms, computers now enable investigations of large macromolecular systems with a simulation time reaching the microsecond range. The reviewed articles cover four years of research to give an overview on the actual impact of MD on the current medicinal chemistry landscape with a particular emphasis on studies of ligand-protein interactions. With a special focus on studies combining computational approaches with data gained from other techniques, this review shows how deeply embedded MD simulations are in drug design strategies and articulates what the future of this technique could be.

Raman micro spectroscopy for in vitro drug screening: subcellular localisation and interactions of doxorubicin

Raman spectroscopy is used for the localization and tracking of chemotherapeutic drug, doxorubicin, in the intracellular environment of lung cancer cell line. Results show the potential of the technique to monitor the mechanisms of action and response on a molecular level, with subcellular resolution.