Understanding The Role of Reline, a Natural DES, on Temperature-Induced Conformational Changes of C-Kit G-Quadruplex DNA: A Molecular Dynamics Study

DNA nanotechnology in ionic liquids and deep eutectic solvents

Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.

Investigating Biomolecules in Deep Eutectic Solvents with Molecular Dynamics Simulations: Current State, Challenges and Future Perspectives

Deep eutectic solvents (DESs) have recently gained increased attention for their potential in biotechnological applications. DESs are binary mixtures often consisting of a hydrogen bond acceptor and a hydrogen bond donor, which allows for tailoring their properties for particular applications. If produced from sustainable resources, they can provide a greener alternative to many traditional organic solvents for usage in various applications (e.g., as reaction environment, crystallization agent, or storage medium). To navigate this large design space, it is crucial to comprehend the behavior of biomolecules (e.g., enzymes, proteins, cofactors, and DNA) in DESs and the impact of their individual components. Molecular dynamics (MD) simulations offer a powerful tool for understanding thermodynamic and transport processes at the atomic level and offer insights into their fundamental phenomena, which may not be accessible through experiments. While the experimental investigation of DESs for various biotechnological applications is well progressed, a thorough investigation of biomolecules in DESs via MD simulations has only gained popularity in recent years. Within this work, we aim to provide an overview of the current state of modeling biomolecules with MD simulations in DESs and discuss future directions with a focus for optimizing the molecular simulations and increasing our fundamental knowledge.

Local and cooperative structural transitions of double-stranded DNA in choline-based deep eutectic solvents

The possibility of using deep eutectic solvents (DESs) as co-solvents for stabilizing and preserving the native structure of DNA provides an attractive opportunity in the field of DNA biotechnology. The rationale of this work is a systematic investigation of the effect of hydrated choline-based DES on the structural stability of a 30-base-pair double-stranded DNA model via a combination of spectroscopic experiments and MD simulations. UV absorption and CD experiments provide evidence of a significant contribution of DESs to the stabilization of the double-stranded canonical (B-form) DNA structure. Multi-wavelength synchrotron UV Resonance Raman (UVRR) measurements indicate that the hydration shell of adenine-thymine pairs is strongly perturbed in the presence of DESs and that the preferential interaction between H-bond sites of guanine residues and DESs is significantly involved in the stabilization of the dsDNA. Finally, MD calculations show that the minor groove of DNA is significantly selective for the choline part of the investigated DESs compared to the major groove. This finding is likely to have a significant impact not only in terms of thermal stability but also in the modulation of ligand-DNA interactions.

Influence of Protonation on the Norepinephrine Inhibiting α-Synuclein 71-82 Oligomerization

The pathogenesis of Parkinson's disease (PD) is closely linked to the massive presence of Lewy vesicles and Lewy axons in the cytoplasm of neurons, mainly consisting of α-synuclein (αS). Norepinephrine (NE), whose secretion can be increased by exercise, has been demonstrated to prevent the fibrillation of αS and to break down the mature αS fibrils. In this work, we focus on the influence of protonation on the inhibitory ability of NE by using amyloid core fragment αS71-82 as a template. All-atom replica-exchange molecular dynamics simulations (accumulating to 33.6 μs) in explicit water were performed to explore the inhibitory effect of protonated and nonprotonated NE on αS oligomerization. Our results show that NE/NE+ can lead to a significant decrease in β-sheet content with increasing temperature, while isolated αS maintains relatively higher β-sheet conformations until 363 K, implying that both NE and NE+ can lower the critical temperature required for αS fibril decomposition. NE and NE+ also lead to the formation of less compact αS oligomers by preventing the backbone hydrogen bonds and the side-chain packing. The protonation would affect the binding affinity, interaction modes, and binding intensity of NE with αS. Interesting, NE and NE+ have a distinct binding free energy in the electrostatic and solvation terms, which mostly counter each other and produce a weak binding intensity with αS. Our work contributes to a better understanding of the inhibitory mechanism of NE and NE+ on αS oligomerization relevant to PD pathogenesis, which may provide clues for the design of antiamyloid medicine.

In silico design and identification of new peptides for mitigating hIAPP aggregation in type 2 diabetes

The aberrant misfolding and self-aggregation of human islet amyloid polypeptide (hIAPP or amylin) into cytotoxic aggregates are implicated in the pathogenesis of type 2 diabetes (T2D). Among various inhibitors, short peptides derived from the amyloidogenic regions of hIAPP have been employed as hIAPP aggregation inhibitors due to their low immunogenicity, biocompatibility, and high chemical diversity. Recently, hIAPP fragment HSSNN18-22 was identified as an amyloidogenic sequence and displayed higher antiproliferative activity to RIN-5F cells. Various hIAPP aggregation inhibitors have been designed by chemical modifications of the highly amyloidogenic sequence (NFGAIL) of hIAPP. In this work, a library of pentapeptides based on fragment HSSNN18-22 was designed and assessed for their efficacy in blocking hIAPP aggregation using an integrated computational screening approach. The binding free energy calculations by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method identified HSSQN and HSSNQ that bind to hIAPP monomer with a binding affinity of -21.25 ± 4.90 and -19.73 ± 3.10 kcal/mol, respectively, which is notably higher as compared to HSSNN (-11.90 ± 4.12 kcal/mol). The sampling of the non aggregation-prone helical conformation was notably increased from 23.5 ± 3.0 in the hIAPP monomer to 38.1 ± 3.6, and 33.8 ± 3.0% on the incorporation of HSSQN, and HSSNQ, respectively, which indicate reduced aggregation propensity of hIAPP monomer. The pentapeptides, HSSQN and HSSNQ, identified as hIAPP aggregation inhibitors in this work can be further conjugated with various metal chelating peptides to yield more efficacious and clinically relevant multifunctional modulators for targeting various pathological hallmarks of T2D.

Exploring the Curvature-Dependence of Boron Nitride Nanoparticles on the Inhibition of hIAPP Aggregation

Nanoparticles, particularly carbon nanoparticles, have gathered significant interest in the field of anti-aggregation research. However, due to their cytotoxicity, the exploration of biocompatible nanoparticles has become a new frontier in the quest for drugs against human amyloid diseases. The application of non-cytotoxic and biocompatible boron nitride (BN) nanoparticles against amyloid aggregation has been probed to tackle this issue. BN nanoparticles displayed inhibitory activity against the aggregation of Aβ and α-syn peptides. In this work, the effect of BN nanoparticles on the dimerization of hIAPP, which is associated with the pathogenesis of type 2 diabetes, is studied. BN nanoparticles prevent the misfolding of hIAPP into β-sheet-rich aggregates. On varying the curvature, the nanoparticles display variation in the interaction preference with hIAPP. Interestingly, as the hydrophobicity of the nanoparticles increases from (5,5) BN nanotube to BN nanosheet, the interaction propensity shifts from N-terminal to the amyloid prone C-terminal of hIAPP. The hydrophobic and aromatic stacking interactions are a contributing factor toward the binding between hIAPP and BN. Due to this, the flat surface of the nanosheet shows better interaction potential toward hIAPP, compared to the nanotubes. Further, the nanoparticles can also disassemble preformed hIAPP fibrils, and the effect is more pronounced for (5,5) nanotube and the nanosheet. This study provides insight into the inhibitory mechanism of hIAPP aggregation by boron nitride nanoparticles and also an understanding of the significance of the curvature of nanoparticles in their interaction with amyloid peptides, which is valuable for the design of antiamyloid drugs.

Insights on choline chloride-based deep eutectic solvent (reline) + primary alcohol mixtures: a molecular dynamics simulation study

Deep eutectic solvents (DESs) emerged as green solvents for new generation technologies owing to their high chemical and thermal stability. Addition of restricted amount of organic solvents into the DESs plays a significant role in the improvement of thermodynamic and the transport properties to work as a potential solvent in process industries. In this paper, molecular dynamics (MD) simulations were performed to understand the thermophysical and transport properties of choline chloride-based DES (reline) and primary alcohol (methanol and ethanol) mixture in relation to microscopic structure. Density, radial distribution function, coordination number, average number of H-bond, diffusion coefficient and spatial distribution function was calculated in order to understand the structure and involvement of H-bond network at an atomic level. H-bond and spatial distribution function analyses revealed that the chloride ion prefers to be spatially distributed around hydroxyl group of alcohol and found to be more pronounced upon increase in alcohol concentration. As a consequence, it was observed that the H-bonds between Cl^- and urea decreases overall with the loading of alcohol and effect is more pronounced beyond a concentration of 0.4. Self-diffusion values for choline, Cl^- and urea were found to be increased significantly upon increase in concentration of alcohol from 0.6 to 0.8. Overall, our simulation points to the interplay and interactions between the chloride ions and the solvents in determining the structural and transport properties of choline chloride-based DES.

Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives

Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications, such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand, which demands the development of new DESs with improved properties. To do so requires an understanding of the fundamental relationship between the structure and properties of DESs. Computer simulation and machine learning techniques provide a fruitful approach as they can predict and reveal physical mechanisms and readily be linked to experiments. This review is devoted to the computational research of DESs and describes technical features of DES simulations and the corresponding perspectives on various DES applications. The aim is to demonstrate the current frontiers of computational research of DESs and discuss future perspectives.

Theoretical investigation of conformational deviation of the human parallel telomeric G-quadruplex DNA in the presence of different salt concentrations and temperatures under confinement

Various experimental reports address the stability of G-quadruplex DNA inside a close confinement such as α-hemolysin, nanocavity water pool and different metal-organic-frameworks (MOFs). To understand the conformational change of G-quadruplex DNA at the atomistic level, we have carried out a total of 40 μs simulation run under both non-polar and polar confinement conditions. To investigate the dynamics, we have considered two different KCl salt concentrations, i.e., 0.47 M (minimal salt concentration) and higher than 2 M (higher salt concentration), at two distinct temperatures, 300 K and 350 K. Here, we have observed that the human telomeric G-quadruplex DNA deviates more from its crystal structure at minimal salt concentration under both non-polar and polar confinement conditions. Besides, the loop regions deviate and fluctuate more compared to the other regions, i.e., sugar-phosphate backbone and tetrad regions. The presence of K+ ions is found to be primarily responsible for this phenomenon. From the spatial density function (SDF) plots, a higher density of K+ ions is observed in the backbone region. Furthermore, from the residue-wise first solvation shell estimation, we have noticed that the K+ ions mainly accumulate in the tetrad region under both non-polar and polar confinement conditions due to which the tetrad regions are more rigid than the loop regions. Higher salt concentration results in increased rigidity of the G-quadruplex DNA. Our study provides valuable insight into the conformational deviation of the G-quadruplex DNA under nanoconfinement conditions.

Functional Nucleic Acids Under Unusual Conditions

Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.

Deep Eutectic Solvents (DESs) and Their Application in Biosensor Development

Deep Eutectic Solvents (DESs) are a new class of solvents characterized by a remarkable decrease in melting point compared to those of the starting components. The eutectic mixtures can be simply prepared by mixing a Hydrogen Bond Acceptor (HBA) with a Hydrogen Bond Donor (HBD) at a temperature of about 80 °C. They have found applications in different research fields; for instance, they have been employed in organic synthesis, electrochemistry, and bio-catalysis, showing improved biodegradability and lower toxicity compared to other solvents. Herein, we review the use of DESs in biosensor development. We consider the emerging interest in different fields of this green class of solvents and the possibility of their use for the improvement of biosensor performance. We point out some promising examples of approaches for the assembly of biosensors exploiting their compelling characteristics. Furthermore, the extensive ability of DESs to solubilize a wide range of molecules provides the possibility to set up new devices, even for analytes that are usually insoluble and difficult to quantify.

Hydrogen Bond Kinetics, Ionic Dynamics, and Voids in the Binary Mixtures of Protic Ionic Liquids with Alkanolamines

Classical molecular dynamics simulations were used to investigate the structural and dynamical properties of the mixtures of ionic liquids (ILs) with the conjugate forms of the cation in a 1:1 molar ratio. The experimental studies suggested the combination of ethanolamines and ILs as novel absorbents for acidic gases such as CO₂ and H₂S, which provide the advantage of efficient absorption of gases at low pressures. However, the microscopic properties of the ionic mixtures are not studied. From our computational investigations, the densities of mixtures are reported and compared with the experimental results. The structural evolution of mixtures is reported by radial distribution functions, coordination numbers, void analysis, and spatial distribution functions. The mixtures' dynamic properties were studied by analyzing the hydrogen bond, ion-pair, and ion-cage lifetimes of the system. Monoethanolammonium and triethanolammonium ILs show different types of spatial distribution functions. The cations have lesser effect on dynamics compared with anions. The charge on the anion greatly affects the dynamics of mixtures. The dianion mixtures show slower dynamics than the monoanionic mixtures. The hydrogen bonding between cations and anions is stronger than that between cations and neutral molecules due to strong coulombic attractive forces. The cations spend more time around the dianions as compared to monoanions. The distributions of voids show that the void sizes are smaller in triethanolamine-based mixtures. The sulfobenzoate-based mixtures show voids smaller than those of pyridine-3-carboxylate-based mixtures due to more available free space between the entities, which facilitates the overall dynamics.

Potential of ATP toward Prevention of hIAPP Oligomerization and Destabilization of hIAPP Protofibrils: An In Silico Perspective

The aggregation of an intrinsically disordered protein, human islet amyloid polypeptide (hIAPP), leads to one of the most prevalent endocrine disorders, type II diabetes mellitus (T2DM). Hence inhibition of hIAPP aggregation provides a possible therapeutic approach for the treatment of T2DM. In this regard, a new aspect of adenosine triphosphate (ATP), which is widely known as the energy source for biological reactions, has recently been discovered, where it can inhibit the formation of protein aggregates and simultaneously dissolve preformed aggregates at a millimolar concentration scale. In this work, we investigate the effect of ATP on the aggregation of an amyloidogenic segment of hIAPP, hIAPP_22-28, and also of the full length sequence. Using all-atom classical molecular dynamics simulations, we observe that the tendency of hIAPP to oligomerize into β-sheet conformers is inhibited by ATP, due to which the peptides remain distant, loosely packed random monomers. Moreover, it can also disassemble preformed hIAPP protofibrils. ATP preferentially interacts with the hydrophobic residues of hIAPP_22-28 fragment and the terminal and turn residues of the full length peptide. The hydrogen bonding, hydrophobic, π-π, and N-H-π stacking interactions are the driving forces for the ATP induced inhibition of hIAPP aggregation. Interestingly, the hydrophobic adenosine of ATP is found to be more in contact with the peptide residues than the hydrophilic triphosphate moiety. The insight into the inhibitory mechanism of ATP on hIAPP aggregation can prove to be beneficial for the design of novel amyloid inhibitors in the future.

Microscopic structural features of water in aqueous-reline mixtures of varying compositions

Reline, a mixture of urea and choline chloride in a 2 : 1 molar ratio, is one of the most frequently used deep eutectic solvents. Pure reline and its aqueous solution have large scale industrial use. Owing to the presence of active hydrogen bond formation sites, urea and choline cations can disrupt the hydrogen-bonded network in water. However, a quantitative understanding of the microscopic structural features of water in the presence of reline is still lacking. We carry out extensive all-atom molecular dynamics simulations to elucidate the effect of the gradual addition of co-solvents on the microscopic arrangements of water molecules. We consider four aqueous solutions of reline, between 26.3 and 91.4 wt%. A disruption of the local hydrogen-bonded structure in water is observed upon inclusion of urea and choline chloride. The extent of deviation of the water structure from tetrahedrality is quantified using the tetrahedral order parameter (q_tet). Our analyses show a monotonic increase in the structural disorder as the co-solvents are added. Increase in the q_tet values are observed when highly electro-negative hetero-atoms like nitrogen, oxygen of urea and choline cations are counted as partners of the central water molecules. Further insights are drawn from the characterization of the hydrogen-bonded network in water and we observe the gradual rupturing of water-water hydrogen bonds and their subsequent replacement by the water-urea hydrogen bonds. A negligible contribution from the hydrogen bonds between water and bulky choline cations has also been found. Considering all the constituents as the hydrogen bond partners we calculate the possibility of a successful hydrogen bond formation with a central water molecule. This gives a clear picture of the underlying mechanism of water replacement by urea.

An in silico investigation of the binding modes and pathway of APTO-253 on c-KIT G-quadruplex DNA

The stability of c-KIT G-quadruplex DNA via ligands has been a significant concern in the growing field of cancer therapy. Thus, it is very important to understand the mechanism behind the high binding affinity of the small drug molecules on the c-KIT G-quadruplex DNA. In this study, we have investigated the binding mode and pathway of the APTO-253 ligand on the c-KIT G-quadruplex DNA employing a total of 10 μs all atom molecular dynamics simulations and further 8.82 μs simulations via the umbrella sampling method using both OL15 and BSC1 latest force fields for DNA structures. From the cluster structure analysis, mainly three binding pathways i.e., top, bottom and side loop stacking modes are identified. Moreover, RMSD, RMSF and 2D-RMSD values indicate that the c-KIT G-quadruplex DNA and APTO-253 molecules are stable throughout the simulation run. Furthermore, the number of hydrogen bonds in each tetrad and the distance between the two central K⁺ cations confirm that the c-KIT G-quadruplex DNA maintains its conformation in the process of complex formation with the APTO-253 ligand. The binding free energies and the minimum values in the potential of mean forces suggest that the binding processes are energetically favorable. Furthermore, we have found that the bottom stacking mode is the most favorable binding mode among all the three modes for the OL15 force field. However, for the BSC1 force field, both the top and bottom binding modes of the APTO-253 ligand in c-KIT G-quadruplex DNA are comparable to each other. To investigate the driving force for the complex formation, we have noticed that the van der Waals (vdW) and π-π stacking interactions are mainly responsible. Our detailed studies provide useful information for the discovery of novel drugs in the field of stabilization of G-quadruplex DNAs.

G-Quadruplex loops regulate PARP-1 enzymatic activation

G-Quadruplexes are non-B form DNA structures present at regulatory regions in the genome, such as promoters of proto-oncogenes and telomeres. The prominence in such sites suggests G-quadruplexes serve an important regulatory role in the cell. Indeed, oxidized G-quadruplexes found at regulatory sites are regarded as epigenetic elements and are associated with an interlinking of DNA repair and transcription. PARP-1 binds damaged DNA and non-B form DNA, where it covalently modifies repair enzymes or chromatin-associated proteins respectively with poly(ADP-ribose) (PAR). PAR serves as a signal in regulation of transcription, chromatin remodeling, and DNA repair. PARP-1 is known to bind G-quadruplexes with stimulation of enzymatic activity. We show that PARP-1 binds several G-quadruplex structures with nanomolar affinities, but only a subset promote PARP-1 activity. The G-quadruplex forming sequence found in the proto-oncogene c-KIT promoter stimulates enzymatic activity of PARP-1. The loop-forming characteristics of the c-KIT G-quadruplex sequence regulate PARP-1 catalytic activity, whereas eliminating these loop features reduces PARP-1 activity. Oxidized G-quadruplexes that have been suggested to form unique, looped structures stimulate PARP-1 activity. Our results support a functional interaction between PARP-1 and G-quadruplexes. PARP-1 enzymatic activation by G-quadruplexes is dependent on the loop features and the presence of oxidative damage.

Water in biodegradable glucose–water–urea deep eutectic solvent: modifications of structure and dynamics in a crowded environment

Molecular dynamics simulations have been performed on a highly viscous (η ∼ 255 cP) naturally abundant deep eutectic solvent (NADES) composed of glucose, urea and water in a weight ratio of 6 : 4 : 1 at 328 K.

Neuroprotective immunity by essential nutrient "Choline" for the prevention of SARS CoV2 infections: An in silico study by molecular dynamics approach

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Prenatal Choline level protects the fetus's developing brain from effects of CoV2.

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Choline from many food supplements can protect the fetus from Coronavirus.

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Choline is used for treatment of many neurodegenerative diseases like Alzheimer.

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Natural Choline may regulate 3CL^pro protein’s viral replication.

Prenatal COVID infection is one of the worst affected and least attended aspects of the COVID-19 disease. Like other coronaviruses, CoV2 infection is anticipated to affect fetal development by maternal inflammatory response on the fetus and placenta. Studies showed that higher prenatal choline level in mother’s body can safeguard the developing brain of the fetus from the adverse effects of CoV2 infection. Choline is commonly used as food supplement. By virtual screening, molecular docking and molecular dynamics techniques, we have established a strong inhibitory possibility of choline for SARS 3CL^pro protease which may provide a lead for prenatal COVID-19 treatment.