Exploring the mechanism of action of spirooxindoles as a class of CDK2 inhibitors: a structure-based computational approach.

Cyclin-dependent kinase 2 (CDK2) regulates cell cycle checkpoints in the synthesis and mitosis phases and plays a pivotal role in cancerous cell proliferation. The activation of CDK2, influenced by various protein signaling pathways, initiates the phosphorylation process. Due to its crucial role in carcinogenesis, CDK2 is a druggable hotspot target to suppress cancer cell proliferation. In this context, several studies have identified spirooxindoles as an effective class of CDK2 inhibitors. In the present study, three spirooxindoles (SOI1, SOI2, and SOI3) were studied to understand their inhibitory mechanism against CDK2 through a structure-based approach. Molecular docking and molecular dynamics (MD) simulations were performed to explore their interactions with CDK2 at the molecular level. The calculated binding free energy for the spirooxindole-based CDK2 inhibitors aligned well with experimental results regarding CDK2 inhibition. Energy decomposition (ED) analysis identified key binding residues, including I10, G11, T14, R36, F82, K89, L134, P155, T158, Y159, and T160, in the CDK2 active site and T-loop phosphorylation. Molecular mechanics (MM) energy was identified as the primary contributor to stabilizing inhibitor binding in the CDK2 protein structure. Furthermore, the analysis of binding affinity revealed that the inhibitor SOI1 binds more strongly to CDK2 compared to the other inhibitors under investigation. It demonstrated a robust interaction with the crucial residue T160 in the T-loop phosphorylation site, responsible for kinase activation. These insights into the inhibitory mechanism are anticipated to contribute to the development of potential CDK2 inhibitors using the spirooxindole scaffold.

Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density.

It is very difficult to reconstruct computationally a large biomolecular complex in its biological entirety from experimental data. The resulting atomistic model should not contain gaps structurally and it should yield stable dynamics. We, for the first time, reconstruct from the published incomplete cryo-EM density a complete MS2 virus at atomistic resolution, that is, the capsid with the genome, and validate the result by all-atom molecular dynamics with explicit water. The available experimental data includes a high resolution protein capsid and an inhomogeneously resolved genome map. For the genomic RNA, apart from 16 hairpins with atomistic resolution, the strands near the capsid's inner surface were resolved up to the nucleic backbone level, and the innermost density was completely unresolved. As a result, only 242 nucleotides (out of 3569) were positioned, while only a fragmented backbone was outlined for the rest of the genome, making a detailed model reconstruction necessary. For model reconstruction, in addition to the available atomistic structure information, we extensively used the predicted secondary structure of the genome (base pairing). The technique was based on semi-automatic building of relatively large strands of RNA with subsequent manual positioning over the traced backbone. The entire virus structure (capsid + genome) was validated by a molecular dynamics run in physiological solution with ions at standard conditions confirming the stability of the model.

Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly.

Spatiotemporal regulation of viral capsid assembly ensures the selection of the viral genome for encapsidation. The porcine circovirus 2 is the smallest autonomously replicating pathogenic virus, yet how PCV2 capsid assembly is regulated to occur within the nucleus remains unknown. We report that pure PCV2 capsid proteins, in the absence of nucleic acids, require acidic conditions to assemble into empty capsids in vitro. By employing constant pH replica exchange molecular dynamics, we unveil the atomistic mechanism of pH-dependency for capsid assembly. The results show that an appropriate protonation configuration for a cluster of acidic amino acids is necessary to appropriately position the GH-loop for driving the capsid assembly. We demonstrate that assembly is prohibited at neutral pH because deprotonation of these residues results in their electrostatic repulsion, shifting the GH-loop to a position incompatible with capsid assembly. We propose that encapsulation of nucleic acids overcomes this repulsion to suitably position the GH-loop. Our findings provide the first atomic resolution mechanism of capsid assembly regulation. These findings are useful for the development of therapeutics that inhibit PCV2 self-assembly.

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time.

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported.

Impact of mutations in SARS-CoV-2 recombinant sub-variant XBB.1.16 on the binding affinity with human ACE2 receptor.

Despite the waning threat of the COVID-19 pandemic, its detrimental impact on global health persists. Regardless of natural immunity or immunity obtained through vaccination, emerging variants of the virus continue to undergo mutations and propagate globally. The persistent mutations in SARS-CoV-2, along with the subsequent formation of recombinant sub-variants has become a challenge for researchers and health professionals, raising concerns about the efficacy of current vaccines. Gaining a better understanding of the biochemical interactions between the Spike Protein (RBD) of SARS-CoV-2 variants and the human ACE2 receptor can prove to be beneficial in designing and developing antiviral therapeutics that are equally effective against all strains and emerging variants. Our objective in this study was to investigate the interfacial binding pattern of the SARS-CoV-2 RBD-ACE2 complex of the Wild Type (WT), Omicron, and the Omicron recombinant sub-variant XBB.1.16. We aimed to examine the atomic level factors and observe how mutations influence the interaction between the virus and its host using Molecular Dynamics simulation, MM/GBSA energy calculations, and Principal Component Analysis. Our findings reveal a higher degree of structural deviation and flexibility in XBB.1.16 compared to WT and Omicron. PCA indicated a wider cluster and significant flexibility in the movements of XBB.1.16 which can also be observed in free energy landscapes, while the normal mode analysis revealed converging motions within the RBD-ACE2 complexes which can facilitate the interaction between them. A pattern of decreased binding affinity was observed in case of XBB.1.16 when compared to the WT and Omicron. These observed deviations in XBB.1.16 when compared to its parent lineage Omicron, and WT can be attributed to the mutations specific to it. Collectively, these results enhance our understanding of the impact of mutations on the interaction between this strain and the host, taking us one step closer to designing effective antiviral therapeutics against the continually mutating strains.

Time-spatial drift of decelerating electromagnetic pulses.

A time dependent electromagnetic pulse generated by a current running laterally to the direction of the pulse propagation is considered in paraxial approximation. It is shown that the pulse envelope moves in the time-spatial coordinates on the surface of a parabolic cylinder for the Airy pulse and a hyperbolic cylinder for the Gaussian. These pulses propagate in time with deceleration along the dominant propagation direction and drift uniformly in the lateral direction. The Airy pulse stops at infinity while the asymptotic velocity of the Gaussian is nonzero.

Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome.

For the first time, a complete all-atom molecular dynamics (MD) model of a virus, bacteriophage MS2, in its entirety, including a protein outer shell, native genomic RNA with necessary divalent ions, and surrounding explicit aqueous solution with ions at physiological concentration, was built. The model is based on an experimentally measured cryo-EM structure, which was substantially augmented by reconstructing missing or low-resolution parts of the measured density (where the atomistic structure cannot be fit unambiguously). The model was tested by a quarter of a microsecond MD run, and various biophysical characteristics are obtained and analyzed. The developed methodology of building the model can be used for reconstructing other large biomolecular structures when experimental data are fragmented and/or of varying resolution, while the model itself can be used for studying the biology of MS2, including the dynamics of its interaction with the host bacteria.

The nut-and-bolt motion of a bacteriophage sliding along a bacterial flagellum: a complete hydrodynamics model.

The 'nut-and-bolt' mechanism of a bacteriophage-bacteria flagellum translocation motion is modelled by numerically integrating the 3D Stokes equations using a Finite-Element Method (FEM). Following the works by Katsamba and Lauga (Phys Rev Fluids 4(1): 013101, 2019), two mechanical models of the flagellum-phage complex are considered. In the first model, the phage fiber wraps around the smooth flagellum surface separated by some distance. In the second model, the phage fiber is partly immersed in the flagellum volume via a helical groove imprinted in the flagellum and replicating the fiber shape. In both cases, the results of the Stokes solution for the translocation speed are compared with the Resistive Force Theory (RFT) solutions (obtained in Katsamba and Lauga Phys Rev Fluids 4(1): 013101, 2019) and the asymptotic theory in a limiting case. The previous RFT solutions of the same mechanical models of the flagellum-phage complex showed opposite trends for how the phage translocation speed depends on the phage tail length. The current work uses complete hydrodynamics solutions, which are free from the RFT assumptions to understand the divergence of the two mechanical models of the same biological system. A parametric investigation is performed by changing pertinent geometrical parameters of the flagellum-phage complex and computing the resulting phage translocation speed. The FEM solutions are compared with the RFT results using insights provided from the velocity field visualisation in the fluid domain.

Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes I: In Silico Implementation for Surfactant Micelles.

Surface electrostatic potential Ψ is a key characteristic of colloid particles. Since the surface of the particles adsorbs various compounds and facilitates chemical reactions between them, Ψ largely affects the properties of adsorbed reactants and governs the flow of chemical reactions occurring between them. One of the most popular methods for estimating Ψ in hydrophilic colloids, such as micellar surfactant solutions and related systems, is the application of molecular probes, predominantly acid-base indicator dyes. The Ψ value is calculated from the difference of the probe's indices of the apparent acidity constant between the examined colloid solution and, usually, some other colloid solution with noncharged particles. Here, we show how to implement this method in silico using alchemical free energy calculations within the framework of molecular dynamics simulations. The proposed implementation is tested on surfactant micelles and is shown to predict experimental Ψ values with quantitative accuracy depending on the kind of surfactant. The sources of errors in the method are discussed, and recommendations for its application are given.

Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes II: Insight from Atomistic Simulations of Micelles.

Exploiting acid-base indicators as molecular probes is one of the most popular methods for determining the surface electrostatic potential Ψ in hydrophilic colloids like micellar surfactant solutions and related systems. Specifically, the indicator's apparent acidity constant index is measured in the colloid solution of interest and, as a rule, in a nonionic surfactant solution; the difference between the two is proportional to Ψ. Despite the widespread use of this approach, a major problem remains unresolved, namely, the dissimilarity of Ψ values obtained with different indicators for the same system. The common point of view recognizes the effect of several factors (the choice of the nonionic surfactant, the probe's localization, and the degree of hydration of micellar pseudophase) but does not allow to quantitatively assess their impact and decide which indicator reports the most correct Ψ value. Here, based on the ability to predict the reported Ψ values in silico, we examined the role of these factors using molecular dynamics simulations for five probes and two surfactants. The probe's hydration in the Stern layer was found responsible for approximately half of the dissimilarity range. The probe's localization is found important but hard to quantify because of the irregular structure of the Stern layer. The most accurate indicators among the examined set were identified. Supplementing experiments on measuring Ψ with molecular dynamics simulation is proposed as a way of improving the efficacy of the indicator method: the simulations can guide the choice of the most suitable probe and nonionic surfactant for the given nanoparticles.

Covalent conjugates based on nanodiamonds with doxorubicin and a cytostatic drug from the group of 1,3,5-triazines: Synthesis, biocompatibility and biological activity.

We report the synthesis of covalent conjugates of nanodiamonds with doxorubicin and a cytostatic drug from the class of 1,3,5-triazines. The obtained conjugates were identified using a number of physicochemical methods (IR-spectroscopy, NMR-spectroscopy, XRD, XPS, TEM). As a result of our study, it was found that ND-СONH-Dox and ND-COO-Diox showed good hemocompatibility, since they did not affect plasma coagulation hemostasis, platelet functional activity, and erythrocyte membrane. The ND-COO-Diox conjugates are also capable of binding to human serum albumin due to the presence of ND in their composition. In the study of the cytotoxic properties of ND-СONH-Dox and ND-COO-Diox in the T98G glioblastoma cell line, indicating that ND-СONH-Dox and ND-COO-Diox demonstrate greater cytotoxicity at lower concentrations of Dox and Diox in the composition of the conjugates compared to individual drugs; the cytotoxic effect of ND-COO-Diox was statistically significantly higher than that of ND-СONH-Dox at all concentrations studied. Greater cytotoxicity at lower concentrations of Dox and Diox in the composition of conjugates compared to individual cytostatics makes it promising to further study the specific antitumor activity and acute toxicity of these conjugates in models of glioblastoma in vivo. Our results demonstrated that ND-СONH-Dox and ND-COO-Diox enter HeLa cells predominantly via a nonspecific actin-dependent mechanism, while for ND-СONH-Dox a clathrin-dependent endocytosis pathway. All data obtained provide that the synthesized nanomaterials show a potential application as the agents for intertumoral administration.

Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes. III. Experimental Hydrophobicity/Hydrophilicity and Charge Distribution of MS2 Virus Surface.

MS2 bacteriophage is often used as a model for evaluating pathogenic viruses' behavior in aqueous solution. However, the questions of the virus surface's hydrophilic/hydrophobic balance, the charge distribution, and the binding mechanism are open. Using the dynamic light scattering method and laser Doppler electrophoresis, the hydrodynamic diameter and the ζ-potential of the virus particles were measured at their concentration of 5 × 1011 particles per mL and ionic strength 0.03 M. The values were found to be 30 nm and -29 or -34 mV (by Smoluchowski or Ohshima approximations), respectively. The MS2 bacteriophage surface was also investigated using a series of acid-base indicator dyes of various charge type, size, and structure. Their spectral and acid-base properties (pKa) are very sensitive to the microenvironment in aqueous solution, including containing nanoparticles. The electrostatic potential of the surface Ψ was estimated using the common formula: Ψ = 59 × (pKai - pKa) in mV at 25 °C. The Ψ values were -50 and +10 mV, respectively, which indicate the "mosaic" way of the charge distribution on the surface. These data are in good agreement with the obtained ζ-potential values and provide even more information about the virus surface. It was found that the surface of the MS2 virus is hydrophilic in solution in contrast to the commonly accepted hypothesis of the hydrophobicity of virus particles. No hydrophobic interactions between various molecular probes and the capsid were observed.

Self-assembly of trehalose molecules on a lysozyme surface: the broken glass hypothesis.

To help understand how sugar interactions with proteins stabilise biomolecular structures, we compare the three main hypotheses for the phenomenon with the results of long molecular dynamics simulations on lysozyme in aqueous trehalose solution (0.75 M). We show that the water replacement and water entrapment hypotheses need not be mutually exclusive, because the trehalose molecules assemble in distinctive clusters on the surface of the protein. The flexibility of the protein backbone is reduced under the sugar patches supporting earlier findings that link reduced flexibility of the protein with its higher stability. The results explain the apparent contradiction between different experimental and theoretical results for trehalose effects on proteins.

Computational mechanics of molecular systems: Quantifying high-dimensional dynamics by distribution of Poincaré recurrence times.

A framework that connects computational mechanics and molecular dynamics has been developed and described. As the key parts of the framework, the problem of symbolising molecular trajectory and the associated interrelation between microscopic phase space variables and macroscopic observables of the molecular system are considered. Following Shalizi and Moore, it is shown that causal states, the constituent parts of the main construct of computational mechanics, the ε-machine, define areas of the phase space that are optimal in the sense of transferring information from the micro-variables to the macro-observables. We have demonstrated that, based on the decay of their Poincaré return times, these areas can be divided into two classes that characterise the separation of the phase space into resonant and chaotic areas. The first class is characterised by predominantly short time returns, typical to quasi-periodic or periodic trajectories. This class includes a countable number of areas corresponding to resonances. The second class includes trajectories with chaotic behaviour characterised by the exponential decay of return times in accordance with the Poincaré theorem.

Structural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation.

Tumor Necrosis Factor-alpha (TNF-α), a multifunctional cytokine responsible for providing resistance against infections, inflammation, and cancers. TNF-α has emerged as a promising drug target against several autoimmune and inflammatory disorders. Several synthetic antibodies (Infliximab, Etanercept, and Adalimumab) are available, but their potential to cause severe side effects has prompted them to develop alternative small molecules-based therapies for inhibition of TNF-α. In the present study, combined in silico approaches based on pharmacophore modeling, virtual screening, molecular docking, and molecular dynamics studies were employed to understand significant direct interactions between TNF-α protein and small molecule inhibitors. Initially, four different small molecule libraries (∼17.5 million molecules) were virtually screened against the selected pharmacophore model. The identified hits were further subjected to molecular docking studies. The three potent lead compounds (ZINC05848961, ZINC09402309, ZINC04502991) were further subjected to 100 ns molecular dynamic studies to examine their stability. Our docking and molecular dynamic analysis revealed that the selected lead compounds target the TNF receptor (TNFR) and efficiently block the production of TNF. Moreover, in silico ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) analysis revealed that all the predicted compounds have good pharmacokinetic properties with high gastrointestinal absorption and a decent bioavailability score. Furthermore, toxicity profiles further evidenced that these compounds have no risk of being mutagenic, tumorigenic, reproductive and irritant except ZINC11915498. In conclusion, the present study could serve as the starting point to develop new therapeutic regimens to treat various TNF- related diseases. Communicated by Ramaswamy H. Sarma.

Protein-Ligand Dissociation Rate Constant from All-Atom Simulation.

Dissociation of a ligand isoniazid from a protein catalase was investigated using all-atom molecular dynamics (MD) simulations. Random acceleration MD (τ-RAMD) was used, in which a random artificial force applied to the ligand facilitates its dissociation. We have suggested a novel approach to extrapolate such obtained dissociation times to the zero-force limit assuming never before attempted universal exponential dependence of the bond strength on the applied force, allowing direct comparison with experimentally measured values. We have found that our calculated dissociation time was equal to 36.1 s with statistically significant values distributed in the interval of 0.2-72.0 s, which quantitatively matches the experimental value of 50 ± 8 s despite the extrapolation over 9 orders of magnitude in time.

In Vitro and In Silico Investigation of Water-Soluble Fullerenol C60(OH)24: Bioactivity and Biocompatibility.

Light fullerenes, C60 and C70, have significant potential in biomedical applications due to their ability to absorb reactive oxygen species, inhibit the development of tumors, inactivate viruses and bacteria, and as the basis for developing systems for targeted drug delivery. However, the hydrophobicity of individual fullerenes complicates their practical use; therefore, creating water-soluble derivatives of fullerenes is increasingly important. Currently, the most studied soluble adducts of fullerenes are polyhydroxy fullerenes or fullerenols. Unfortunately, investigations of fullerenol biocompatibility are fragmental. They often lack reproducibility both in the synthesis of the compounds and their biological action. We here investigate the biocompatibility of a well-defined fullerenol C60(OH)24 obtained using methods that minimize the content of impurities and quantitatively characterize the product's composition. We carry out comprehensive biochemical and biophysical investigations of C60(OH)24 that include photodynamic properties, cyto- and genotoxicity, hemocompatibility (spontaneous and photo-induced hemolysis, platelet aggregation), and the thermodynamic characteristics of C60(OH)24 binding to human serum albumin and DNA. The performed studies show good biocompatibility of fullerenol C60(OH)24, which makes it a promising object for potential use in biomedicine.

Graphene Oxide of Extra High Oxidation: A Wafer for Loading Guest Molecules.

We present a new modification of graphene oxide with very high content (85 wt %) of oxygen-containing functional groups (hydroxy, epoxy, lactol, carboxyl, and carbonyl groups) that forms stable aqueous dispersion in up to 9 g·L-1 concentration solutions. A novel faster method of the synthesis is described that produces up to 1 kg of the material and allows controlling the particle size in solution. The synthesized compound was characterized by various physicochemical methods and molecular dynamics modeling, revealing a unique structure in the form of a multilayered wafer of several sheets thick, where each sheet is highly corrugated. The ragged structure of the sheets forms pockets with hindered mobility of water that leads to the possibility of trapping guest molecules.

Identifying and correcting non-Markov states in peptide conformational dynamics.

Conformational transitions in proteins define their biological activity and can be investigated in detail using the Markov state model. The fundamental assumption on the transitions between the states, their Markov property, is critical in this framework. We test this assumption by analyzing the transitions obtained directly from the dynamics of a molecular dynamics simulated peptide valine-proline-alanine-leucine and states defined phenomenologically using clustering in dihedral space. We find that the transitions are Markovian at the time scale of approximately 50 ps and longer. However, at the time scale of 30-40 ps the dynamics loses its Markov property. Our methodology reveals the mechanism that leads to non-Markov behavior. It also provides a way of regrouping the conformations into new states that now possess the required Markov property of their dynamics.