Molecular Dynamics Simulations of Molecules in Uniform Flow

Progress in Multiscale Modeling of Silk Materials

As a result of their hierarchical structure and biological processing, silk fibers rank among nature's most remarkable materials. The biocompatibility of silk-based materials and the exceptional mechanical properties of certain fibers has inspired the use of silk in numerous technical and medical applications. In recent years, computational modeling has clarified the relationship between the molecular architecture and emergent properties of silk fibers and has demonstrated predictive power in studies on novel biomaterials. Here, we review advances in modeling the structure and properties of natural and synthetic silk-based materials, from early structural studies of silkworm cocoon fibers to cutting-edge atomistic simulations of spider silk nanofibrils and the recent use of machine learning models. We explore applications of modeling across length scales: from quantum mechanical studies on model peptides, to atomistic and coarse-grained molecular dynamics simulations of silk proteins, to finite element analysis of spider webs. As computational power and algorithmic efficiency continue to advance, we expect multiscale modeling to become an indispensable tool for understanding nature's most impressive fibers and developing bioinspired functional materials.

The role of flow in the self-assembly of dragline spider silk proteins

Hydrodynamic flow in the spider duct induces conformational changes in dragline spider silk proteins (spidroins) and drives their assembly, but the underlying physical mechanisms are still elusive. Here we address this challenging multiscale problem with a complementary strategy of atomistic and coarse-grained molecular dynamics simulations with uniform flow. The conformational changes at the molecular level were analyzed for single-tethered spider silk peptides. Uniform flow leads to coiled-to-stretch transitions and pushes alanine residues into β sheet and poly-proline II conformations. Coarse-grained simulations of the assembly process of multiple semi-flexible block copolymers using multi-particle collision dynamics reveal that the spidroins aggregate faster but into low-order assemblies when they are less extended. At medium-to-large peptide extensions (50%-80%), assembly slows down and becomes reversible with frequent association and dissociation events, whereas spidroin alignment increases and alanine repeats form ordered regions. Our work highlights the role of flow in guiding silk self-assembly into tough fibers by enhancing alignment and kinetic reversibility, a mechanism likely relevant also for other proteins whose function depends on hydrodynamic flow.

Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism

Proteins are natural polymers that play an essential role in both living organisms and biotechnological applications. During certain bioprocessing steps, they can be exposed to significant mechanical stress induced by, for example, shear flow or sonication, resulting in reduced therapeutic efficacy, aggregation, or even a loss of activity. For this reason, there is a need to understand and determine the susceptibility of the protein activity to the experienced mechanical stress. To acquire this knowledge, it is necessary to study the rotational dynamics of the protein. Commonly, the rotational dynamics of soft molecules is interpreted based on a theoretical analysis performed in an inertial laboratory frame. However, the obtained angular velocity mixes pure rotations and vibrations with angular momentum, consequently lacking a clear dynamical interpretation. On the other hand, the use of the noninertial internal Eckart frame allows the determination of pure angular velocity as it minimizes the coupling between the rotational and vibrational degrees of freedom. In the present work, by conducting open-boundary molecular dynamics simulations and exploiting the Eckart frame formalism, we study the rotational dynamics of a small protein under the shear flow of various strengths. Our results show that the angular velocity increases nonlinearly with increasing shear rate. Furthermore, the protein gains vibrational angular momentum at higher shear rates, which is reflected in the higher angular velocity computed by employing the Eckart frame formalism and confirmed by analysis of the contributions to the total kinetic energy of the biomolecule.

Biohybrid Membrane Formation by Directed Insertion of Aquaporin into a Solid-State Nanopore

Biohybrid nanopores combine the durability of solid-state nanopores with the precise structure and function of biological nanopores. Particular care must be taken to control how biological nanopores adapt to their surroundings once they come into contact with the solid-state nanopores. Two major challenges are to precisely control this adaptability under dynamic conditions and provide predesigned functionalities that can be manipulated for engineering applications. In this work, we report on the computational design of a distinctive class of biohybrid active membrane layers, built from the directed-insertion of an aquaporin-incorporated lipid nanodisc into a model alkyl-functionalized silica pore. We show that in an aqueous environment when a pressure difference exists between the two sides of the solid-state nanopore, the preferential interactions between the hydrocarbon tail of the lipid molecules that surround the aquaporin protein and the alkyl group functionalizing the interior surface of the silica nanopore enable the insertion of the aquaporin-incorporated lipid shell into the nanopore by forcing out the water molecules. The same preferential interactions are responsible for the structural stability of the inserted aquaporin-incorporated lipid shell as well as the water sealing properties of the lipid-alkyl interface. We further show that the aquaporin protein stabilized in the alkyl-functionalized silica nanopore preserves its biological structure and function in both pure and saline water, and, remarkably, its water permeability is equal to the one measured in the biological environment. The designed biohybrid membrane could pave the way for the development of durable transformative devices for water filtration.

Identification of potential antivirals against 3CLpro enzyme for the treatment of SARS-CoV-2: A multi-step virtual screening study

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak is posing a serious public health threat worldwide in the form of COVD-19. Herein, we have performed two-dimensional quantitative structure-activity relationship (2D-QSAR) and three-dimensional pharmacophore modelling analysis employing inhibitors of 3-chymotrypsin-like protease (3CLpro), the leading protease that is crucial for the replication of SARS-CoV-2. The investigation aims to identify the important structural features responsible for the enzyme inhibition and the search for novel 3CLpro enzyme inhibitors as effective therapeutics for treating SARS-CoV-2. Furthermore, we carried out molecular docking studies using the most and least active compounds in the dataset, aiming to validate the contributions of various features as appeared in the QSAR models. Later, the stringently validated 2D-QSAR model was used to estimate the 3CLpro inhibitory activity of compounds from five chemical databases. Compounds with the significant predicted activity were then subjected to pharmacophore-based virtual screening to screen the top-rated compounds, which were then further subjected to molecular docking analysis, absorption, distribution, metabolism, excretion - toxicity (ADMET) profiling, and molecular dynamics (MD) simulation. The multi-step virtual screening analyses suggested that compounds CASAntiV-865453-58-3, CASAntiV-865453-40-3, and CASAntiV-2043031-84-9 could be used as effective therapeutic agents for the treatment of SARS-CoV-2.

Optimization of the Urea Removal in a Wearable Dialysis Device Using Nitrogen-Doped and Phosphorus-Doped Graphene

Dialysis has been recognized as an essential treatment for end-stage renal disease (ESRD). This therapy, however, suffers from several limitations leading to numerous complications in the patients. As dialysis cannot completely substitute healthy kidney functions, the health condition of an ESRD patient is ultimately affected. Wearable artificial kidney (WAK) can resolve the restrictions of blood purification by the dialysis method. However, absorbing large amounts of urea produced in the body is one of the main challenges of these WAK and overcoming this is necessary to improve both functionality and footprint of the device. This study investigates the adsorption capabilities of N- and P-doped graphene nanosorbents for the first time by using molecular dynamic simulation. Urea removal on carbon nanosheets was simulated with different percentages of phosphorus and nitrogen dopants along with the pristine graphene. Specifically, the effects of interaction energy, adsorption percentage, gyration radius, hydrogen bonding, and other molecular dynamic analyses on urea removal were also investigated. The results from this study match well with the existing research, demonstrating the accuracy of the model. The results further suggest that graphene nanosheets doped by 10% nitrogen are likely the most effective in removing urea given that it is associated with the maximum radial distribution function (RDF), the maximum reduction in gyration radius, a high number of hydrogen bonds, and the most negative adsorption energy. This molecular study offers attractive suggestions for the novel adsorbents of artificial kidney devices and paves the way for the development of novel and enhanced urea adsorbents.

Longitudinal strand ordering leads to shear thinning in Nafion

Proton-exchange membrane fuel cells (PEMFC) offer a promising energy generation alternative for a wide range of technologies thanks to their ecological friendliness and unparalleled efficiency. At the heart of these electrochemical cells lies the membrane electrode assembly with its most important energy conversion components, the Proton Exchange Membrane. This component is created through the use of printing techniques and Nafion inks. The physicochemical properties of the ink, such as its viscosity under shear, are critical for the finished product. In this work we present non-equilibrium Molecular Dynamics simulations using a MARTINI based coarse-grained model for Nafion to understand the mechanism governing the shear viscosity of Nafion solutions. By simulating a Couette flow and calculating density maps of the Nafion chains in these simulations we shed light on the process that leads to the experimentally observed shear thinning effects of Nafion solutions under flow. We observe rod-shaped Nafion microstructures, 3 nm in size on average, when shear flow is absent or low. Higher shear rates instead break these structures and align Nafion strands along the direction of the flow, resulting in lower shear viscosities. Our work paves the way for a deeper understanding of the dynamic and mechanical properties of Nafion including studies of more complex CL and PEM inks.

β-Blockers bearing hydroxyethylamine and hydroxyethylene as potential SARS-CoV-2 Mpro inhibitors: rational based design, in silico, in vitro, and SAR studies for lead optimization

The global COVID-19 pandemic became more threatening especially after the introduction of the second and third waves with the current large expectations for a fourth one as well. This urged scientists to rapidly develop a new effective therapy to combat SARS-CoV-2. Based on the structures of β-adrenergic blockers having the same hydroxyethylamine and hydroxyethylene moieties present in the HIV-1 protease inhibitors which were found previously to inhibit the replication of SARS-CoV, we suggested that they may decrease the SARS-CoV-2 entry into the host cell through their ability to decrease the activity of RAAS and ACE2 as well. Herein, molecular docking of twenty FDA-approved β-blockers was performed targeting SARS-CoV-2 Mpro. Results showed promising inhibitory activities especially for Carvedilol (CAR) and Nebivolol (NEB) members. Moreover, these two drugs together with Bisoprolol (BIS) as an example from the lower active ones were subjected to molecular dynamics simulations at 100 ns. Great stability across the whole 100 ns timeframe was observed for the top docked ligands, CAR and NEB, over BIS. Conformational analysis of the examined drugs and hydrogen bond investigation with the pocket's crucial residues confirm the great affinity and confinement of CAR and NEB within the Mpro binding site. Moreover, the binding-free energy analysis and residue-wise contribution analysis highlight the nature of ligand-protein interaction and provide guidance for lead development and optimization. Furthermore, the examined three drugs were tested for their in vitro inhibitory activities towards SARS-CoV-2. It is worth mentioning that NEB achieved the most potential anti-SARS-CoV-2 activity with an IC50 value of 0.030 μg ml-1. Besides, CAR was found to have a promising inhibitory activity with an IC50 of 0.350 μg ml-1. Also, the IC50 value of BIS was found to be as low as 15.917 μg ml-1. Finally, the SARS-CoV-2 Mpro assay was performed to evaluate and confirm the inhibitory effects of the tested compounds (BIS, CAR, and NEB) towards the SARS-CoV-2 Mpro enzyme. The obtained results showed very promising SARS-CoV-2 Mpro inhibitory activities of BIS, CAR, and NEB (IC50 = 118.50, 204.60, and 60.20 μg ml-1, respectively) compared to lopinavir (IC50 = 73.68 μg ml-1) as a reference standard.

Graphene-Based Nanoparticles as Potential Treatment Options for Parkinson's Disease: A Molecular Dynamics Study

INTRODUCTION

The study of abnormal aggregation of proteins in different tissues of the body has recently earned great attention from researchers in various fields of science. Concerning neurological diseases, for instance, the accumulation of amyloid fibrils can contribute to Parkinson's disease, a progressively severe neurodegenerative disorder. The most prominent features of this disease are the degeneration of neurons in the substantia nigra and accumulation of α-synuclein aggregates, especially in the brainstem, spinal cord, and cortical areas. Dopamine replacement therapies and other medications have reduced motor impairment and had positive consequences on patients' quality of life. However, if these medications are stopped, symptoms of the disease will recur even more severely. Therefore, the improvement of therapies targeting more basic mechanisms like prevention of amyloid formation seems to be critical. It has been shown that the interactions between monolayers like graphene and amyloids could prevent their fibrillation.

METHODS

For the first time, the impact of four types of last-generation graphene-based nanostructures on the prevention of α-synuclein amyloid fibrillation was investigated in this study by using molecular dynamics simulation tools.

RESULTS

Although all monolayers were shown to prevent amyloid fibrillation, nitrogen-doped graphene (N-Graphene) caused the most instability in the secondary structure of α-synuclein amyloids. Moreover, among the four monolayers, N-Graphene was shown to present the highest absolute value of interaction energy, the lowest contact level of amyloid particles, the highest number of hydrogen bonds between water and amyloid molecules, the highest instability caused in α-synuclein particles, and the most significant decrease in the compactness of α-synuclein protein.

DISCUSSION

Ultimately, it was concluded that N-Graphene could be the most effective monolayer to disrupt amyloid fibrillation, and consequently, prevent the progression of Parkinson's disease.