Density functional theory studies on C20 with substitutional TinNn impurities

In this paper, we have performed systematic theoretical surveys of C₂₀ and its C_20-2nTi_nN_n nanocages with n = 1-8 at DFT. Full optimization indicates none of the structures collapse to open deformed as segregated heterofullerene. Also, in order to avoid the resulted strain of fused five-pentagon configuration, some of them deform their cage at the Ti-N bonds and appear cubic-like. Binding energy (E_b) increases, and the absolute heat of atomization │ΔH_at│ of the designed C_20-2nTi_nN_n structures decreases, respectively, as the number of substituting Ti-N units increases. The calculated E_b of 57.05 eV/atom and │ΔH_at│ of 2437.40 kcal/mol display C₄Ti₈N₈ as the most thermodynamic stable heterofullerene where including eight separated Ti-N units through two double C═C bonds. In contrast, the calculated band gap of 2.06 eV shows C₁₈Ti₁N₁ as the best-insulated heterofullerene. Here isolable or extractable open-shell C₁₈Ti₁N₁ heterofullerene must be kinetic stable species, and closed-shell C₄Ti₈N₈ should be thermodynamic stable species. Compared to the suggested Ti-decorated B₃₈ fullerene as a high capacity hydrogen storage material with large E_b (5.67 eV/atom), our studied C_20-2nTi_nN_n heterofullerenes show the higher E_b with a range of 13.78 to 57.05 eV/atom, the higher stability, and the higher capacity hydrogen storage. Each Ti-N unit can bind up to two hydrogen molecules with an average adsorption energy of 0.073 eV/H₂. While the C₄Ti₈N₈ fullerene substituted with 8 Ti-N units can store 16 H₂ molecules, the hydrogen gravimetric density (the hydrogen storage capacity) reaches up to 5.61 wt% with an average adsorption energy of 0.587 eV/H₂. Based on these results, we infer that C₄Ti₈N₈ fullerene is a potential material for hydrogen storage with high capacity and might motivate active experimental efforts in designing hydrogen storage media.

Photophysics of nanographenes: from polycyclic aromatic hydrocarbons to graphene nanoribbons

Graphene quantum dots (GQDs) and nanoribbons (GNRs) are classes of nanographene molecules that exhibit highly tunable photophysical properties. There have been great strides in recent years to advance our understanding of nanographene photophysics and develop their use in light-harvesting systems, such as artificial photosynthesis. Here, we review the latest studies of GQDs and GNRs which have shed new light onto their photophysical underpinnings through computational and advanced spectroscopic techniques. We discuss how the size, symmetry, and shape of nanographenes influence their molecular orbital structures and, consequentially, their spectroscopic signatures. The scope of this review is to comprehensively lay out the general photophysics of nanographenes starting with benzene and building up to larger polycyclic aromatic hydrocarbons, GQDs, and GNRs. We also explore a collection of publications from recent years that build upon the current understanding of nanographene photophysics and their potential application in light-driven processes from display, lasing, and sensing technology to photocatalytic water splitting.

Simultaneous enantioseparation and simulation studies of atenolol, metoprolol and propranolol on Chiralpak® IG column using supercritical fluid chromatography

Enantioseparation of three β-blockers, i.e., atenolol, metoprolol and propranolol, was studied on amylose tris(3-chloro-5-methylphenylcarbamate) immobilized chiral stationary phase using supercritical fluid chromatography (SFC). The effect of organic modifiers (methanol, isopropanol and their mixture), column temperature and back pressure on chiral separation of β-blockers was evaluated. Optimum chromatographic separation with respect to resolution, retention, and analysis time was achieved using a mixture of CO₂ and 0.1% isopropyl amine in isopropanol: methanol (50:50, V/V), in 75:25 (V/V) ratio. Under the optimized conditions, the resolution factors (R_s) and separation factors (α) were greater than 3.0 and 1.5, respectively. Further, with increase in temperature (25–45 °C) and pressure (100–150 bars) there was corresponding decrease in retention factors (k), α and R_s. However, a reverse trend (α and R_s) was observed for atenolol with increase in temperature. The thermodynamic data from van't Hoff plots revealed that the enantioseparation was enthalpy driven for metoprolol and propranolol while entropy driven for atenolol. To understand the mechanism of chiral recognition and the elution behavior of the enantiomers, molecular docking studies were performed. The binding energies obtained from simulation studies were in good agreement with the elution order found experimentally and also with the free energy values. The method was validated in the concentration range of 0.5–10 μg/mL for all the enantiomers. The limit of detection and limit of quantitation ranged from 0.126 to 0.137 μg/mL and 0.376–0.414 μg/mL, respectively. The method was used successfully to analyze these drugs in pharmaceutical preparations.

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Simultaneous enantioseparation of three β-blockers in a single analysis using chiral SFC

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Separation efficiency was mainly dependent on the nature and composition of mobile phase

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van't Hoff plots revealed enthalpy driven process for metoprolol and propranolol and entropy driven for atenolol

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Binding energies from molecular docking study were in good agreement with the elution order

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The results suggested hydrogen bonding and hydrophobic interactions, as the dominant interaction modes.

Identification of Cytochrome P450 Isozymes Involved in Enantioselective Metabolism of Fipronil in Fish Liver: In Vitro Metabolic Kinetics and Molecular Modeling

Fipronil has been frequently detected in waterways worldwide at concentrations that threaten aquatic organisms, yet the metabolic behavior of fipronil enantiomers in aquatic organisms is largely unknown, which is of significance in enantioselective toxicity evaluation. We quantitatively identified the specific cytochrome P450 (CYP) isozymes involved in metabolizing fipronil enantiomers in tilapia by combining in vitro metabolic kinetic assays and molecular docking. Inhibition studies suggested that CYP1A enzyme was the main isoform catalyzing metabolism of fipronil and that CYP3A contributed in a limited way to the metabolism in fish liver S9. Both the dissipation rate constant and the maximum metabolic velocity of R-(-)-fipronil were greater than those of S-(+)-fipronil in tilapia liver S9, suggesting that tilapia selectively metabolized R-(-)-fipronil. The CYP1A1 isozyme exhibited the highest binding capacity to R-(-)-fipronil and S-(+)-fipronil (binding energy -9.39 and -9.17 kcal/mol, respectively), followed by CYP1A2 (-7.30 and -6.94 kcal/mol, respectively) and CYP3A4 (-7.16 and -6.91 kcal/mol, respectively). The results of in vitro metabolic assays and molecular docking were consistent, that is, CYP1A, specifically CYP1A1, exhibited a higher metabolic capacity to fipronil than CYP3A, and fish liver S9 selectively metabolized R-(-)-fipronil. The present study provides insight into the enantioselective metabolic behavior and toxicological implications of the in vitro metabolic kinetics of fipronil in fish. Environ Toxicol Chem 2022;41:230-239. © 2021 SETAC.

A Microcolumn DC Graphene Sensor for Rapid, Sensitive, and Universal Chemical Vapor Detection

Nearly all existing direct current (DC) chemical vapor sensing methodologies are based on charge transfer between sensor and adsorbed molecules. However, the high binding energy at the charge-trapped sites, which is critical for high sensitivity, significantly slows sensors' responses and makes the detection of nonpolar molecules difficult. Herein, by exploiting the incomplete screening effect of graphene, we demonstrate a DC graphene electronic sensor for rapid (subsecond) and sensitive (ppb) detection of a broad range of vapor analytes, including polar, nonpolar, organic, and inorganic molecules. Molecular adsorption induced capacitance change in the graphene transistor is revealed to be the main sensing mechanism. A novel sensor design, which integrates a centimeter-scale graphene transistor and a microfabricated flow column, is pioneered to enhance the fringing capacitive gating effect. Our work provides an avenue for a broad spectrum real-time gas sensing technology and serves as an ideal testbed for probing molecular physisorption on graphene.

The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2

Mutations in the receptor binding domain (RBD) in SARS-CoV-2 are shown to enhance its replication, transmissibility, and binding to host cells. Recently, a new strain is reported in India that includes a mutation (T478K, and L452R) in the RBD, that is possibly increasing the infection rate. Here, using Molecular Mechanics (MM) and Monte Carlo (MC) sampling, we show that the double mutant variant of SARS-CoV-2 induced conformational change in ACE2-E37, which enhanced the electrostatic interactions by the formation of a salt-bridge with SARS-CoV-2-R403. In addition, we observed that the double mutated structure induced a significant change in the salt-bridge electrostatic interaction between RBD-T500 and ACE2-D355. Where that this interaction lost more than 70% of its value compared to its value in WT protein.

Thermal stability of water polyhedra with square faces

The ability to form numerous crystalline modifications of ice and gas hydrate frameworks is a characteristic feature of water. In fact, this structural variety is much wider due to the proton disorder. Configurations with different arrangements of hydrogen atoms (protons) in hydrogen bonds are not equivalent in their properties. Polyhedral water clusters are convenient objects for studying the effect of proton disorder on the properties of ice-like systems. It was previously established that the stability of water polyhedra is determined by the competition of two factors. The geometric factor gives preference to tetrahedrally coordinated structures with a large number of pentagonal faces. The topological factor takes into account the number of energetically most favorable types of H-bonds. This number increases with the number of square faces. It was found that tetrahedrally coordinated structures are not the most stable. However, these calculations were performed without taking thermal effects into account (Kirov M. V., J Phys Chem A, 124:4463 - 4470, 2020). The purpose of the present article is to study the structural stability of various water polyhedra at different temperatures. In the course of modeling, using the Amoeba force field, the advantage of configurations with a large number of square faces is demonstrated. The structure and energetics of surface defects are studied. Several very stable structures of unusual shape were found, including polyhedra which contain 4-coordinated molecules and polyhedra whose O-H groups are directed to the cluster center. The comparative analysis of cluster stability includes the temperature intervals of melting-like transitions.

Exploration of In-silico screening of therapeutic agents against SARS-CoV-2

In the present investigation, molecular docking studies have been performed using AutoDock Vina to investigate the role of ligand-binding affinity at the hydrophobic pocket of COVID-19. The knowledge of the binding of protein receptors with ligand molecules is essential in drug discovery processes. Hydroxamic acids with reported biological activity, have been investigated for docking to an important target, SARS-CoV-2, in order to predict their therapeutic efficacy. The spike protein of the coronavirus is responsible for the attachment to host cells and a positive-sense single-strand RNA, (+)ssRNA, is a genetic material that can be translated into protein in the host cell. We modeled the structure of SARS-CoV-2 with the ligands, hydroxamic acids. They show binding capability with both, Spike protein and (+)ssRNA. The twain exhibit negative binding energies which signify that reactions are spontaneous, strong, and fast. The present research proposed hydroxamic acids as molecules which can be used for the development of anti-virals therapeutics against SARS-CoV-2.

Antiproliferative, apoptosis-inducing activity and molecular docking studies of sydnones compounds

Objective

To evaluate the antiproliferative and apoptosis inducing activity of different sydnones on cancer cell lines and their interaction with cancer proteins by molecular docking studies.

Material and Methods

Antiproliferative activity was carried out by MTT assay and apoptosis inducing activity was performed by DAPI and Annexin V and propidium iodide staining. Molecular docking studies were performed using AutoDock Tools 1.5.6. Pharmacokinetics properties like ADME and toxicity were analysed by pkCSM web server.

Result

In this study, four new sydnone compounds 3-(4-nonylbiphenyl-4'-yl) sydnone (MC-182), 3-(4-propylbiphenyl-4'-yl) sydnone (MC-454), 3-(4-hexylbiphenyl-4'-yl) sydnone (MC-433), and 3-(4-methylbiphenyl-4'-yl) sydnone (MC-431) were screened for antiproliferative and apoptotic effect against BT-474 (human breast cancer), HeLa (human cervical cancer) and Jurkat (human myeloid leukemia) Mostly, all the sydnone compounds exhibited decent antiproliferative effectiveness, but compound MC-431, MC-433, and MC-454 showed more antiproliferative activity (IC50 1.71, 10.09 and 2.87 μM against BT-474, Hela and Jurkat cell line, respectively). The changes of morphological characteristics of cancer cells determined by staining techniques indicate the apoptotic cell death. The molecular docking and interaction studies were carried out between sydnones with cancer proteins (epidermal growth factor domain receptor tyrosine kinase [EGF-TK], tumor necrosis factor-alpha [TNF-α] and Caspase3. Among all four sydnone molecules, two compounds MC-454 and MC-431 showed good binding energy with targeted proteins. Drug-like property was predicted by ADME toxicity study.

Conclusion

The results indicate sydnone compounds were found to exhibit anticancer activity by inducing apoptosis. The molecular docking study of sydnones with cancer proteins showed a decent interaction affinity. The results of absorption, distribution, metabolism, excretion and toxicity studies by the Insilco approach also proved that MC-454 sydnone showed better In-Vivo administration. Thus, the current research work indicates that these sydnone compounds would be prospective in developing anticancer medicines.

Identification of Mpro inhibitors of SARS-CoV-2 using structure based computational drug repurposing

The recent outbreak of COVID-19, caused by the novel pathogen SARS-coronavirus 2 (SARS-CoV-2) is a severe health emergency. In this pandemic, drug repurposing seems to be the most promising alternative to identify effective therapeutic agents for immediate treatment of infected patients. The present study aimed to evaluate all the drugs present in drug bank as potential novel SARS-CoV-2 inhibitors, using computational drug repurposing studies. Docking-based virtual screening and binding energy prediction were performed, followed by Absorption Distribution Metabolism Excretion calculation. Hydroxychloroquine and Nelfinavir have been identified as the best potential inhibitor against the SARS-CoV-2, therefore, they were used as reference compounds in computational DR studies. The docking study revealed 13 best compounds based on their highest binding affinity, binding energy, and dock score concerning the other screened compounds. Out of 13, only 4 compounds were further shortlisted based on their binding energy and best ADME properties. The hierarchical virtual screening yielded the best 04 drugs, DB07042 (compound 2), DB13035 (compound 3), DB13604 (compound 5) and DB08253 (compound 6), with commendable binding energies in kcal/mol, i.e. −65.45, −62.01, −52.09 and −51.70 respectively. Further, Molecular dynamics simulation with 04 best-retrieved hits has confirmed stable trajectories in protein in terms of root mean square deviation and root mean square fluctuation. During 30 ns simulation, the interactions were also found similar to the docking-based studies. However, clinical studies are necessary to investigate their therapeutic use against this outbreak.

Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function

In order to evaluate the interactions between a potential drug candidate like inhibitor N3 and the residues in substrate binding site of SARS-CoV-2 main protease (M pro ), we used molecular docking and dynamics simulations. The structural features describing the degrees of folding states ofM pro formed by beta-barrels and alpha-helices were analyzed by means of root mean square deviation, root mean square fluctuation, radius of gyration, residue velocity, H-bonding, dihedral angle distributions and radial distribution function. All of the residues forming ligand binding domain (LBD) ofM pro lie within the allowed region of the dihedral angle distributions as observed from the equilibrating best pose ofM pro -N3 system. Sharp peaks of radial distribution function (RDF) for H-bonding atom pairs (about 2 Å radial distance apart) describe the strong interactions between inhibitor and SARS-CoV-2M pro . During MD simulations, HSE163 has the lowest residue speed offering a sharp RDF peak whereas GLN192 has the highest residue speed resulting a flat RDF peak for the H-bonding atom pairs ofM pro -N3 system. Along with negative values of coulombic and Lenard-Jones energies, MM/PBSA free energy of binding contributed by the non-covalent interactions betweenM pro and N3 has been obtained to be -19.45 ± 3.6 kcal/mol. These physical parameters demonstrate the binding nature of an inhibitor inM pro -LBD. This study will be helpful in evaluating the drug candidates which are expected to inhibit the SARS-CoV-2 structural proteins.

Balanced lipase interactions for degradation-controlled paclitaxel release from lipid cubic phase formulations

Lipid cubic phase (LCP) formulations enhance the intestinal solubility and bioavailability of hydrophobic drugs by reducing precipitation and facilitating their mass transport to the intestinal surface for absorption. LCPs with an ester linkage connecting the acyl chain to the glycerol backbone (monoacylglycerols), are susceptible to chemical digestion by several lipolytic enzymes including lipases, accelerating the release of hydrophobic agents from the lipid bilayers of the matrix. Unlike regular enzymes that transform soluble substrates, lipolytic enzymes act at the interface of water and insoluble lipid. Therefore, compounds that bind to this interface can enhance or inhibit the activity of enzymes to varying extent. Here, we explore how the lipolysis rate can be tuned by the interfacial interaction of porcine pancreatic lipase with monoolein LCPs containing a known lipase inhibitor, tetrahydrolipstatin. Release of the Biopharmaceutical Classification System (BCS) class IV drug, paclitaxel, from the inhibitor-modified LCP was examined in the presence of lipase and its effectors colipase and calcium. By combining experimental dynamic digestion studies, thermodynamic measurements and molecular dynamics simulations of the competitive inhibition of lipase by tetrahydrolipstatin, we reveal the role and mode of action of lipase effectors in creating a precisely-balanced degradation-controlled LCP release system for the poorly soluble paclitaxel drug.

Molecular dynamics investigation of structural and mechanical properties of silica nanorod reinforced dental resin composites

In this work, molecular dynamics simulations are conducted to investigate the structural and mechanical properties of dental materials, i.e., the silica nanorod reinforced Bis-GMA/TEGDMA resin composite. The effects of loading content and size of the silica nanorods on the composite stiffness were performed by examining resin chain conformation, hydrogen bonds and matrix/filler binding energy. It is revealed that the presence of the silica nanorod causes polymer chain expansion, endowing the resins with higher stiffness. Moreover, the volumetric hydrogen bonds and binding energy increase considerably with the loading content, but decrease gradually with the diameter or show almost independence of the length. Furthermore, the composite moduli were quantified by the micromechanics models and the transverse moduli were well predicted by the Counto model, signifying a perfect bonding between the matrix and nanorod. The chain expansion and energetic matrix/filler interactions are believed to contribute to the significant mechanical reinforcement of the composites with the loading content. However, the length of the nanorod has a little effect on the composite moduli due to the unaltered interfacial interaction. In contrast, a smaller diameter is supposed to give a larger modulus, and this is not observed in this work due to the synergic effects of improved matrix/filler interaction and actual reduced filler volume fraction. The mechanical enhancement by the rod-like structures is more influenced by the loading content, but less so by the size of the nanorod, and it also exhibits superior mechanical performance as compared to nanoparticles. The findings thus extend the current understanding of the nanostructure and mechanical properties of silica nanorod reinforced dental resin composites from an atomic/molecular perspective.

Theoretical study of the interactions between peptide tyrosine tyrosine [PYY (1-36)], a newly identified modulator in type 2 diabetes pathophysiology, with receptors NPY1R and NPY4R

PURPOSE

Diabetes mellitus is a common condition in the clinically obese. Bariatric surgery is one of the ways to put type 2 diabetes in remission. Recent findings propose the appetite-regulator peptide tyrosine tyrosine (PYY) as a therapeutic option for patients with type 2 diabetes. This novel gut hormone restores impaired insulin and glucagon secretion in pancreatic islets and is implicated in type 2 diabetes reversal after bariatric surgery. The current study elucidates the interactions between PYY and the NPY1R and NPY4R receptors using computational methods.

METHODS

Protein structure prediction, molecular docking simulation, and molecular dynamics (MD) simulation were performed to elucidate the interactions of PYY with NPY1R and NPY4R.

RESULTS

The predicted binding models of PYY-NPY receptors are in agreement with those described in the literature, although different interaction partners are presented for the C-terminal tail of PYY. Non-polar interactions are predicted to drive the formation of the protein complex. The calculated binding energies show that PYY has higher affinity for NPY4R (ΔG_GBSA = -65.08 and ΔG_PBSA = -87.62 kcal/mol) than for NPY1R (ΔG_GBSA = -23.11 and ΔG_PBSA = -50.56 kcal/mol).

CONCLUSIONS

Based on the constructed models, the binding conformations obtained from docking and MD simulation for both the PYY-NPY1R and PYY-NPY4R complexes provide a detailed map of possible interactions. The calculated binding energies show a higher affinity of PYY for NPY4R. These findings may help to understand the mechanisms behind the improvement of diabetes following bariatric surgery.

Computational Studies of Selected Transition Metal Complexes as Potential Drug Candidates against the SARS-CoV-2 Virus

The earth has witnessed the greatest global health crisis due to the outbreak of the SARS-CoV-2 virus in late 2019, resulting in the pandemic COVID-19 with 3.38 million mortality and 163 million infections across 222 nations. Therefore, there is an urgent need for an effective therapeutic option against the SARS-CoV-2 virus. Transition metal complexes with unique chemical, kinetic and thermodynamic properties have recently emerged as the viable alternative for medicinal applications. Herein, the potential application of selected antiviral transition metal-based compounds against the SARS-CoV-2 virus was explored in silico. Initially, the transition metal-based antiviral compounds (1-5) were identified based on the structural similarity of the viral proteins (proteases, reverse transcriptase, envelop glycoproteins, etc.) of HIV, HCV, or Influenza virus with the proteins (S-protein, RNA-dependent RNA polymerase, proteases, etc) of SARS-CoV-2 virus. Hence the complexes (1-5) were subjected to ADME analysis for toxicology and pharmacokinetics report and further for the molecular docking calculations, selectively with the viral proteins of the SARS-CoV-2 virus. The molecular docking studies revealed that the iron-porphyrin complex (1) and antimalarial drug, ferroquine (2) could be the potential inhibitors of Main protease (Mpro) and spike proteins respectively of SARS-CoV-2 virus. The complex 1 exhibited high binding energy of -11.74 kcal/mol with the Mpro of SARS-CoV-2. Similarly ferroquine exhibitred binding energy of -7.43 kcal/mol against spike protein of SARS-CoV-2. The complex 5 also exhibited good binding constants values of -7.67, -8.68 and -7.82 kcal/mol with the spike protein, Mpro and RNA dependent RNA polymerase (RdRp) proteins respectively. Overall, transition metal complexes could provide an alternative and viable therapeutic solution for COVID-19.

In-silico study of peptide-protein interaction of antimicrobial peptides potentially targeting SARS and SARS-CoV-2 nucleocapsid protein

This study is an attempt to find a suitable therapy using antimicrobial peptides (AMPs) by identifying peptide-protein interaction of AMPs and nucleocapsid protein of SARS and SARS-CoV- 2. The AMPs were shortlisted from the APD3 database (Antimicrobial peptide database) based on various physicochemical parameters. The binding efficacy of AMPs was measured using the lowest energy score of the docked complexes with 10 selected AMPs. For SARS-CoV, AP00180 showed the best pose with a binding affinity value of - 6.4 kcal/mol. Prominent hydrogen bonding interactions were observed between Lys85 (nucleocapsid receptor) and Arg13 (antimicrobial peptide ligand) having the least intermolecular distance of 1.759 Å. For SARS-CoV-2, AP00549 was docked with a binding affinity value of - 3.4 kcal/mol and Arg119 and Glu14 of receptor nucleocapsid protein and ligand AMP having the least intermolecular distance of 2.104 The dynamic simulation was performed at 50 ns to check the stability of the final docked complexes, one with each protein. The two best AMPs were AP00180 (Human Defensin-5) for SARS and AP00549 (Plectasin) for SARS-CoV-2. From positive results of dynamic simulation and previously known knowledge that some AMPs interact with the nucleocapsid of coronaviruses, these AMPs might be used as a potential therapeutic agent for the treatment regime of SARS-CoV-2 and SARS infection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-021-00103-z.

The impact of curcumin derived polyphenols on the structure and flexibility COVID-19 main protease binding pocket: a molecular dynamics simulation study

The newly occurred SARS-CoV-2 caused a leading pandemic of coronavirus disease (COVID-19). Up to now it has infected more than one hundred sixty million and killed more than three million people according to 14 May 2021 World Health Organization report. So far, different types of studies have been conducted to develop an anti-viral drug for COVID-19 with no success yet. As part of this, silico were studied to discover and introduce COVID-19 antiviral drugs and results showed that protease inhibitors could be very effective in controlling. This study aims to investigate the binding affinity of three curcumin derived polyphenols against COVID-19 the main protease (Mpro), binding pocket, and identification of important residues for interaction. In this study, molecular modeling, auto-dock coupled with molecular dynamics simulations were performed to analyze the conformational, and stability of COVID-19 binding pocket with diferuloylmethane, demethoxycurcumin, and bisdemethoxycurcumin. All three compounds have shown binding affinity −39, −89 and −169.7, respectively. Demethoxycurcumin and bisdemethoxycurcumin showed an optimum binding affinity with target molecule and these could be one of potential ligands for COVID-19 therapy. And also, COVID-19 main protease binding pocket binds with the interface region by one hydrogen bond. Moreover, the MD simulation parameters indicated that demethoxycurcumin and bisdemethoxycurcumin were stable during the simulation run. These findings can be used as a baseline to develop therapeutics with curcumin derived polyphenols against COVID-19.

A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution

Conformational search for the most stable geometry connection of 16 sets of polydopamine (PDA) tetramer subunits has been systematically investigated using density functional theory (DFT) calculations. Our results indicated that the more planar subunits are, the more stable they are. This finding is in good agreement with recent experimental observations, which have suggested that PDA are composed of the nearly planar subunits that appear to be stacked together via the π-π interactions to form graphite-like layered aggregates associated with the balance of the intramolecular hydrogen bonds and steric effects from the indole and catechol moieties. Molecular dynamics (MD) simulations of 16 spherical clusters of the tetramer subunits of PDA in the gas and aqueous phase were performed at 298 K and confirmed the stability of supramolecular tetramer aggregates. The complex formation and binding energy of all 16 clusters are very strong although the shapes of the clusters in aqueous solution are not spherical and are very much different from those in the gas phase. The aggregations of all 16 clusters in aqueous solution were also confirmed from the profiles of the Kratky plot and the radius of gyration of all clusters. Our MD results in both gas phase and aqueous solution pointed out that there are high possibilities of aggregations of the 16 kinds of tetramer subunits although the conformations of each tetramer subunit are not flat. In summary, this work brings an insight into the controversial structure of PDA tetramer units and explains some of the important structural features found in the aqueous phase in comparison to the gas phase.

Dataset on structure and physical properties of stable diatomic systems based on van der Waals density functional method

With the influence of progress in the materials informatics, development of fundamental database has been attracting growing interest. The bonding between atoms is essential component of all kinds of materials and govern their structure, stability, and properties. When we try to understand a material by breaking it down into microscopic components, bonding of diatomic system is the most fundamental. In the field of spectroscopy, diatomic molecular spectroscopy data has been studied well, and the diatomic molecular spectroscopy database [1] has been constructed recently. Concerning electronic structure, however, there is no easily accessible database of diatomic system. In order to develop a database of diatomic systems, it is important to consider adequate interaction. In addition to covalent bonding, van der Waals (vdW) interaction is also known to play an essential role especially in describing weak bonding systems such as noble gas dimers, atomic or molecular absorption, and layered materials. Thus, vdW interaction must be considered to develop database of diatomic systems so that it can be used for general purposes. One of its theoretical implementations is vdW density functional (vdW-DF) method [2], which has been developed within the framework of density functional theory 3 (DFT) and has been showing its effectiveness as general-purpose method. In this data article, we provide a vdW-DF-based calculation dataset focusing on diatomic systems. All diatomic systems containing atoms from H (Z = 1) to Ra (Z = 88) were considered, and stable structures and properties of more than 2,900 stable diatomic systems has been calculated correctly. This cyclopedic dataset of diatomic systems with consideration of vdW interaction can be useful building blocks for understanding, describing, and predicting interaction of atoms.

Interlayer engineering of molybdenum disulfide toward efficient electrocatalytic hydrogenation

Electrocatalytic hydrogenation (ECH) enables the sustainable production of chemicals under ambient condition; however, suffers from serious competition with hydrogen (H₂) evolution and the use of precious metals as electrocatalysts. Herein, molybdenum disulfide is for the first time developed as an efficient and noble-metal-free catalyst for ECH via in situ intercalation of ammonia or alkyl-amine cations. This interlayer engineering regulates phase transition (2H → 1 T), and effectively ameliorates electronic configurations and surface hydrophobicity to promote the ECH of biomass-derived oxygenates, while prohibiting H₂ evolution. The optimal one intercalated by dimethylamine (MoS₂-DMA) is capable of hydrogenating furfural (FAL) to furfuryl alcohol with high Faradaic efficiency of 86.3%-73.3% and outstanding selectivity of >95.0% at -0.25 to -0.65 V (vs. RHE), outperforming MoS₂ and other conventional metals. Such prominent performance stems from the enhanced chemisorption and surface hydrophobicity. The chemisorption of H intermediate and FAL, synchronously strengthened on the edge-sites of MoS₂-DMA, accelerates the surface elementary step following Langmuir-Hinshelwood mechanism. Moreover, the improved hydrophobicity benefits FAL affinity to overcome diffusion limitation. Discovering the effective modulation of MoS₂ from a typical H₂ evolution electrocatalyst to a promising candidate for ECH, this study broadens the scope to exploit catalysts used for electrochemical synthesis.

Characterization of titanium influences on structure and thermodynamic stability of novel C20-nTin nanofullerenes (n=1-5): a density functional perspective

In this survey, effects of titanium heteroatom(s) on structural parameters and thermodynamic stability of C₂₀ fullerene and its C_20-nTi_n derivatives (n = 1-5) are compared and contrasted, at DFT levels of theory. The results show that in going from C₁₉Ti₁ to C₁₅Ti₅, binding energy increases while absolute value heat of atomization decreases. According to vibrational frequency analysis, excepting C₁₆Ti_4-1, the other optimized structures give no imaginary frequency as true minima. The calculated binding energy of 887.12 kcal mol^-1/atom displays C₁₅Ti₅ as the most thermodynamically stable heterofullerene. It has C_s symmetry and contains five titanium atoms alternatively in equatorial position. The substitutional doping of C₂₀ fullerene leads to high Mülliken charge distribution upon the surfaces of the resulted heterofullerenes especially C₁₉Ti₁ as suitable hydrogen storage. The contour plots indicate the most negative electrostatic potential by red color for C atoms, whereas the most positive electrostatic potential by yellow color for Ti heteroatoms. The contour plots and multiwfn analysis exhibit charge transfer from titanium heteroatoms to the neighboring carbon atoms. Furthermore, the resulted electron density maps from multiwfn qualitatively confirm the contour plot's findings. The hydrogen adsorption is an endothermic process for C₂₀ fullerene and exothermic process for C_20-nTi_n heterofullerenes. Major criteria examined for thermodynamic stability; from C₁₉Ti₁ to C₁₅Ti₅, binding energy and hydrogen adsorption increase while heat of atomization decreases.

Molecular simulation studies of the interactions between the human/pangolin/cat/bat ACE2 and the receptor binding domain of the SARS-CoV-2 spike protein

The recent outbreak of SARS-CoV-2 has had a profound effect on the world. Similar to that in SARS-CoV, the entry receptor of SARS-CoV-2 is ACE2. The binding of SARS-CoV-2 spike protein to ACE2 is the critical to the virus infection. Recently multiple species (human, Chinese chrysanthemum, Malay pangolin and cat) have been reported to be susceptible to the virus infection. However, the binding capacity and the detailed binding mechanism of SARS-CoV-2 spike protein to ACE2 of these species remains unexplored. Herein free energy calculations with MM-GBSA and Potential of Mean Forces together reveal that the Human-SARS-CoV-2 has a higher stability tendency than Human-SARS-CoV. Meanwhile, we uncover that SARS-CoV-2 has an enhanced ability to bind with the ACE2 in humans, pangolins and cats compared to that in bats. Analysis of key residues with energy decomposition and residue contact maps reveal several important consensus sites in ACE2s among the studied species, and determined the more favorable specified residues among the different types of amino acids. These results provide important implications for understanding SARS-CoV-2 host range which will make it possible to control the spread of the virus and use of animal models, targeted drug screening and vaccine candidates against SARS-CoV-2.

Thermodynamic stability, structural and electronic properties for the C20-nAln heterofullerenes (n = 1-5): a DFT study

DFT calculations are utilized to compare and contrast the substituted aluminum-heterofullerenes, C_20-nAl_n (with n = 1-5) from thermodynamically view point, at density functional theory (DFT). Vibrational frequency analysis confirms that apart from C₁₅Al₅, all studied species are true minima. Considering the optimized geometries shows that all heterofullerenes are isolated-pentagon cage and none collapse to open deformed as segregated structure. The highest binding energy (5.56 eV/atom) and absolute heat of atomization (3323.68 kcal mol^-1) reveals open-shell C₁₉Al₁ as the most stable thermodynamic heterofullerene. The most NICS (0) (isotropic and anisotropic parameters, -49.58 and - 46.47 ppm, respectively) introduces closed-shell C₁₈Al_2-2 as the most aromatic structure. Also, closed-shell C₁₆Al_4-1 heterofullerene emerges with the most polarizability (307.71 a.u.) and hence activity to interact with the surrounding polar species. The lowest and the highest charge transfer on the surfaces of C₂₀ and C₁₆Al_4-2 without weak Al-Al bond, as the worst and the best candidate, respectively, provokes further investigation on impossible and possible application for hydrogen storage, respectively. We wish that the present survey will stimulate new experiments.

In silico analysis of carbohydrate-binding pockets in the lectin genes from various species of Canavalia

Legumes are endowed with an opulent class of proteins called lectins that can detect tenuous variations in carbohydrate structures and bind them reversibly with high affinity and specificity. The genus Canavalia, in the family of Leguminosae, is considered to be an affluent source of lectin. An effort has been made to analyse the sequences encoded by the lectin gene and its carbohydrate binding pockets from three species of Canavalia, including C. virosa, C. rosea, and C. pubescens. Crude seed extract showed highest haemagglutination titer against buffalo RBCs and has high affinity to mannose and trehalose. Amplification of the lectin gene by gene-specific primers showed the presence of an 870 bp amplicon. Physicochemical characterization using various bioinformatic tools showed that the isoelectric point was below 7, suggesting that lectin molecules were acidic. A high aliphatic index and high instability index were observed, which indicated that lectin molecules were stable towards a wide range of temperatures. The occurrence of N-glycosylation sites at two sites was also identified in all three species. Prediction of secondary structure showed that approximately 59.05 %, 56.76 % and 54.88 % of the elements were random coils in the case of C. virosa, C. pubescens and C. rosea, respectively. Comparative modelling of the proteins and docking of hypothetical models with sugar moieties that inhibited the agglutination activity suggested that asparagine, serine, alanine, valine, tyrosine and threonine were the major residues involved in hydrogen bonding and other stacking interactions. This can further provide insights on its prospective antibiosis property.

In silico studies of selected multi-drug targeting against 3CLpro and nsp12 RNA-dependent RNA-polymerase proteins of SARS-CoV-2 and SARS-CoV

An outbreak of a cluster of viral pneumonia cases, subsequently identified as coronavirus disease 2019 (COVID-19), due to a novel SARS-CoV-2 necessitates an urgent need for a vaccine to prevent infection or an approved medication for a cure. In our in silico molecular docking study, a total of 173 compounds, including FDA-approved antiviral drugs, with good ADME descriptors, and some other nucleotide analogues were screened. The results show that these compounds demonstrate strong binding affinity for the residues at the active sites of RNA-dependent RNA-polymerase (RdRp) modelled structures and Chymotrypsin-like cysteine protease (3CLpro) of the HCoV proteins. Free energies (ΔG's) of binding for SARS-CoV-2 and SARS-CoV RdRp range from - 5.4 to - 8.8 kcal/mol and - 4.9 to - 8.7 kcal/mol, respectively. Also, SARS-CoV-2 and SARS-CoV 3CLpro gave ΔG values ranging from - 5.1 to - 8.4 kcal/mol and - 5.5 to - 8.6 kcal/mol, respectively. Interesting results are obtained for ivermectin, an antiparasitic agent with broad spectrum activity, which gave the highest binding energy value (- 8.8 kcal/mol) against the 3CLpro of SARS-CoV-2 and RdRps of both SARS-CoV and SARS-CoV-2. The reason for such high binding energy values is probably due to the presence of hydroxy, methoxy and sugar moieties in its structure. The stability of the protein-ligand complexes of polymerase inhibitors considered in this investigation, such as Sofosbuvir, Remdesivir, Tenofovir, Ribavirin, Galidesivir, 5c3, 5h1 and 7a1, show strong to moderate hydrogen bonding and hydrophobic interactions (π-π stacked, π-π T-shaped, π-sigma and π-alkyl). The stability provided from such interactions translate into greater antiviral activity or inhibitory effect of the ligands. Assessment of the average free energies of binding of the FDA approved drugs are highly comparable for conformers of a particular inhibitor, indicating similar modes of binding within the pockets.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13721-021-00299-2.