Atomistic De-novo Inhibitor Generation-Guided Drug Repurposing for SARS-CoV-2 Spike Protein with Free-Energy Validation by Well-Tempered Metadynamics

Computational drug design is increasingly becoming important with new and unforeseen diseases like COVID-19. In this study, we present a new computational de novo drug design and repurposing method and applied it to find plausible drug candidates for the receptor binding domain (RBD) of SARS-CoV-2 (COVID-19). Our study comprises three steps: atom-by-atom generation of new molecules around a receptor, structural similarity mapping to existing approved and investigational drugs, and validation of their binding strengths to the viral spike proteins based on rigorous all-atom, explicit-water well-tempered metadynamics free energy calculations. By choosing the receptor binding domain of the viral spike protein, we showed that some of our new molecules and some of the repurposable drugs have stronger binding to RBD than hACE2. To validate our approach, we also calculated the free energy of hACE2 and RBD, and found it to be in an excellent agreement with experiments. These pool of drugs will allow strategic repurposing against COVID-19 for a particular prevailing conditions.     

A Cationic Zinc Hydride Cluster Stabilized by an N‐Heterocyclic Carbene: Synthesis,Reactivity, and Hydrosilylation Catalysis

The trinuclear cationic zinc hydride cluster [(IMes)₃Zn₃H₄(THF)](BPh₄)₂ ( 1 ) was obtained either by protonation of the neutral zinc dihydride [(IMes)ZnH₂]₂ with a Brønsted acid or by addition of the putative zinc dication [(IMes)Zn(THF)]²⁺. A triply bridged thiophenolato complex 2 was formed upon oxidation of 1 with PhS? SPh. Protonolysis of 1 by methanol or water gave the corresponding trinuclear dicationic derivatives. At ambient temperature, 1 catalyzed the hydrosilylation of aldehydes, ketones, and nitriles. Carbon dioxide was also hydrosilylated under forcing conditions when using (EtO)₃SiH, giving silylformate as the main product.     

Metal‐like Ductility in Organic Plastic Crystals: Role of Molecular Shape and Dihydrogen Bonding Interactions in Aminoboranes

Ductility is a common phenomenon in many metals but is difficult to achieve in molecular crystals. Organic crystals bend plastically on one or two face‐specific directions but fracture when stressed in any other arbitrary directions. An exceptional metal‐like ductility and malleability in the isomorphous crystals of two globular molecules, BH₃NMe₃ and BF₃NMe₃, is reported, with characteristic tensile stretching, compression, twisting, and thinning. The mechanically deformed samples, which transition to lower symmetry phases, retain good long‐range order amenable to structure determination by single‐crystal X‐ray diffraction. Molecules in these high‐symmetry crystals interact through electrostatic forces (B^??N⁺) to form columnar structures with multiple slip planes and weak dispersive forces between columns. On the other hand, the limited number of facile slip planes and strong dihydrogen bonding in BH₃NHMe₂ negates ductility. Our study has implications for the design of soft ferroelectrics, solid electrolytes, barocalorics, and soft robotics.     

Metabolite profiling and in-vitro colon cancer protective activity of Cycas revoluta cone extract

Abstract

The methanolic extract of Cycas revoluta cone (MECR) was analyzed by GC-MS and UHPLC for metabolite profiling and was evaluated for anti-colon cancer property by using in vitro assays like Cell Viability Assay, Colony Formation Assay, ROS Determination, Flowcytometry, DAPI staining assay, Tunel assay. GC-MS and HPLC analysis confirmed the presence of different phytochemicals in the extract of Cycas revoluta cone. In-vitro studies showed MECR extract showed significant anti-colon cancer activity by reducing proliferation and inducing apoptosis in colon cancer cell (HCT-8) line, but no such activity was seen in normal colon cell (CCD-18Co) line. The investigation confirms that MECR may be a promising candidate in colon cancer protection.     

DIC Challenge 2.0: Developing Images and Guidelines for Evaluating Accuracy and Resolution of 2D Analyses

Experimental Mechanics - The DIC Challenge 2.0 follows on from the work accomplished in the first Digital Image Correlation (DIC) Challenge Reu et al. (Experimental Mechanics 58(7):1067, 1). The...     

达芬奇效应:简便的数字视频

数字视频将引发人们与电子产品交互方式的变革。实现数字视频不但复杂,而且费时费钱。而这一切难题在达芬奇技术面前全部烟消云散。     

Advantage of Quantum Theory over Nonclassical Models of Communication

Quantum correlations provide dramatic advantage over the corresponding classical resources in several communication tasks. However, a broad class of probabilistic theories exists that attributes greater success than quantum theory in many of these tasks by allowing supra-quantum correlations in “space-like” and/or “time-like” paradigms. In this letter, a communication task involving three spatially separated parties is proposed where one party (verifier) aims to verify whether the bit strings possessed by the other two parties (terminals) are equal or not. This task is called authentication with limited communication, the restrictions on communication being: i) the terminals cannot communicate with each other, but (ii) each of them can communicate with the verifier through single use of channels with limited capacity. Manifestly, classical resources are not sufficient for perfect success of this task. Moreover, it is also not possible to perform this task with certainty in several nonclassical theories although they might possess stronger “space-like” and/or “time-like” correlations. Surprisingly, quantum resources can achieve the perfect winning strategy. The proposed task thus stands apart from all previously known communication tasks as it exhibits quantum advantage over other nonclassical strategies.     

Copper(I) complexes of N-(aryl)pyridine-2-aldimines: Spectral, electrochemical and catalytic properties

The reactions of N-(aryl)pyridine-2-aldimines (L-R; R = OCH₃, CH₃, H, Cl and NO₂), derived from pyridine-2-aldehyde and para-substituted anilines, with CuI in methanol under ambient conditions afford a series of brown complexes of the type [{Cu(L-R)I}₂]. The structure of the [{Cu(L-OCH₃)I}₂] complex has been determined by X-ray crystallography. In these dimeric complexes the two copper centers are linked through an iodo-bridge, and the L-R ligands are coordinated to the metal center through the pyridine-nitrogen and imine-nitrogen. All the complexes show characteristic ¹H NMR signals and intense MLCT transitions in the visible region. These complexes also show an emission near 465 nm, whilst they are excited at 340 nm, with relatively poor quantum yields (φ ∼0.002 at 298 K). Cyclic voltammetry on all the complexes shows two successive Cu(I)-Cu(II) oxidations on the positive side of SCE, and a reduction of the coordinated imine ligand on the negative side. These copper(I) complexes are found to efficiently catalyze Suzuki type C-C coupling reactions.     

Efficacious Anticancer Drug Delivery Mediated by a pH‐Sensitive Self‐Assembly of a Conserved Tripeptide Derived from Tyrosine Kinase NGF Receptor

We present herein a short tripeptide sequence (Lys–Phe–Gly or KFG) that is situated in the juxtamembrane region of the tyrosine kinase nerve growth factor (Trk NGF) receptors. KFG self‐assembles in water and shows a reversible and concentration‐dependent switching of nanostructures from nanospheres (vesicles) to nanotubes, as evidenced by dynamic light scattering, transmission electron microscopy, and atomic force microscopy. The morphology change was associated with a transition in the secondary structure. The tripeptide vesicles have inner aqueous compartments and are stable at pH 7.4 but rupture rapidly at pH≈6. The pH‐sensitive response of the vesicles was exploited for the delivery of a chemotherapeutic anticancer drug, doxorubicin, which resulted in enhanced cytotoxicity for both drug‐sensitive and drug‐resistant cells. Efficient intracellular release of the drug was confirmed by fluorescence‐activated cell sorting analysis, fluorescence microscopy, and confocal microscopy.     

Third body modeling in fretting using the combined finite-discrete element method

A new approach was developed for modeling the effect of the third body on fretting. This was accomplished using the combined finite-discrete element method (FDEM) in which the third body is analyzed as discrete elements while the first bodies are modeled using finite elements. This approach provides a link between large scale models which treat the mass of wear debris as a single or small number of bodies and small scale models which only study a control volume. The FDEM was used to analyze the behavior of third body particles between flat sliding surfaces. When the third body mass is composed of unconnected particles, it behaves as a Newtonian fluid, but this behavior ceases when the particles are connected into platelets. The FDEM was also used to study the behavior of third body particles inside a Hertzian line contact. As the number of particles and platelet size increase the load carried by the worn slip zone grows larger in relationship to the unworn stick zone.