Evidence for Multiple Binding Modes in the Initial Contact Between SARS-CoV-2 Spike S1 Protein and Cell Surface Glycans**

Infection of host cells by SARS-CoV-2 begins with recognition by the virus S (spike) protein of cell surface heparan sulfate (HS), tethering the virus to the extracellular matrix environment, and causing the subunit S1-RBD to undergo a conformational change into the ‘open’ conformation. These two events promote the binding of S1-RBD to the angiotensin converting enzyme 2 (ACE2) receptor, a preliminary step toward viral-cell membrane fusion. Combining ligand-based NMR spectroscopy with molecular dynamics, oligosaccharide analogues were used to explore the interactions between S1-RBD of SARS CoV-2 and HS, revealing several low-specificity binding modes and previously unidentified potential sites for the binding of extended HS polysaccharide chains. The evidence for multiple binding modes also suggest that highly specific inhibitors will not be optimal against protein S but, rather, diverse HS-based structures, characterized by high affinity and including multi-valent compounds, may be required.     

Thermal and biological studies of Schiff bases of chitosan derived from heteroaryl aldehydes

Journal of Thermal Analysis and Calorimetry - The synthesis of Schiff bases of chitosan is performed by the reaction of chitosan with different heteroaryl aldehydes, i.e., furfuraldehyde,...     

Discovery of novel inhibitors for <Emphasis Type="Italic">Leishmania</Emphasis> nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization

Nucleoside diphosphate kinases (NDKs) are ubiquitous enzymes that catalyze the transfer of the γ-phosphate moiety from an NTP donor to an NDP acceptor, crucial for maintaining the cellular level of nucleoside triphosphates (NTPs). The inability of trypanosomatids to synthesize purines de novo and their dependence on the salvage pathway makes NDK an attractive target to develop drugs for the diseases they cause. Here we report the discovery of novel inhibitors for Leishmania NDK based on the structural and functional characterization of purified recombinant NDK from Leishmania amazonensis. Recombinant LaNDK possesses auto-phosphorylation, phosphotransferase and kinase activities with Histidine 117 playing an essential role. LaNDK crystals were grown by hanging drop vapour diffusion method in a solution containing 18% PEG-MME 500, 100 mM Bis-Tris propane pH 6.0 and 50 mM MgCl₂. It belongs to the hexagonal space group P6₃22 with unit cell parameters a?=?b?=?115.18, c?=?62.18 Å and α?=?β?=?90°, γ?=?120°. The structure solved by molecular replacement methods was refined to crystallographic R-factor and R_free values of 22.54 and 26.52%, respectively. Molecular docking and dynamics simulation-based virtual screening identified putative binding compounds. Protein inhibition studies of selected hits identified five inhibitors effective at micromolar concentrations. One of the compounds showed ~45% inhibition of Leishmania promastigotes proliferation. Analysis of inhibitor-NDK complexes reveals the mode of their binding, facilitating design of new compounds for optimization of activities as drugs against leishmaniasis.     

A computational two scaled model for the simulation of micro-heterogeneous low-alloyed TRIP steels

In transformation induced plasticity (TRIP) steel a diffusionless austenitic-martensitic phase transformation induced by plastic deformation can be observed, resulting in excellent macroscopic properties. In particular low-alloyed TRIP steels, which can be obtained at lower production costs than high-alloyed TRIP steel, combine this mechanism with a heterogeneous arrangement of different phases at the microscale, namely ferrite, bainite, and retained austenite. The macroscopic behavior is governed by a complex interaction of the phases at the micro-level and the inelastic phase transformation from retained austenite to martensite. A reliable model for low-alloyed TRIP steel should therefore account for these microstructural processes to achieve an accurate macroscopic prediction. To enable this, we focus on a multiscale method often referred to as FE² approach, see [6]. In order to obtain a reasonable representative volume element, a three-dimensional statistically similar representative volume element (SSRVE) [1] can be used. Thereby, also computational costs associated with FE² calculations can be significantly reduced at a comparable prediction quality. The material model used here to capture the above mentioned microstructural phase transformation is based on [3] which was proposed for high alloyed TRIP steels, see also e.g. [8]. Computations based on the proposed two-scale approach are presented here for a three dimensional boundary value problem to show the evolution of phase transformation at the microscale and its effects on the macroscopic properties. (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Stability-Indicating High-Performance Thin-Layer Chromatographic Method for the Estimation of Ambroxol Hydrochloride and Doxofylline in a Pharmaceutical Formulation Using Experimental Design in Robustness Study

JPC – Journal of Planar Chromatography – Modern TLC - A sensitive, specific, and accurate stability-indicating high-performance thin-layer chromatographic method for the analysis of...     

The probability analysis of opening of DNA

We have studied the separation of a double stranded DNA (dsDNA), which is driven by either the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends not only on the sequence but also on the constraints on the chain in the experimental setups. Our results clearly demonstrate that the force-induced melting of dsDNA, whose one of the ends is constrained, is significantly different from the thermal melting, when both ends are free.     

Composition of a monoterpenoid-rich essential oil from the rhizome of Zingiber officinale from north western Himalayas

The chemical composition of the essential oil from the rhizome of ginger (Zingiber officinale Roscoe), collected from Nahan, Himachal Pradesh, India, was determined by gas chromatography and GC-MS. Fifty-one compounds, representing 95.1% of the oil, were identified. The oil was characterized by relatively large amounts of the monoterpenoids 1,8-cineole (10.9%), linalool (4.8%), borneol (5.6%), alpha-terpineol (3.6%), neral (8.1%), geraniol (14.5%), geranial (9.5%), trans-dimethoxy citral (5.0%) and geranyl acetate (6.3%). Five compounds, namely trans-linalool oxide, trans-linalool oxide acetate, (Z)-dimethoxycitral, (E)-dimethoxy citral and epi-zingiberenol are reported for the first time in oil of ginger.