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.     

Enhancement of β-Glucan Biological Activity Using a Modified Acid-Base Extraction Method from Saccharomyces cerevisiae

Beta glucan (β-glucan) has promising bioactive properties. Consequently, the use of β-glucan as a food additive is favored with the dual-purpose potential of increasing the fiber content of food products and enhancing their health properties. Our aim was to evaluate the biological activity of β-glucan (antimicrobial, antitoxic, immunostimulatory, and anticancer) extracted from Saccharomyces cerevisiae using a modified acid-base extraction method. The results demonstrated that a modified acid-base extraction method gives a higher biological efficacy of β-glucan than in the water extraction method. Using 0.5 mg dry weight of acid-base extracted β-glucan (AB extracted) not only succeeded in removing 100% of aflatoxins, but also had a promising antimicrobial activity against multidrug-resistant bacteria, fungi, and yeast, with minimum inhibitory concentrations (MIC) of 0.39 and 0.19 mg/mL in the case of resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa, respectively. In addition, AB extract exhibited a positive immunomodulatory effect, mediated through the high induction of TNFα, IL-6, IFN-γ, and IL-2. Moreover, AB extract showed a greater anticancer effect against A549, MDA-MB-232, and HepG-2 cells compared to WI-38 cells, at high concentrations. By studying the cell death mechanism using flow-cytometry, AB extract was shown to induce apoptotic cell death at higher concentrations, as in the case of MDA-MB-231 and HePG-2 cells. In conclusion, the use of a modified AB for β-glucan from Saccharomyces cerevisiae exerted a promising antimicrobial, immunomodulatory efficacy, and anti-cancer potential. Future research should focus on evaluating β-glucan in various biological systems and elucidating the underlying mechanism of action.     

Polyethylene Glycol Functionalized Graphene Oxide Nanoparticles Loaded with Nigella sativa Extract: A Smart Antibacterial Therapeutic Drug Delivery System

Flaky graphene oxide (GO) nanoparticles (NPs) were synthesized using Hummer’s method and then capped with polyethylene glycol (PEG) by an esterification reaction, then loaded with Nigella sativa (N. sativa) seed extract. Aiming to investigate their potential use as a smart drug delivery system against Staphylococcus aureus and Escherichia coli, the spectral and structural characteristics of GO-PEG NPs were comprehensively analyzed by XRD, AFM, TEM, FTIR, and UV- Vis. XRD patterns revealed that GO-PEG had different crystalline structures and defects, as well as a higher interlayer spacing. AFM results showed GONPs with the main grain size of 24.41 nm, while GONPs–PEG revealed graphene oxide aggregation with the main grain size of 287.04 nm after loading N. sativa seed extract, which was verified by TEM examination. A strong OH bond appeared in FTIR spectra. Furthermore, UV- Vis absorbance peaks at (275, 284, 324, and 327) nm seemed to be correlated with GONPs, GO–PEG, N. sativa seed extract, and GO –PEG- N. sativa extract. The drug delivery system was observed to destroy the bacteria by permeating the bacterial nucleic acid and cytoplasmic membrane, resulting in the loss of cell wall integrity, nucleic acid damage, and increased cell-wall permeability.     

基于图像的二维剪纸自动生成方法

中国剪纸的设计极具挑战性, 要求画面简洁、直观, 还需要表达特定的文化内涵, 且整张剪纸须整体连通。提出了一种基于图像的二维剪纸自动生成方法, 能够将任意数码照片自动转化为剪纸图形。首先,利用图像分割方法建立区域连接图; 接着, 基于该连接图对颜色、边界对比度和区域连通性进行数学建模, 并获得优化目标函数; 最后, 通过模拟退火算法求解目标方程, 自动生成保持图像内容的剪纸图形。还开发了连通性后处理和区域指定等用户交互工具, 允许用户在自动生成的剪纸图形中方便地加入个人设计。实验表明, 所生成的剪纸图形画面简洁、整体连通。 本方法在降低剪纸设计难度的同时还可满足个性化的设计需求, 有助于传播和传承我国的民间剪纸艺术。     

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.     

Zur Existenz von k-Kurven in endlichen Ebenen

We prove the existence of k-arcs in finite planes of order q with a lower bound b=b(q) for k.