Establishing an Analogue Based In Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease

The ongoing coronavirus pandemic has been a burden on the worldwide population, with mass fatalities and devastating socioeconomic consequences. It has particularly drawn attention to the lack of approved small-molecule drugs to inhibit SARS coronaviruses. Importantly, lessons learned from the SARS outbreak of 2002–2004, caused by severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), can be applied to current drug discovery ventures. SARS-CoV-1 and SARS-CoV-2 both possess two cysteine proteases, the main protease (M^pro) and the papain-like protease (PL^pro), which play a significant role in facilitating viral replication, and are important drug targets. The non-covalent inhibitor, GRL-0617, which was found to inhibit replication of SARS-CoV-1, and more recently SARS-CoV-2, is the only PL^pro inhibitor co-crystallised with the recently solved SARS-CoV-2 PL^pro crystal structure. Therefore, the GRL-0617 structural template and pharmacophore features are instrumental in the design and development of more potent PL^pro inhibitors. In this work, we conducted scaffold hopping using GRL-0617 as a reference to screen over 339,000 ligands in the chemical space using the ChemDiv, MayBridge, and Enamine screening libraries. Twenty-four distinct scaffolds with structural and electrostatic similarity to GRL-0617 were obtained. These proceeded to molecular docking against PL^pro using the AutoDock tools. Of two compounds that showed the most favourable predicted binding affinities to the target site, as well as comparable protein-ligand interactions to GRL-0617, one was chosen for further analogue-based work. Twenty-seven analogues of this compound were further docked against the PL^pro, which resulted in two additional hits with promising docking profiles. Our in silico pipeline consisted of an integrative four-step approach: (1) ligand-based virtual screening (scaffold-hopping), (2) molecular docking, (3) an analogue search, and, (4) evaluation of scaffold drug-likeness, to identify promising scaffolds and eliminate those with undesirable properties. Overall, we present four novel, and lipophilic, scaffolds obtained from an exhaustive search of diverse and uncharted regions of chemical space, which may be further explored in vitro through structure-activity relationship (SAR) studies in the search for more potent inhibitors. Furthermore, these scaffolds were predicted to have fewer off-target interactions than GRL-0617. Lastly, to our knowledge, this work contains the largest ligand-based virtual screen performed against GRL-0617.     

非肽类SARS冠状病毒3CL蛋白酶抑制剂的设计与活性表征

SARS冠状病毒3CL蛋白酶是SARS病毒复制过程中的主要蛋白酶, 针对其开展药物设计有望得到有效的抗SARS病毒药物. 本文基于SARS冠状病毒3CL蛋白酶的三维结构, 对现有化学试剂及临床用药数据库进行虚拟筛选, 选出可能对SARS冠状病毒3CL蛋白酶有抑制的非肽化合物进行初步活性测试, 并研究了已知的人鼻病毒3C蛋白酶抑制剂对SARS冠状病毒3CL蛋白酶的活性, 合成了两种母环的衍生物, 得到靛红和哌嗪两类SARS冠状病毒3CL蛋白酶的抑制剂, 其中一个靛红类化合物的IC₅₀为0.76 µmol•L^－1; 而抗组胺药哌嗪类化合物对SARS冠状病毒3CL蛋白酶及细胞培育的SARS病毒的抑制作用, 提示了老药可以开发出新的用途.     

SARS病毒核衣壳蛋白的表达与鉴定

依据Genebank中SARS基因组序列和酵母菌对密码子的选择性,采用人工合成的方法,合成了优化的SARS病毒核衣壳蛋白(N)的全基因(1296bp),与CTL表位基因(195bp)重组后,将其克隆到酵母分泌型表达载体pPIC9K中,构建成重组表达载体pPIC9K-N.重组载体转化毕赤酵母GS115,并经MD平板和MM平板筛选及PCR鉴定,得到阳性重组酵母工程菌GS115-pPIC9K-N.用甲醇诱导其分泌表达目的蛋白并对表达产物进行分析、浓缩与鉴定.结果表明,SARS病毒核衣壳蛋白能实现在毕赤酵母中高效表达,表达量达到20%,初步纯化后的产物具有良好的抗原特异性.     

Titanium (IV) complexes of some tetra‐dentate symmetrical bis‐Schiff bases of 1,6‐hexanediamine: Synthesis,characterization, and in silico prediction of potential inhibitor against coronavirus (SARS‐CoV‐2)

Symmetrical bis‐Schiff bases (LH ₂) have been synthesized by the condensation of 1,6‐hexanediamine (hn) and carbonyl or dicarbonyl. One of the synthesized Schiff bases has been subjected to the molecular docking for the prediction of their potentiality against coronavirus (SARS‐CoV‐2). Molecular docking revealed that tested Schiff base possessed high binding affinity with the receptor protein of SARS CoV‐2 compared with hydroxychloroquine (HCQ). The ADMET analysis showed that ligand is non‐carcinogenic and less toxic than standard HCQ. Schiff bases acting as dibasic tetra‐dentate ligands formed titanium (IV) complexes of the type [TiL(H₂O)₂Cl₂] or [TiL(H₂O)₂]Cl₂ being coordinated through ONNO donor atoms. Ligands and complexes were characterized by the elemental analysis and physicochemical and spectroscopic data including FTIR, ¹H NMR, mass spectra, UV‐Visible spectra, molar conductance, and magnetic measurement. Optimized structures obtained from quantum chemical calculations supported the formation of complexes. Antibacterial, antifungal, and anti‐oxidant activity assessments have been studied for synthesized ligands and complexes.     

新型全新风"免疫"空调系统的初步研究

提出了一种新型的,基于高效换热和间接蒸发冷却的全新风免疫空调系统,从理论和热力计算等方面对全新风系统和回风系统做了比较。初步研究结果表明,该新型全新风系统不但可以从根本上改善室内空气品质,而且其能量消耗水平与现有回风空调系统相接近,具有良好的研究开发前景。     

Biosensors and rapid diagnostic tests on the frontier between analytical and clinical chemistry for biomolecular diagnosis of dengue disease: a review

The past decades have witnessed enormous technological improvements towards the development of simple, cost-effective and accurate rapid diagnostic tests for detection and identification of infectious pathogens. Among them is dengue virus, the etiologic agent of the mosquito-borne dengue disease, one of the most important emerging infectious pathologies of nowadays. Dengue fever may cause potentially deadly hemorrhagic symptoms and is endemic in the tropical and sub-tropical world, being also a serious threat to temperate countries in the developed world. Effective diagnostics for dengue should be able to discriminate among the four antigenically related dengue serotypes and fulfill the requirements for successful decentralized (point-of-care) testing in the harsh environmental conditions found in most tropical regions. The accurate identification of circulating serotypes is crucial for the successful implementation of vector control programs based on reliable epidemiological predictions. This paper briefly summarizes the limitations of the main conventional techniques for biomolecular diagnosis of dengue disease and critically reviews some of the most relevant biosensors and rapid diagnostic tests developed, implemented and reported so far for point-of-care testing of dengue infections. The invaluable contributions of microfluidics and nanotechnology encompass the whole paper, while evaluation concerns of rapid diagnostic tests and foreseen technological improvements in this field are also overviewed for the diagnosis of dengue and other infectious and tropical diseases as well.     

关于SARS的预测模型

建立了确诊病例和疑似病例累计人数随时间变化的差分方程模型.通过对其求解和合理的假设讨论了确诊病例数在不同的阶段随时间变化的情况.进一步,用我们的模型来模拟北京疫情(2003.4.20—2003.5.29)的变化情况.说明我们的模型具有一定的实用性.     

Asymptotic behavior of an SEI epidemic model with diffusion

An SEI epidemic model with constant recruitment and infectious force in the latent period is investigated. This model describes the transmission of diseases such as SARS. The behavior of positive solutions to a reaction–diffusion system with homogeneous Neumann boundary conditions are investigated. Sufficient conditions for the local and global asymptotical stability are given by linearization and by the method of upper and lower solutions and its associated monotone iterations. Our result shows that the disease-free equilibrium is globally asymptotically stable if the contact rate is small.     

用常微分方程模型分析预防和隔离措施对SARS发病率的影响

通过建立常微分方程模型 ,分析了预防和隔离措施对 SARS发病率的影响 ,并把计算结果与实际统计数据进行了比较 ,结果表明 ,及时高效的预防和隔离措施能够有效地控制 SARS的传播 .     

Computational simulation of interactions between SARS coronavirus spike mutants and host species-specific receptors

As a critical adaptive mechanism, amino acid replacements on the severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein could alter the receptor-binding specificity of this envelope glycoprotein and in turn lead to the emergence or reemergence of this viral zoonosis. Based on the X-ray structures of SARS-CoV spike receptor-binding domain (RBD) in complex with its functional receptor (angiotensin-converting enzyme 2, ACE2), we perform computational simulations of interactions between three representative RBD mutants and four host species-specific receptors. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics approaches. And the predictions further indicate that some viral prototypes might utilize the rat ACE2 while rats might serve as a vector or reservoir of SARS-CoV.