Harnessing Protein-Ligand Interaction Fingerprints to Predict New Scaffolds of RIPK1 Inhibitors

Necroptosis has emerged as an exciting target in oncological, inflammatory, neurodegenerative, and autoimmune diseases, in addition to acute ischemic injuries. It is known to play a role in innate immune response, as well as in antiviral cellular response. Here we devised a concerted in silico and experimental framework to identify novel RIPK1 inhibitors, a key necroptosis factor. We propose the first in silico model for the prediction of new RIPK1 inhibitor scaffolds by combining docking and machine learning methodologies. Through the data analysis of patterns in docking results, we derived two rules, where rule #1 consisted of a four-residue signature filter, and rule #2 consisted of a six-residue similarity filter based on docking calculations. These were used in consensus with a machine learning QSAR model from data collated from ChEMBL, the literature, in patents, and from PubChem data. The models allowed for good prediction of actives of >90, 92, and 96.4% precision, respectively. As a proof-of-concept, we selected 50 compounds from the ChemBridge database, using a consensus of both molecular docking and machine learning methods, and tested them in a phenotypic necroptosis assay and a biochemical RIPK1 inhibition assay. A total of 7 of the 47 tested compounds demonstrated around 20–25% inhibition of RIPK1’s kinase activity but, more importantly, these compounds were discovered to occupy new areas of chemical space. Although no strong actives were found, they could be candidates for further optimization, particularly because they have new scaffolds. In conclusion, this screening method may prove valuable for future screening efforts as it allows for the exploration of new areas of the chemical space in a very fast and inexpensive manner, therefore providing efficient starting points amenable to further hit-optimization campaigns.     

硅烷化磁铁粉固定胰蛋白酶的研究

分别以硅烷化磁铁粉、硅烷磁化脱乙酰几丁质及脱乙酰几丁质作载体,甲醛或戊二醛为交联剂,对胰蛋白酶的固定化条件及所制备的固定化酶的性质进行了研究．研究了载体种类、交联剂和ｐＨ值以及载体与酶比例等因素对胰蛋白酶固定化的影响．研究了不同载体固定胰蛋白酶的特点,证明以硅烷化试剂和甲醛作交联剂的硅烷化磁铁粉作胰蛋白酶固定化的载体具有明显优点,所制备的硅烷化磁铁粉固定化胰蛋白酶酶学性质明显优于可溶性胰蛋白酶     

The Pathophysiology of Long COVID throughout the Renin-Angiotensin System

COVID-19 has expanded across the world since its discovery in Wuhan (China) and has had a significant impact on people’s lives and health. Long COVID is a term coined by the World Health Organization (WHO) to describe a variety of persistent symptoms after acute SARS-CoV-2 infection. Long COVID has been demonstrated to affect various SARS-CoV-2-infected persons, independently of the acute disease severity. The symptoms of long COVID, like acute COVID-19, consist in the set of damage to various organs and systems such as the respiratory, cardiovascular, neurological, endocrine, urinary, and immune systems. Fatigue, dyspnea, cardiac abnormalities, cognitive and attention impairments, sleep disturbances, post-traumatic stress disorder, muscle pain, concentration problems, and headache were all reported as symptoms of long COVID. At the molecular level, the renin-angiotensin system (RAS) is heavily involved in the pathogenesis of this illness, much as it is in the acute phase of the viral infection. In this review, we summarize the impact of long COVID on several organs and tissues, with a special focus on the significance of the RAS in the disease pathogenesis. Long COVID risk factors and potential therapy approaches are also explored.     

Computational Insight into Biotransformation Profiles of Organophosphorus Flame Retardants to Their Diester Metabolites by Cytochrome P450

Biotransformation of organophosphorus flame retardants (OPFRs) mediated by cytochrome P450 enzymes (CYPs) has a potential correlation with their toxicological effects on humans. In this work, we employed five typical OPFRs including tris(1,3-dichloro-2-propyl) phosphate (TDCIPP), tris(1-chloro-2-propyl) phosphate (TCIPP), tri(2-chloroethyl) phosphate (TCEP), triethyl phosphate (TEP), and 2-ethylhexyl diphenyl phosphate (EHDPHP), and performed density functional theory (DFT) calculations to clarify the CYP-catalyzed biotransformation of five OPFRs to their diester metabolites. The DFT results show that the reaction mechanism consists of Cα-hydroxylation and O-dealkylation steps, and the biotransformation activities of five OPFRs may follow the order of TCEP ≈ TEP ≈ EHDPHP > TCIPP > TDCIPP. We further performed molecular dynamics (MD) simulations to unravel the binding interactions of five OPFRs in the CYP3A4 isoform. Binding mode analyses demonstrate that CYP3A4-mediated metabolism of TDCIPP, TCIPP, TCEP, and TEP can produce the diester metabolites, while EHDPHP metabolism may generate para-hydroxyEHDPHP as the primary metabolite. Moreover, the EHDPHP and TDCIPP have higher binding potential to CYP3A4 than TCIPP, TCEP, and TEP. This work reports the biotransformation profiles and binding features of five OPFRs in CYP, which can provide meaningful clues for the further studies of the metabolic fates of OPFRs and toxicological effects associated with the relevant metabolites.     

7-Aminoalkoxy-Quinazolines from Epigenetic Focused Libraries Are Potent and Selective Inhibitors of DNA Methyltransferase 1

Inhibitors of epigenetic writers such as DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug and probe discovery. To advance epigenetic probes and drug discovery, chemical companies are developing focused libraries for epigenetic targets. Based on a knowledge-based approach, herein we report the identification of two quinazoline-based derivatives identified in focused libraries with sub-micromolar inhibition of DNMT1 (30 and 81 nM), more potent than S-adenosylhomocysteine. Also, both compounds had a low micromolar affinity of DNMT3A and did not inhibit DNMT3B. The enzymatic inhibitory activity of DNMT1 and DNMT3A was rationalized with molecular modeling. The quinazolines reported in this work are known to have low cell toxicity and be potent inhibitors of the epigenetic target G9a. Therefore, the quinazoline-based compounds presented are attractive not only as novel potent inhibitors of DNMTs but also as dual and selective epigenetic agents targeting two families of epigenetic writers.     

脉冲电场对木瓜蛋白酶影响的荧光光谱分析

木瓜蛋白酶溶液在电场强度为50 kV·cm-1,频率1 500 Hz,脉冲宽度40 μs的脉冲电场下接受19 800个脉冲处理后,其活性降低了56.5％。文章采用荧光偏光光谱对处理前后的样品进行了分析。 处理后酶样的荧光强度明显大于处理前,在峰值位置其荧光强度增加超过50％,峰位从342 nm移到了346 nm左右,其荧光偏振幅度明显减小。由此推断出木瓜蛋白酶经脉冲电场处理后酶蛋白的α-螺旋结构松散拉伸,分子内部的氨基酸残基暴露于分子表面,并有部分发生离解游离于溶液中,导致活性部位的结构发生变化,最终导致酶失活。     

An improved ensemble learning machine for biological activity prediction of tyrosine kinase inhibitors

Boosting is one of the most important strategies in ensemble learning because of its ability to improve the stability and performance of weak learners. It is nonparametric, multivariate, fast and interpretable but is not robust against outliers. To enhance its prediction accuracy as well as immunize it against outliers, a modified version of a boosting algorithm (AdaBoost R2) was developed and called AdaBoost R3. In the sampling step, extremum samples were added to the boosting set. In the robustness step, a modified Huber loss function was applied to overcome the outlier problem. In the output step, a deterministic threshold was used to guarantee that bad predictions do not participate in the final output. The performance of the modified algorithm was investigated with two anticancer data sets of tyrosine kinase inhibitors, and the mechanism of inhibition was studied using the relative weighted variable importance procedure. Investigating the effect of base learner's strength reveals that boosting is only successful using the classification and regression tree method (a weak to moderate learner) and does not have a significant effect using the radial basis functions partial least square method (a strong base learners). Copyright © 2015 John Wiley & Sons, Ltd.     

CONFORMATIONAL PREFERENCES ABOUT Cpy-S BONDS IN DI-2-PYRIDYL DISULFIDE

Abstract

The total energy, dipole moment and electron densities for each possible rotational conformation about the C_py-S bonds of di-2-pyridyl disulfide were evaluated by using the semi-quantitative CNDO/2 method. The conformations in which the pyridine rings are coplanar with the valency plane of the bonded sulfur atom (cis-cis, cis-trans and trans-trans) were predicted to be the most favored ones.

Results of the theoretical study, when compared to some experimental determinations such as dipole moment and variable temperature pmr spectra, provided evidence that easy interconversion between these conformations can occur.     

Synthesis and Properties of Self‐doped Polyaniline with Polycationic Templates via Biocatalysis

The enzyme horseradish peroxidase (HRP) was used to polymerize acid‐functionalized anilines to make self‐doped polymer in the presence of a polycationic template. Anionic templates such as sulfonated polystyrene (SPS) could not function as a suitable template for the polymerization of acid‐functionalized aniline derivatives. Several types of polyelectrolytes were used as templates to observe the structural effects and doping behavior of polyaniline/template complexes. The synthesis is straightforward and the conditions are mild in that the polymerization of conducting polyanilines may be carried out in buffered solutions as high as pH 6, with a stoichiometric amount of hydrogen peroxide and catalytic amount of enzyme. The conductivity of these enzymatically synthesized self‐doped polymers was relatively high without additional doping due to the self‐doping of the acid moieties. The conductivity did not decrease dramatically at pH 3 as is the usual case of unsubstituted HCl‐doped polyaniline and maintained good conductivity even at pH 6. The measured conductivity at pH 4～pH 6 is around 10^?4 S/cm to 10^?6 S/cm.