Exploring the relationship between hub proteins and drug targets based on GO and intrinsic disorder

Protein–protein interactions (PPIs) play essential roles in many biological processes. In protein–protein interaction networks, hubs involve in numbers of PPIs and may constitute an important source of drug targets. The intrinsic disorder proteins (IDPs) with unstable structures can promote the promiscuity of hubs and also involve in many disease pathways, so they also could serve as potential drug targets. Moreover, proteins with similar functions measured by semantic similarity of gene ontology (GO) terms tend to interact with each other. Here, the relationship between hub proteins and drug targets based on GO terms and intrinsic disorder was explored. The semantic similarities of GO terms and genes between two proteins, and the rate of intrinsic disorder residues of each protein were extracted as features to characterize the functional similarity between two interacting proteins. Only using 8 feature variables, prediction models by support vector machine (SVM) were constructed to predict PPIs. The accuracy of the model on the PPI data from human hub proteins is as high as 83.72%, which is very promising compared with other PPI prediction models with hundreds or even thousands of features. Then, 118 of 142 PPIs between hubs are correctly predicted that the two interacting proteins are targets of the same drugs. The results indicate that only 8 functional features are fully efficient for representing PPIs. In order to identify new targets from IDP dataset, the PPIs between hubs and IDPs are predicted by the SVM model and the model yields a prediction accuracy of 75.84%. Further research proves that 3 of 5 PPIs between hubs and IDPs are correctly predicted that the two interacting proteins are targets of the same drugs. All results demonstrate that the model with only 8-dimensional features from GO terms and intrinsic disorder still gives a good performance in predicting PPIs and further identifying drug targets.     

Virtual screening of protein kinase C inhibitors from natural product library to modulate general anaesthetic effects

Protein kinase C (PKC) plays a key role in neurotransmission in the central nervous system, and targeting PKC domain is considered as a strategy to modulate the anaesthetic effects. In this study, we described a synthetic pipeline to perform high-throughput virtual screening against a large library of 3D structural natural products released recently in order to discover those potential PKC modulators. A total of 100 natural products with top scores were raised, from which 12 promising candidates were tested to determine their inhibitory potencies against PKC. As might be expected, the promiscuous kinase inhibitor staurosporine showed a high PKC inhibitory activity (IC₅₀ = 64 nM), and other two tested compounds, i.e. fisetin and tetrahydropapaverine, were also highly potent with their activities at nanomolar level (IC₅₀ = 370 and 190, respectively).     

Inhibition of thermal induced protein denaturation of extract/fractions of Withania somnifera and isolated withanolides

This study describes the in vitro inhibition of protein denaturation of extract/fractions of Withania somnifera and isolated withanolides including 20β hydroxy-1-oxo(22R)-witha-2,5,24 trienolide (1), (20R,22R-14α,20α)-dihydroxy-1-oxowitha-2,5,16,24 tetraenolide (2). The results showed that the extract/fractions of the plant evoked profound inhibitory effect on thermal-induced protein denaturation. The chloroform fraction caused the most dominant attenuation of 68% at 500 μg/mL. The bioactivity-guided isolation from chloroform fraction led to the isolation of compounds 1 and 2 that showed profound protein inhibition with 78.05% and 80.43% effect at 500 μg/mL and thus strongly complimented the activity of extract/fractions. In conclusion, extract/fractions of W. somnifera possessed strong inhibition of protein denaturation that can be attributed to these isolated withanolides.     

Synthesis of N,N‐Dialkylamino‐nor‐Dihydroxanthene‐Hemicyanine Fused Near‐Infrared Fluorophores and Their First Water‐Soluble and/or Bioconjugatable Analogues

The effective synthesis of extended conjugated N ,N ‐dialkylamino‐nor ‐dihydroxanthene‐based fluorophores is described from diversely functionalized salicylic aldehydes. The access to these original fluorescent derivatives proceeded in two steps through a one‐pot construction of the unusual nor ‐dihydroxanthene (nor ‐DHX) scaffold followed by a diversification step providing a wide variety of nor ‐DHX‐hemicyanine fused dyes emitting in the range of 730–790 nm. The versatility of our approach has enabled a further extension to the late‐stage introduction of negatively/positively charged polar groups onto their terminal nitrogen heterocyclic subunit, thereby giving access to the first water‐soluble and/or bioconjugatable members of this emerging class of NIR fluorophores. Our water‐solubilizing method is easily implementable, and the nor ‐DHX‐hemicyanine skeleton maintains satisfying fluorescence quantum yields (5–20 %) under physiological conditions. Finally, the bioconjugation ability of fluorescent derivatives bearing a free carboxylic acid was demonstrated through the covalent labeling of a model protein, namely, bovine serum albumin.     

Precisely Designed Isopeptide Bridge‐Crosslinking Endows Artificial Hydrolases with High Stability and Catalytic Activity under Extreme Denaturing Conditions

Enzymes normally lose their activities under extreme conditions due to the dissociation of their active tertiary structure. If an enzyme could maintain its catalytic activity under non‐physiological or denaturing conditions, it might be used in more applications in the pharmaceutical and chemical industries. Recently, we reported a coiled‐coil six‐helical bundle (6HB) structure as a scaffold for designing artificial hydrolytic enzymes. Here, intermolecular isopeptide bonds were incorporated to enhance the stability and activity of such biomolecules under denaturing conditions. These isopeptide bridge‐tethered 6HB enzymes showed exceptional stability against unfolding and retained or even had increased catalytic activity for a model hydrolysis reaction under thermal and chemical denaturing conditions. Thus, isopeptide bond‐tethering represents an efficient route to construct ultrastable artificial hydrolases, with promising potential to maintain biocatalysis under extreme conditions.     

Unambiguous Determination of Protein Arginine Ionization States in Solution by NMR Spectroscopy

Because arginine residues in proteins are expected to be in their protonated form almost without exception, reports demonstrating that a protein arginine residue is charge‐neutral are rare and potentially controversial. Herein, we present a ¹³C‐detected NMR experiment for probing individual arginine residues in proteins notwithstanding the presence of chemical and conformational exchange effects. In the experiment, the ¹⁵N^η and ¹⁵N^ϵ chemical shifts of an arginine head group are correlated with that of the directly attached ¹³C^ζ. In the resulting spectrum, the number of protons in the arginine head group can be obtained directly from the ¹⁵N–¹H scalar coupling splitting pattern. We applied this method to unambiguously determine the ionization state of the R52 side chain in the photoactive yellow protein from Halorhodospira halophila . Although only three H^η atoms were previously identified by neutron crystallography, we show that R52 is predominantly protonated in solution.     

Palladium in the Chemical Synthesis and Modification of Proteins

The field of site‐specific modification of proteins has drawn significant attention in recent years owing to its importance in various research areas such as the development of novel therapeutics and understanding the biochemical and cellular behaviors of proteins. The presence of a large number of reactive functional groups in the protein of interest and in the cellular environment renders modification at a specific site a highly challenging task. With the development of sophisticated chemical methodologies it is now possible to target a specific site of a protein with a desired modification, however, many challenges remain to be solved. In this context, transition metals in particular palladium‐mediated C−C bond‐forming and C−O bond‐cleavage reactions gained great interest owing to the unique catalytic properties of palladium. Palladium chemistry is being explored for protein modifications in vitro, on the cell surface, and within the cell. Very recently, palladium complexes have been applied for the rapid deprotection of several widely utilized cysteine protecting groups as well as in the removal of solubilizing tags to facilitate chemical protein synthesis. This Minireview highlights these advances and how the accumulated knowledge of palladium chemistry for small molecules is being impressively transferred to synthesis and modification of chemical proteins.     

Selenium and Selenocysteine in Protein Chemistry

Selenocysteine, the selenium‐containing analogue of cysteine, is the twenty‐first proteinogenic amino acid. Since its discovery almost fifty years ago, it has been exploited in unnatural systems even more often than in natural systems. Selenocysteine chemistry has attracted the attention of many chemists in the field of chemical biology owing to its high reactivity and resulting potential for various applications such as chemical modification, chemical protein (semi)synthesis, and protein folding, to name a few. In this Minireview, we will focus on the chemistry of selenium and selenocysteine and their utility in protein chemistry.