Downfalls of Chemical Probes Acting at the Kinase ATP-Site: CK2 as a Case Study

Protein kinases are a large class of enzymes with numerous biological roles and many have been implicated in a vast array of diseases, including cancer and the novel coronavirus infection COVID-19. Thus, the development of chemical probes to selectively target each kinase is of great interest. Inhibition of protein kinases with ATP-competitive inhibitors has historically been the most widely used method. However, due to the highly conserved structures of ATP-sites, the identification of truly selective chemical probes is challenging. In this review, we use the Ser/Thr kinase CK2 as an example to highlight the historical challenges in effective and selective chemical probe development, alongside recent advances in the field and alternative strategies aiming to overcome these problems. The methods utilised for CK2 can be applied to an array of protein kinases to aid in the discovery of chemical probes to further understand each kinase’s biology, with wide-reaching implications for drug development.     

Functional analysis of repositioned anilide derivatives as anticancer compounds

Off the different types cancers 40% of the population have been observed to be affected by leukemia. Contemporary therapeutics is focusing on generation of new synthetic analogues that can exert maximum positive physiological effect with minimum dosage and negligible deleterious side effects. New generation pharmacists are focusing on such promising effects of Imatinib (a potential anti-cancer drug molecule), Dasatinib, Pelitinib and Nilotinib. The present research study focuses on novel synthesized anilides derivative against BCR-ABL kinase as potential anti-leukemic agent. Validation of the compounds by molecular docking with specific BCR-ABL kinase confirmed their activity. Toxicity prediction of these compounds helped to identify sustainability as therapeutic molecules. The IC₅₀ values were calculated (211 ug, 175 ug, 272ug for compounds A, B, C resp.) and the mode of cell death was gauged by DNA laddering assay. The cells were observed to be induced for programmed cell death. By validating and in-vivo testing of three synthesized compounds, the compound B was observed to be more stable thermodynamically with a potentially vital active site and appears to be a promising anti-leukemic factor. The present research thus lays a preliminary platform in world of pharmaceutics, where these new analogues appear to be efficient, target specific and less toxic molecules.     

Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity

The histidine residue has an exceptional affinity for metals, but solution structure of its complexes are difficult to study. For zinc and nickel complexes, Raman and Raman optical activity (ROA) spectroscopy methods to investigate the link between spectral shapes and the geometry were used. The spectra were recorded and interpreted on the basis of ionic equilibria, molecular dynamics, ab initio molecular dynamics, and density functional theory. For zwitterionic histidine the dominant tautomer was determined by the decomposition of experimental spectra into calculated subspectra. An octahedral structure was found to prevail for the ZnHis₂ complex in solution, in contrast to a tetrahedral arrangement in the crystal phase. The solution geometry of NiHis₂ is more similar to the octahedral structure found by X-ray. The Raman and ROA structural determinations of metal complexes are dependent on extensive computations, but reveal unique information about the studied systems.     

Selective Aptamer‐Based Control of Intraneuronal Signaling

Cellular behavior is orchestrated by the complex interactions of a myriad of intracellular signal transduction pathways. To understand and investigate the role of individual components in such signaling networks, the availability of specific inhibitors is of paramount importance. We report the generation and validation of a novel variant of an RNA aptamer that selectively inhibits the mitogen‐activated kinase pathway in neurons. We demonstrate that the aptamer retains function under intracellular conditions and that application of the aptamer through the patch‐clamp pipette efficiently inhibits mitogen‐activated kinase‐dependent synaptic plasticity. This approach introduces synthetic aptamers as generic tools, readily applicable to inhibit different components of intraneuronal signaling networks with utmost specificity.     

CH Oxidation of Ingenanes Enables Potent and Selective Protein Kinase C Isoform Activation

Ingenol derivatives with varying degrees of oxidation were prepared by two‐phase terpene synthesis. This strategy has allowed access to analogues that cannot be prepared by semisynthesis from natural ingenol. Complex ingenanes resulting from divergent C? H oxidation of a common intermediate were found to interact with protein kinase C in a manner that correlates well with the oxidation state of the ingenane core. Even though previous work on ingenanes has suggested a strong correlation between potential to activate PKCδ and induction of neutrophil oxidative burst, the current study shows that the potential to activate PKCβII is of key importance while interaction with PKCδ is dispensable. Thus, key modifications of the ingenane core allowed PKC isoform selectivity wherein PKCδ‐driven activation of keratinocytes is strongly reduced or even absent while PKCβII‐driven activation of neutrophils is retained.     

The Identification of a Novel Highly Condensed Pentacyclic Heteroaromatic Ring System 1,3,5,5b,6,8,10,10b‐Octaazacyclopenta[h,i]Aceanthrylene and its Application in the Synthesis of 5,7‐Substituted Pyrazolo[4,3‐d]Pyrimidines

Pyrazolo[4,3‐d]pyrimidines are of interest as potential kinase inhibitors. This article describes the formation of a novel highly conjugated, condensed, centrosymmetric heteroaromatic compound, 4,9‐dichloro‐2,7‐diisopropyl‐1,3,5,5b,6,8,10,10b‐octaazacyclopenta[h,i]aceanthrylene ( 3 ), during the chlorination of 5,7‐dihydroxypyrazolo[4,3‐d]pyrimidine ( 1 ) with phenylphosphonic dichloride. The nucleophilic attack of benzylamine on 3 afforded N‐benzyl‐5‐chloro‐3‐isopropyl‐1H‐pyrazolo[4,3‐d]pyrimidin‐7‐amine ( 6 ), which was further substituted to yield a pyrazolo[4,3‐d]pyrimidine analogue of roscovitine, a well‐known cyclin‐dependent kinase inhibitor.     

Quantitation of sunitinib,an oral multitarget tyrosine kinase inhibitor,and its metabolite in urine samples by nonaqueous capillary electrophoresis time of flight mass spectrometry

A rapid, sensitive, and specific method was developed and validated using a nonaqueous‐capillary electrophoresis method with TOF‐MS for determination of sunitinib and N‐desethyl sunitinib in human urine. In order to avoid ionic suppression a urine samples dilution with methanol 1:10 previous step was used. This was the only treatment step to urine samples before the injection. Despite this dilution of the urine, the detection limit was as low as 0.07 mg/L for sunitinib and 0.15 mg/L for N‐desethyl sunitinib. Separation of compounds was achieved with a mixture of 5 mM ammonium formate in methanol. The calibration curves were linear over the range of 0.5–50.0 mg/L for the two analyzed compounds. The within‐run and between‐run precisions were within 5%, while the accuracy ranged from 96.0 to 100.4%. This method can be used in routine clinical practice to monitor sunitinib and N‐desethyl sunitinib drugs in the urine of cancer patients treated with once daily administration.     

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).     

De Novo Design and Synthesis of a γ‐Turn Peptidomimetic Scaffold and Its Application as JNK3 Allosteric Ligand

As a way to develop a neuroprotective agent for the JNK3‐JIP1‐binding site, peptidomimetics of JIP‐1 as JNK3 allosteric regulators have been examined. The study consisted of in silico scaffold hopping, molecular docking, solution and solid‐phase peptide syntheses, and K_d measurements using surface plasmon resonance. As a peptidomimetic of JIP1, heptamer mimetic 16 (K_d=2.72 μm ) displayed a higher affinity than decamer JIP1 (K_d=23.6 μm ). The high affinity of 16 implies that the characteristic γ‐turn mimetic structure, “”Φ‐X‐Φ“ hydrophobic motif in 16 , increased its affinity toward the JIP‐site of JNK3.