Probing the Binding Site of Abl Tyrosine Kinase Using in Situ Click Chemistry

Modern combinatorial chemistry is used to discover compounds with desired function by an alternative strategy, in which the biological target is directly involved in the choice of ligands assembled from a pool of smaller fragments. Herein, we present the first experimental result where the use of in situ click chemistry has been successfully applied to probe the ligand-binding site of Abl and the ability of this enzyme to form its inhibitor. Docking studies show that Abl is able to allow the in situ click chemistry between specific azide and alkyne fragments by binding to Abl-active sites. This report allows medicinal chemists to use protein-directed in situ click chemistry for exploring the conformational space of a ligand-binding pocket and the ability of the protein to guide its inhibitor. This approach can be a novel, valuable tool to guide drug design synthesis in the field of tyrosine kinases

High-throughput docking for the identification of new influenza A virus polymerase inhibitors targeting the PA-PB1 protein-protein interaction

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Allosteric Inhibition of Abl Kinase

Since the mechanism of allosteric regulation was postulated for the first time in 1965 by Monod, Wyman and Changeux, 50 years have passed. From that moment our vision and understanding of the ligand–protein interaction process have been completely changed. Proteins started to be considered to be not fixed biological entities but flexible structures endowed with an activity which could be finely tuned by interaction with other proteins or new small molecules able to bind pockets different from the catalytic sites. In this chapter an in-depth description of one of the most studied allosteric modulation mechanisms will be provided. Abelson murine-leukemia viral-oncogene homolog-1 (c-Abl) protein kinase represents a noteworthy example of how a small post-translational modification (myristoylation of the N-terminal region of the protein sequence) can drive a mechanism of complex domain rearrangements, determining the activation state of the enzyme. Many efforts have been devoted, by scientists all around the world, to studying the molecular basis for the autoinhibition mechanism of c-Abl, and its derived oncogenic fusion protein breakpoint cluster region–Abl (Bcr–Abl), leading to the identification of the first allosteric inhibitor GNF-5, currently undergoing a Phase I clinical trial for the treatment of chronic myelogenous leukemia (CML).</jats:p

Application of Molecular Modelling to Speed-up the Lead Discovery Process

By transforming many life-threatening diseases to almost negligible problems, drug discovery has improved life expectancy and our quality-of-life in general. However, in recent years, the flat trend of new drugs reaching the market, coupled with the increase of costs of this long process has led the pharmaceutical sector to a ‘crisis’. For this reason, research and development has turned to cutting-edge technology to reduce time and expense. In this chapter, we will discuss how the impressive improvements in both structure- and ligand-based molecular modelling approaches can help to drive and speed up drug discovery, making important contributions at all levels of the process.</jats:p

Inhibitors of Tau-Phosphorylating Kinases

The phosphorylation of tau protein is finely regulated by a balance between phosphorylation and dephosphorylation processes carried out by kinases and phosphatases. It has been suggested that the disruption of this equilibrium and consequent abnormal tau phosphorylation contribute to the aggregation of tau. The understanding of this important mechanism is of high interest because of the implication of tau aggregates in the development of Alzheimer’s disease (AD). In the last few years, among the possible strategies which could be used to reduce tau phosphorylation, the inhibition of certain tyrosine kinases has been suggested as a promising alternative to the common therapeutic approaches. In this chapter we will first give an overview of the tau protein kinases, their roles in cells, regulation and importance in AD. This will be followed by a more detailed description of the role of Fyn, a member of the Src family kinases, in the physiological development of CNS and the pathological progress of AD. How the inhibition of Fyn could be used as a new strategy in the fight against AD will be discussed

Inhibitors of tau-phosphorylating kinases

The phosphorylation of tau protein is finely regulated by a balance between phosphorylation and dephosphorylation processes carried out by kinases and phosphatases. It has been suggested that the disruption of this equilibrium and consequent abnormal tau phosphorylation contribute to the aggregation of tau. The understanding of this important mechanism is of high interest because of the implication of tau aggregates in the development of Alzheimer’s disease (AD). In the last few years, among the possible strategies which could be used to reduce tau phosphorylation, the inhibition of certain tyrosine kinases has been suggested as a promising alternative to the common therapeutic approaches. In this chapter we will first give an overview of the tau protein kinases, their roles in cells, regulation and importance in AD. This will be followed by a more detailed description of the role of Fyn, a member of the Src family kinases, in the physiological development of CNS and the pathological progress of AD. How the inhibition of Fyn could be used as a new strategy in the fight against AD will be discussed

Insight into the Allosteric Inhibition of Abl Kinase

5Abl kinase inhibitors targeting the ATP binding pocket are currently used as a front-line therapy for the treatment of chronic myelogenous leukemia (CML), but their use has significant limitation because of the development of drug resistance (especially due to the T315I mutation). Two compounds (GNF-2 and BO1) have been found able to inhibit the Abl activity through a peculiar mechanism of action. Particularly, GNF-2 acts as allosteric inhibitor against Bcr-Abl wild type (wt), but it has no activity against the gatekeeper mutant T315I. Its activity against the last mutant reappears when used together with an ATP-competitive inhibitor such as Imatinib or Nilotinib. A crystal structure of GNF-2 bound to the Abl myristoyl pocket (MP) has been released. On the contrary, BO1 shows an ATP-competitive/mixed mechanism of action against the wt, while it acts as an allosteric inhibitor against T315I. In order to better understand the mechanism of Abl allosteric inhibition, MD simulations and MM/GBSA analysis were performed on Abl wt and T315I in complex with GNF-2 and BO1, and the results were compared to those found for the natural myristoyl ligand. Similarly to that observed for the myristoyl group, the binding of an allosteric inhibitor to the MP promotes the formation of a compact and inhibited conformation of the wt protein, characterized by the stabilization of the intramolecular interactions that occur between SH2-SH3 and kinase domains. Conversely, an overall higher flexibility was observed with the Abl T315I mutant, especially in the case of GNF-2. Our analysis highlighted differences in the dynamic behavior of GNF-2 and BO1 which could explain the different biological profiles of the two allosteric inhibitors against the T315I mutant.nonenoneFallacara, Anna Lucia; Tintori, Cristina; Radi, Marco; Schenone, Silvia; Botta, MaurizioFallacara, Anna Lucia; Tintori, Cristina; Radi, Marco; Schenone, Silvia; Botta, Maurizi

Protein-protein interactions and human cellular cofactors as new targets for HIV therapy

Two novel approaches for the development of new drugs against AIDS are summarized each leading to the achievement of important discoveries in anti-HIV therapy. Despite the success of HAART in reducing mortality, resistant strains continue to emerge in the clinic, underscoring the importance of developing next-generation drugs. Protein-protein interactions and human cellular cofactors represent the new targets of tomorrow in HIV research. The most relevant results obtained in the last few years by the two new strategies are described herein

Protein-protein interactions and human cellular cofactors as new targets for HIV therapy

Two novel approaches for the development of new drugs against AIDS are summarized each leading to the achievement of important discoveries in anti-HIV therapy. Despite the success of HAART in reducing mortality, resistant strains continue to emerge in the clinic, underscoring the importance of developing next-generation drugs. Protein protein interactions and human cellular cofactors represent the new targets of tomorrow in HIV research. The most relevant results obtained in the last few years by the two new strategies are described herein