Modeling complex metabolic reactions, ecological systems, and financial and legal networks with MIANN models based on Markov-Wiener node descriptors

[Abstract] The use of numerical parameters in Complex Network analysis is expanding to new fields of application. At a molecular level, we can use them to describe the molecular structure of chemical entities, protein interactions, or metabolic networks. However, the applications are not restricted to the world of molecules and can be extended to the study of macroscopic nonliving systems, organisms, or even legal or social networks. On the other hand, the development of the field of Artificial Intelligence has led to the formulation of computational algorithms whose design is based on the structure and functioning of networks of biological neurons. These algorithms, called Artificial Neural Networks (ANNs), can be useful for the study of complex networks, since the numerical parameters that encode information of the network (for example centralities/node descriptors) can be used as inputs for the ANNs. The Wiener index (W) is a graph invariant widely used in chemoinformatics to quantify the molecular structure of drugs and to study complex networks. In this work, we explore for the first time the possibility of using Markov chains to calculate analogues of node distance numbers/W to describe complex networks from the point of view of their nodes. These parameters are called Markov-Wiener node descriptors of order kth (Wk). Please, note that these descriptors are not related to Markov-Wiener stochastic processes. Here, we calculated the Wk(i) values for a very high number of nodes (>100,000) in more than 100 different complex networks using the software MI-NODES. These networks were grouped according to the field of application. Molecular networks include the Metabolic Reaction Networks (MRNs) of 40 different organisms. In addition, we analyzed other biological and legal and social networks. These include the Interaction Web Database Biological Networks (IWDBNs), with 75 food webs or ecological systems and the Spanish Financial Law Network (SFLN). The calculated Wk(i) values were used as inputs for different ANNs in order to discriminate correct node connectivity patterns from incorrect random patterns. The MIANN models obtained present good values of Sensitivity/Specificity (%): MRNs (78/78), IWDBNs (90/88), and SFLN (86/84). These preliminary results are very promising from the point of view of a first exploratory study and suggest that the use of these models could be extended to the high-throughput re-evaluation of connectivity in known complex networks (collation)

Third-generation CDK inhibitors: A review on the synthesis and binding modes of Palbociclib, Ribociclib and Abemaciclib

The role of cyclin-dependent kinases (CDKs) in regulating the transition of cell cycle steps makes thisclass of enzymes a suitable target for cancer therapy. Three different generations of CDKs inhibitors havebeen developed so far. Third-generation compounds (i.e.selective CDK4/6 inhibitors) are the mostpromising ones, due to their limited toxicity and highin vivoactivity. To date, three compounds haveentered the therapy, namely Palbociclib, Ribociclib and Abemaciclib. Herein we review the medicinalchemistry aspects of these drugs, with some references to very similar analogues that have been publishe

SAM50, a side door to the mitochondria: The case of cytotoxic proteases

SAM50, a 7\u20138 nm diameter \u3b2-barrel channel of the mitochondrial outer membrane, is the central channel of the sorting and assembly machinery (SAM) complex involved in the biogenesis of \u3b2-barrel proteins. Interestingly, SAM50 is not known to have channel translocase activity; however, we have recently found that this channel is necessary and sufficient for mitochondrial entry of cytotoxic proteases. Cytotoxic lymphocytes eliminate cells that pose potential hazards, such as virus- and bacteria-infected cells as well as cancer cells. They induce cell death following the delivery of granzyme cytotoxic proteases into the cytosol of the target cell. Although granzyme A and granzyme B (GA and GB), the best characterized of the five human granzymes, trigger very distinct apoptotic cascades, they share the ability to directly target the mitochondria. GA and GB do not have a mitochondrial targeting signal, yet they enter the target cell mitochondria to disrupt respiratory chain complex I and induce mitochondrial reactive oxygen species (ROS)-dependent cell death. We found that granzyme mitochondrial entry requires SAM50 and the translocase of the inner membrane 22 (TIM22). Preventing granzymes\u2019 mitochondrial entry compromises their cytotoxicity, indicating that this event is unexpectedly an important step for cell death. Although mitochondria are best known for their roles in cell metabolism and energy conversion, these double-membrane organelles are also involved in Ca2+ homeostasis, metabolite transport, cell cycle regulation, cell signaling, differentiation, stress response, redox homeostasis, aging, and cell death. This multiplicity of functions is matched with the complexity and plasticity of the mitochondrial proteome as well as the organelle's morphological and structural versatility. Indeed, mitochondria are extremely dynamic and undergo fusion and fission events in response to diverse cellular cues. In humans, there are 1500 different mitochondrial proteins, the vast majority of which are encoded in the nuclear genome and translated by cytosolic ribosomes, after which they must be imported and properly addressed to the right mitochondrial compartment. To this end, mitochondria are equipped with a very sophisticated and highly specific protein import machinery. The latter is centered on translocase complexes embedded in the outer and inner mitochondrial membranes working along five different import pathways. We will briefly describe these import pathways to put into perspective our finding regarding the ability of granzymes to enter the mitochondria

METABOLIC DEPLETION EFFECT ON SERINE THREONINE-PHOSPHORYLATION AND TYROSINE-PHOSPHORYLATION OF MEMBRANE-PROTEINS IN HUMAN ERYTHROCYTES

The response of serine/threonine-phosphorylation of the major transmembrane protein (band 3) in human erythrocytes to the metabolic state of the cells is different from that exhibited by the tyrosine-phosphorylation of the same protein. Precisely, both serine- and tyrosine-phosphorylation are decreased during metabolic depletion of the erythrocytes. However, the depletion-induced tyrosine-phosphorylation decrease of band 3 is not reversed by the subsequent metabolic repletion of the depleted cells, being accompanied by an irreversible inactivation of both membrane-bound and cytosolic tyrosine-protein kinase(s). By contrast, the depletion-induced phosphoserine-dephosphorylation is reversed by the following repletion, being accompanied by a reversible translocation of casein kinase(s) between cytosolic and membrane compartments. A possible functional correlation between the serine-phosphorylation state of band 3 protein and the band 3-mediated anion transport across the membrane is discussed

Effect of intracellular pH changes on the distribution of tyrosine- and serine/threonine-protein kinase activities in human erythrocytes

The pH-dependence of the distribution of Tyr- and Ser/Thr-protein kinases between cytosol and membrane in human erythrocytes was investigated. When the internal pH of human erythrocytes is decreased from 8 to 7.3 the membrane-associated Tyr-protein kinase activity markedly increases at expense of the cytosolic counterpart, whereas the membrane-bound and cytosolic casein kinase activity are unaffected. This different response of the two kinase activities to the imposed variation of intracellular pH may explain why the Tyr-phosphorylation of cytoplasmic domain of band 3 results to be much higher in the ghosts from erythrocytes whose internal pH was 7.3 than that in the ghosts from erythrocytes whose internal pH was 8. By contrast, the Ser-phosphorylation of spectrin beta-subunit (band 2) and band 3 results to be practically unchanged in the ghosts from the erythrocytes treated at both pH values

A novel convenient synthesis of benzoquinazolines

A novel synthetic pathway to benzoquinazolines from naphthylamines is reported. Benzoquinazoline nucleus was cyclized in good yield from N-protected naphthylamines using hexamethylenetetramine in TFA and potassium ferricyanide in aqueous ethanolic KOH. This method is efficient and convenient with respect to previously reported synthetic pathways

A novel approach to quinazolin-4(3H)-one via quinazoline oxidation: an improved synthesis of 4-anilinoquinazolines

A novel strategy to prepare 4-anilinoquinazoline derivatives based on the oxidation of the quinazoline ring is described. Quinazoline oxidation has been investigated and improved, thus leading to an efficient and high yielding method to quinazolin-4(3H)-ones. Efficiency of this approach has been evaluated synthesizing four well known tyrosine kinase inhibitors and comparing the obtained yields with those achievable through conventional synthetic methods