Computing Integrated Information (Φ) in Discrete Dynamical Systems with Multi-Valued Elements

Integrated information theory (IIT) provides a mathematical framework to characterize the cause-effect structure of a physical system and its amount of integrated information (Φ). An accompanying Python software package (“PyPhi”) was recently introduced to implement this framework for the causal analysis of discrete dynamical systems of binary elements. Here, we present an update to PyPhi that extends its applicability to systems constituted of discrete, but multi-valued elements. This allows us to analyze and compare general causal properties of random networks made up of binary, ternary, quaternary, and mixed nodes. Moreover, we apply the developed tools for causal analysis to a simple non-binary regulatory network model (p53-Mdm2) and discuss commonly used binarization methods in light of their capacity to preserve the causal structure of the original system with multi-valued elements.     

A certain critical density property for invariant Harnack inequalities in H-type groups

We consider second order linear degenerate elliptic operators which are elliptic with respect to horizontal directions generating a stratified algebra of H-type. Extending a result by Gutiérrez and Tournier (2011) for the Heisenberg group, we prove a critical density estimate by assuming a condition of Cordes–Landis type. We then deduce an invariant Harnack inequality for the non-negative solutions from a result by Di Fazio, Gutiérrez, and Lanconelli (2008).     

Platinated copper(3-clip-phen) complexes as effective DNA-cleaving and cytotoxic agents

The synthesis and biological activity of three heteronuclear platinum-copper complexes based on 3-Clip-Phen are reported. These rigid complexes have been designed to alter the intrinsic mechanism of action of both the platinum moiety and the Cu(3-Clip-Phen) unit. The platinum centers of two of these complexes are coordinated to a 3-Clip-Phen moiety, an ammine ligand and two chlorides, which are either cis or trans to each other. The third complex comprises two 3-Clip-Phen units and two chloride ligands bound in a trans fashion to the platinum ion. DNA-cleavage experiments show that the complexes are highly efficient nuclease agents. In addition, a markedly difference in their aptitude to perform direct double-strand cleavage is observed, which appears to be strongly related to the ability of the platinum unit to coordinate to DNA. Indeed, complex 6 is unable to coordinate to DNA, which is reflected by its incapability to carry out double-strand breaks. Nonetheless, this complex exhibits efficient DNA-cleavage activity, and its cytotoxicity is high for several cell lines. Complex 6 shows better antiproliferate activity than both cisplatin and Cu(3-Clip-Phen) toward most cancer cell lines. Furthermore, the cytotoxicity observed for 1 is for most cell lines close to that of cisplatin, or even better. Cu(3-Clip-Phen) induces very low cytotoxic effects, but a marked migratory activity. Complex 6 presents DNA-cleavage properties comparable to the one of Cu(3-Clip-Phen), but it does not show any migratory activity. Interestingly, both Cu(3-Clip-Phen) and 6 induces vacuolisation processes in the cell in contrast to complex 1 and cisplatin. Thus, the four complexes cisplatin tested, Cu(3-Clip-Phen), 1 and 6 stimulate different cellular responses.     

Photochemical Bromination of 2,5-Dimethylbenzoic Acid as Key Step of an Improved Alkyne-Functionalized Blue Box Synthesis**

Cyclobis(paraquat-p-phenylene), also known as “blue box”, is a highly electron-deficient macrocycle, widely used as a molecular receptor for small electron-rich molecules. Inserting a reactive functional group onto the molecular structure of this cyclophane is paramount for its inclusion into complex architectures. To this aim, including an alkyne moiety would be ideal, because it can participate in click reactions. However, the synthesis of such alkyne-functionalized cyclophane suffers from several drawbacks: the use of toxic and expensive CCl₄, the need for high-pressure reactors, and overall low yield. We have revised the existing synthesis of this cyclophane derivative bearing an alkyne moiety, to overcome all these limitations. In particular, photochemical radical bromination is adopted to obtain a sensitive intermediate. We demonstrated that the synthesized host molecule can be functionalized via click reactions and take part in radical-radical interactions. Our work makes a key functionalized paraquat macrocycle more accessible, facilitating the development of novel redox-responsive systems.     

Tumor Carbohydrate Associated Antigen Analogs as Potential Binders for Siglec-7

We investigated two recently synthesized and characterized sialyl derivatives, bearing the Neu5Ac-α-(2-6)-Gal epitope, as promising binders for Siglec-7, an inhibitory Siglec mainly found on natural killer cells. A variety of sialoglycan structures can be recognized by Siglec-7 with implications in the modulation of immune responses. Notably, overexpression of sialylated glycans recognized by Siglec-7 can be associated with the progression of several tumors, including melanoma and renal cell carcinoma. NOE-based NMR techniques, including Saturation Transfer Difference and transferred-NOESY NMR, together with molecular docking and dynamic simulations were combined to shed light on the molecular basis of Siglec-7 recognition of two conformationally constrained Sialyl-Tn antigen analogs. We, therefore, identify the ligands epitope mapping and their conformational features and propose 3D models accurately describing the protein-ligand complexes. We found that the binding site of Siglec-7 can accommodate both synthetic analogs, with the sialic acid mainly involved in the interaction. Moreover, the flexibility of Siglec-7 loops allows a preferred accommodation of the more rigid compound bearing a biphenyl moiety at position 9 of the sialic acid that contributed to the interaction to a large extent. Our findings provided insights for developing potential novel high affinity ligands for Siglec-7 to hinder tumor evasion.     

Data‐Driven Optimal Transport

The problem of optimal transport between two distributions ρ(x) and μ(y) is extended to situations where the distributions are only known through a finite number of samples {x_i} and {y_j}. A weak formulation is proposed, based on the dual of the Kantorovich formulation, with two main modifications: replacing the expected values in the objective function by their empirical means over the {x_i} and {y_j}, and restricting the dual variables u(x) and v(y) to a suitable set of test functions adapted to the local availability of sample points. A procedure is proposed and tested for the numerical solution of this problem, based on a fluidlike flow in phase space, where the sample points play the role of active Lagrangian markers. © 2016 Wiley Periodicals, Inc.     

Chemoinformatics Analyses of Tau Ligands Reveal Key Molecular Requirements for the Identification of Potential Drug Candidates against Tauopathies

Tau is a highly soluble protein mainly localized at a cytoplasmic level in the neuronal cells, which plays a crucial role in the regulation of microtubule dynamic stability. Recent studies have demonstrated that several factors, such as hyperphosphorylation or alterations of Tau metabolism, may contribute to the pathological accumulation of protein aggregates, which can result in neuronal death and the onset of a number of neurological disorders called Tauopathies. At present, there are no available therapeutic remedies able to reduce Tau aggregation, nor are there any structural clues or guidelines for the rational identification of compounds preventing the accumulation of protein aggregates. To help identify the structural properties required for anti-Tau aggregation activity, we performed extensive chemoinformatics analyses on a dataset of Tau ligands reported in ChEMBL. The performed analyses allowed us to identify a set of molecular properties that are in common between known active ligands. Moreover, extensive analyses of the fragment composition of reported ligands led to the identification of chemical moieties and fragment combinations prevalent in the more active compounds. Interestingly, many of these fragments were arranged in recurring frameworks, some of which were clearly present in compounds currently under clinical investigation. This work represents the first in-depth chemoinformatics study of the molecular properties, constituting fragments and similarity profiles, of known Tau aggregation inhibitors. The datasets of compounds employed for the analyses, the identified molecular fragments and their combinations are made publicly available as supplementary material.     

Antioxidant and Antisteatotic Activities of Fucoidan Fractions from Marine and Terrestrial Sources

Fucoidan is a fucose-rich sulfated polysaccharide typically found in the cell wall of marine algae but also recently isolated from terrestrial sources. Due to a variety of biological activities, including antioxidant properties, fucoidan exhibits an attractive therapeutic potential against a wide array of metabolic diseases associated with oxidative stress. We used FTIR, ¹H NMR and ¹³C NMR spectroscopy to investigate the structural features of a fucoidan fraction extracted from the brown alga Cystoseira compressa (CYS). The antioxidant potential of CYS was measured by DPPH, ABTS and FRAP assays, which revealed a radical scavenging capacity that was confirmed in in vitro cellular models of hepatic and endothelial cells. The same antioxidant effects were observed for another fucoidan fraction previously identified in the terrestrial tree Eucalyptus globulus (EUC). Moreover, in hepatic cells, CYS and EUC exhibited a significant antisteatotic action, being able to reduce intracellular triglyceride content through the regulation of key genes of hepatic lipid metabolism. EUC exerted stronger antioxidant and antisteatotic effects as compared to CYS, suggesting that both marine and terrestrial sources should be considered for fucoidan extraction and therapeutic applications.