On the Motive Power of Chemical Transformations in?Open Systems

The classical basic concepts of cyclic processes and the efficiency of heat engines are used here to conjecture about the laws of thermodynamics for open systems that can exchange matter with a surrounding environment. An ideal chemomechanical elastic bar is envisioned that changes its stiffness while undergoing a chemical transformation which is, in turn, influenced by the axial strain of the bar. Stable equilibrium states are identified as minimizers of the total energy, which is assumed to be nonconvex in type. If the bar is loaded and then alternatively placed in environments at chemical potentials either ?? _i or ?? _s >?? _i , a reversible cycle analogous to the classical Carnot cycle may be traced. In this case, the environmental ??chemical potential?? plays the role of the temperature and the ??chemical work?? the role of heat. For the system, the main form of interaction with the exterior, other than mechanical work, is the exchange of mass of a component at different environmental chemical potentials. It is then possible to obtain an elementary theory of chemical engines in which efficiency estimates (in terms of environmental chemical potentials) and related pertinent issues can be discussed. This model may serve as a basis for analyzing coupled chemo-mechanical processes occurring in materials such as ionized gels for possible applications as actuators, and to interpret complex phenomena in biological systems, such as the chemical kinetics of smooth muscles.     

Metal-based antitumour drugs in the post-genomic era: what comes next?

In our Dalton Transactions Perspective article entitled, 'Metal-based antitumour drugs in the post genomic era', (Dalton Trans., 2006, 1929-1933) we discussed metal-based drugs in light of past decades of research. We concluded that the post-genomic era would dictate a change in the direction of the field with knowledge of the genome increasingly allowing protein targets to be identified and not simply assuming that DNA is the only relevant target of metal-based drugs. Since our article was published new insights into the mode of action of metal-based drugs have emerged making some older findings increasingly relevant to current drug design. In this article we discuss these developments in terms of what we believe should be the future direction for the field.     

Ruthenium anticancer compounds: myths and realities of the emerging metal-based drugs

Ruthenium anticancer drugs have attracted an increasing interest in the last 20 years and two of them have entered clinical trials. Compared to platinum drugs, the complexes based on ruthenium are often identified as less toxic and capable of overcoming the resistance induced by platinum drugs in cancer cells. These activities were attributed to the transportation to tumour cells by transferrin and to the selective activation to more reactive species by the reducing environment of solid tumours as compared to healthy tissues. Ruthenium anticancer drugs have been almost always designed to mimic platinum drugs, particularly for targeting DNA. Indeed, none of the above properties has never been clearly demonstrated even for the ruthenium drugs that entered clinical trials. The suggestion for the future is to change the perspective when designing new chemical entities, abandoning the philosophy that guided the actual panel of ruthenium drugs and to look further into the fine mechanism by which the most relevant ruthenium complexes available kill the target tumour cells, then focusing on targets selective of tumour cells and responsible for cell growth and malignancy.     

Organometallic ruthenium-based antitumor compounds with novel modes of action

Both metal complexes and organic molecules are widely used for the treatment of various diseases including cancer - in addition to surgery and radiotherapy. Recent years have witnessed a surge of interest in the application of organometallic compounds to treat cancer and other diseases. Indeed, the unique properties of organometallic compounds, intermediate between those of classical inorganic and organic materials provide new opportunities in medicinal chemistry. In this review, based on the award lecture at ICBOMC’10, we describe a class of ruthenium(II)-arene complexes that are weakly cytotoxic in vitro, but show selective antimetastatic activity in vivo. These compounds, [Ru(η⁶-p-arene)Cl₂(pta)] termed RAPTA, interact strongly with proteins, with the ability to discriminate binding to different proteins, but show a relatively low propensity to bind DNA, which is considered to be the main target of many metal-based drugs. The basic RAPTA structure is quite stable in physiological environments, and studies have shown that aquation of the chloride bonds occurs, it may not be an essential step for anticancer drug activity - direct substitution with biomolecular targets is also possible. Based on the favorable physicochemical properties of RAPTA compounds, combined with their highly promising pharmacological properties, the structure represents an ideal scaffold for rational drug design. Thus far, strategies to overcome drug resistance, by interference with critical enzymes responsible for drug deactivation, and tumor targeting, by tethering to human serum albumin via hydrolyzable linkers, have been demonstrated. However, many more approaches can be envisaged. In any case, the net result are a type of hybrid compounds, that occupy a niche somewhere between classical cisplatin-type anticancer agents that are widely applied to many tumor types and targeted therapies based on organic structures used to inhibit specific enzymes. As such, should these compounds prove themselves in the clinic it is not inconceivable that they could be rapidly refined to form personalized chemotherapies.     

Specificity in the Cu interactions with prion protein fragments and related His-rich peptides from mammals to fishes

The prion proteins may play a critical role in copper homeostasis and the antioxidant activity in the brain. This review presents the state of art in the studies on Cu²⁺ prion systems. The proteins discussed are from different species from mammals to fishes. All proteins are His-rich and the research discussed clearly indicates the basic role of imidazole side chains and the adjacent amide nitrogen atoms in metal ion binding. Prions represent the family of proteins with new mode of Cu²⁺ binding which includes the amide nitrogen coordination. The multi-imidazole coordination is also likely and it can play a critical role in the antioxidant activity of the copper–prion complexes. The combination of the imidazole and amide nitrogen atoms to Cu²⁺ ions could also be relevant in histidine-rich peptide antibiotics including demegen. The impact of peptide sequence and His positions on copper binding ability is also discussed.     

InCl3 and ZrCl4 catalyzed regioselective reaction of 2,2′-dihydroxybiphenyl with terminal alkynes: synthesis of new dibenzo[d,f][1,3]dioxepines

The regioselective reaction of 2,2′-dihydroxybiphenyl with terminal alkynes was found to be rapidly catalyzed by InCl₃ and ZrCl₄. The chemoselectivity of catalysts and alkynes for biphenol over water, together with the reaction mechanism are discussed in details.     

Ready Biodegradability study and insights with ultra-high-performance liquid chromatograph coupled to a quadrupole time of flight of a Metformin-based drug and of Metarecod,a natural substance-based medical device

Drugs are indispensable products with incontrovertible benefits to human health and lifestyle. However, due to their overuse and improper disposal, unwanted residues of active pharmaceutical ingredients (APIs) have been found in different compartments of the environment and now are considered as contaminants of emerging concern (CECs). Therefore, they are very likely to have a boomerang effect on human health, because they can enter into the food cycle. In the current legislation framework, one of the tests first used to evaluate biodegradation of APIs as well as chemical compounds is the ready biodegradability test (RBT). This test can be performed according to a series of protocols prepared by Organization for Economic Co-operation and Development (OECD) and usually is carried out on pure compounds. RBTs, largely used due to their relatively low cost, perceived standardization, and straightforward implementation and interpretation, are known to have a number of well-documented limitations. In this work, following a recently reported approach, we propose to improve the evaluation of the RBT results applying advanced analytical techniques based on mass spectrometry, not only to the APIs but also to complex formulated products, as the biodegradability can potentially be affected by the formulation. We evaluated the ready biodegradability of two therapeutic products, Product A —a drug based on Metformin—and Product B —Metarecod a natural substance-based medical device—through the acquisition of the fingerprint by ultra-high-performance chromatograph coupled to a quadrupole time of flight (UHPLC-qToF) of samples coming from the RBT OECD 301F. Untargeted and targeted evaluation confirmed the different behavior of the two products during the respirometry-manometric test, which showed a difficulty of the Metformin-based drug to come back in the life cycle, whereas Metarecod resulted ready biodegradable. The positive results of this research will hopefully be useful in the future for a better evaluation of the risk/benefit ratio of APIs extended to the environment.     

Bifurcated hydrogen bond in lithium nitrate trihydrate probed by ab initio molecular dynamics

The hydrogen-bond dynamics of lithium nitrate trihydrate has been studied by a combined approach based on ab initio molecular dynamics simulations and wavelet analysis. The simultaneous bifurcated interaction between one hydrogen atom of water molecules and two oxygen atoms of nitrate ions is the pivotal feature of the crystal structure: this bifurcated interaction has deep effects on the O-H stretching region of the vibrational spectrum. The structural, dynamic, spectroscopic, and electronic properties of the bifurcated hydrogen bond have been investigated computationally, elucidating at the molecular level the differences with weak and strong hydrogen bonds present in the crystal. These studies corroborate the very recent IR experiments performed on the lithium nitrate trihydrate crystal, offering new perspectives to interpreting the vibrational spectra. In fact, this approach allows obtaining two-dimensional plots, which summarize the essential features of both the hydrogen-bond network and IR spectra, resulting in a peculiar "signature" of the bifurcated interaction.     

Dense trees: a new look at degenerate graphs

Dense trees are undirected graphs defined as natural extensions of trees. They are already known in the realm of graph coloring under the name of k-degenerate graphs. For a given integer k1, a k-dense cycle is a connected graph, where the degree of each vertex is greater than k. A k-dense forest F=(V,E) is a graph without k-dense cycles as subgraphs. If F is connected, then is a k-dense tree. 1-dense trees are standard trees. We have |E|k|V|−k(k+1)/2. If equality holds F is connected and is called a maximal k-dense tree. k-trees (a subfamily of triangulated graphs) are special cases of maximal k-dense trees.We review the basic theory of dense trees in the family of graphs and show their relation with k-trees. Vertex and edge connectivity is thoroughly investigated, and the role of maximal k-dense trees as “reinforced” spanning trees of arbitrary graphs is presented. Then it is shown how a k-dense forest or tree can be decomposed into a set of standard spanning trees connected through a common “root” of k vertices. All sections include efficient construction algorithms. Applications of k-dense trees in the fields of distributed systems and data structures are finally indicated.