Francesco Musiani

Polysaccharides for the Delivery of Antitumor Drugs

Among the several delivery materials available so far, polysaccharides represent very attractive molecules as they can undergo a wide range of chemical modifications, are biocompatible, biodegradable, and have low immunogenic properties. Thus, polysaccharides can contribute to significantly overcome the limitation in the use of many types of drugs, including anti-cancer drugs. The use of conventional anti-cancer drugs is hampered by their high toxicity, mostly depending on the indiscriminate targeting of both cancer and normal cells. Additionally, for nucleic acid based drugs (NABDs), an emerging class of drugs with potential anti-cancer value, the practical use is problematic. This mostly depends on their fast degradation in biological fluids and the difficulties to cross cell membranes. Thus, for both classes of drugs, the development of optimal delivery materials is crucial. Here we discuss the possibility of using different kinds of polysaccharides, such as chitosan, hyaluronic acid, dextran, and pullulan, as smart drug delivery materials. We first describe the main features of polysaccharides, then a general overview about the aspects ruling drug release mechanisms and the pharmacokinetic are reported. Finally, notable examples of polysaccharide-based delivery of conventional anti-cancer drugs and NABDs are reported. Whereas additional research is required, the promising results obtained so far, fully justify further efforts, both in terms of economic support and investigations in the field of polysaccharides as drug delivery materials.

Kinetic and Structural Studies Reveal a Unique Binding Mode of Sulfite to the Nickel Center in Urease.

Urease is the most efficient enzyme known to date, and catalyzes the hydrolysis of urea using two Ni(II) ions in the active site. Urease is a virulence factor in several human pathogens, while causing severe environmental and agronomic problems. Sporosarcina pasteurii urease has been used extensively in the structural characterization of the enzyme. Sodium sulfite has been widely used as a preservative in urease solutions to prevent oxygen-induced oxidation, but its role as an inhibitor has also been suggested. In the present study, isothermal titration microcalorimetry was used to establish sulfite as a competitive inhibitor for S. pasteurii urease, with an inhibition constant of 0.19mM at pH7. The structure of the urease-sulfite complex, determined at 1.65Å resolution, shows the inhibitor bound to the dinuclear Ni(II) center of urease in a tridentate mode involving bonds between the two Ni(II) ions in the active site and all three oxygen atoms of the inhibitor, supporting the observed competitive inhibition kinetics. This coordination mode of sulfite has never been observed, either in proteins or in small molecule complexes, and could inspire synthetic coordination chemists as well as biochemists to develop urease inhibitors based on this chemical moiety.

Novel Lipid and Polymeric Materials as Delivery Systems for Nucleic Acid Based Drugs.

Nucleic acid based drugs (NADBs) are short DNA/RNA molecules that include among others, antisense oligonucleotides, aptamers, small interfering RNAs and micro-interfering RNAs. Despite the different mechanisms of actions, NABDs have the ability to combat the effects of pathological gene expression in many experimental systems. Thus, nowadays, NABDs are considered to have a great therapeutic potential, possibly superior to that of available drugs. Unfortunately, however, the lack of effective delivery systems limits the practical use of NABDs. Due to their hydrophilic nature, NABDs cannot efficiently cross cellular membrane; in addition, they are subjected to fast degradation by cellular and extracellular nucleases. Together these aspects make the delivery of NABDs as naked molecules almost un-effective. To optimize NABD delivery, several solutions have been investigated. From the first attempts described in the beginning of the 1980s, a burst in the number of published papers occurred in the beginning of 1990 s reaching a peak in 2012-13. The extensive amount of work performed so far clearly witnesses the interest of the scientific community in this topic. In the present review, we will concentrate on the description of the most interesting advances in the field. Particular emphasis will be put on polymeric and lipid materials used alone or in combination with a promising delivery strategy based on the use of carbon nanotubes. The data presented suggest that, although further improvements are required, we are not far from the identification of effective delivery systems for NABDs thus making the clinical use of these molecules closer to reality.

Transient Interactions of a Cytosolic Protein with Macromolecular and Vesicular Cosolutes: Unspecific and Specific Effects.

Cytosolic proteins do not occur as isolated but are exposed to many interactions within a crowded cellular environment. We investigated the associations between a test cytosolic protein, human ileal bile acid binding protein (IBABP), and model cosolutes mimicking macromolecular and lipid membrane intracellular components. Using fluorescence spectroscopy, heteronuclear NMR, and molecular dynamics, we found that IBABP associated weakly with anionic lipid vesicles and experienced transient unspecific contacts with albumin. Localized dynamic perturbations were observed even in the case of apparent unspecific binding. IBABP and ubiquitin did not display mutually attractive forces, whereas IBABP associated specifically with lysozyme. A structural model of the IBABP–lysozyme complex was obtained by data‐driven docking simulation. Presumably, all the interactions shown here contribute to modulating functional communication of a protein in its native environment.

On the interaction of Helicobacter pylori NikR, a Ni(II)-responsive transcription factor, with the urease operator: in solution and in silico studies

Helicobacter pylori (Hp) is a carcinogen that relies on Ni(II) to survive in the extreme pH conditions of the human guts. The regulation of genes coding for Ni(II) enzymes and proteins is effected by the nickel-responsive transcription factor NikR, composed of a DNA-binding domain (DBD) and a metal-binding domain (MBD). The scope of this study is to obtain the molecular details of the HpNikR interaction with the urease operator OPureA, in solution. The size of the full-length protein prevents the characterization of the HpNikR–OPureA interaction using NMR. We thus investigated the two separate domains of HpNikR. The conservation of their oligomeric state was established by multiple-angle light scattering. Isothermal calorimetric titrations indicated that the thermodynamics of Ni(II) binding to the isolated MBD is independent of the presence of the adjacent DBDs. The NMR spectra of the isolated DBD support considerable conservation of its structural properties. The spectral perturbations induced on the DBD by OPureA provided information useful to calculate a structural model of the HpNikR–OPureA complex using a docking computational protocol. The NMR assignment of the residues involved in the protein–DNA interaction represents a starting point for the development of drugs potentially able to eradicate H. pylori infections. All evidences so far collected, in this and previous studies, consistently indicate that binding of Ni(II) to the MBD increases the HpNikR–DNA affinity by modulating the dynamic, and not the structural, properties of the protein, suggesting that the formation of a stable complex relies upon an induced fit mechanism.

Chemosensorial G-proteins-Coupled Receptors: A Perspective from Computational Methods

G-protein coupled receptors (GPCRs) constitute the targets of about 40 % of all the pharmaceutical drugs in the market and, among other functions, a large portion of the family detects odorants and a variety of tastant molecules. Computational techniques are instrumental to understand structure, dynamics and function of the cascades triggered by these receptors. As an example, here we report our own computational work aimed to dissect GPCR molecular mechanisms for chemical senses. The implications of our work for systems biology and for pharmacology are discussed.

Molecular Mechanics/Coarse-Grained Simulations as a Structural Prediction Tool for GPCRs/Ligand Complexes

G-protein coupled receptors (GPCRs) are the most common family of transmembrane receptors in humans. Bioinformatics-based approaches have provided accurate structural predictions of these proteins in complex with their agonist/antagonists when reliable template could be identified. Unfortunately, the average sequence identity across GPCR’s is in the majority of cases below 20%. In these cases, target selection and alignment required for homology modelling is nontrivial, and subsequent standard docking procedures may suffer from severe limitations. A hybrid “Molecular Mechanics/Coarse-Grained” (MM/CG) scheme, developed by some of us and reviewed here, has been shown to improve the quality of structural predictions in few cases and holds promises for high-throughput investigations of GPCR/ligand complexes which do not possess a highly reliable structural template.

Dynamic characterization and substrate binding of cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase—an enzyme used in bioremediation

AbstractIn recent years, techniques involving the use of organisms to remove or neutralize pollutants from contaminated sites have attracted great attention. The aim of bioremediation is to use naturally occurring organisms to degrade dangerous substances to less toxic or non toxic molecules. The gram-negative bacterium Pandoraea pnomenusa strain B-356 (Pp) has been found to be able to transform a persistent class of organic pollutant compounds, namely the biphenyl and polychlorinated biphenyls (PCBs). A key enzyme in the PCB catabolic pathway is NAD-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (BphB), for which the crystal structure from Pp has been crystallized in apo-, NAD-bound and biphenyldiol-/NAD-bound forms. The substrate binding loop structure has not been completely resolved to date in the former two bound states. Here we report the results of the first extensive molecular dynamics simulations on the three different states of PpBphB. This allowed an in depth characterization of the mechanism of ligand uptake and binding, including unraveling of the gating mechanism. Our simulations give a deep insight into several dynamic features of the enzyme that were not captured by crystal structures. Graphical AbstractStarting geometries (in grey) and representative structures of the substrate binding loop of the most populated cluster of structures found in the apo (left), binary(center) and holo (right) forms of PpBphB

Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria

The interaction between macromolecules is a fundamental aspect of most biological processes. The computational techniques used to study protein-protein and protein-nucleic acid interactions have evolved in the last few years because of the development of new algorithms that allow the a priori incorporation, in the docking process, of experimentally derived information, together with the possibility of accounting for the flexibility of the interacting molecules. Here we review the results and the evolution of the techniques used to study the interaction between metallo-proteins and DNA operators, all involved in the nickel and iron metabolism of pathogenic bacteria, focusing in particular on Helicobacter pylori (Hp). In the first part of the article we discuss the methods used to calculate the structure of complexes of proteins involved in the activation of the nickel-dependent enzyme urease. In the second part of the article, we concentrate on two applications of protein-DNA docking conducted on the transcription factors HpFur (ferric uptake regulator) and HpNikR (nickel regulator). In both cases we discuss the technical expedients used to take into account the conformational variability of the multi-domain proteins involved in the calculations.

On the role of a specific insert in acetate permeases (ActP) for tellurite uptake in bacteria: Functional and structural studies.

The oxyanion tellurite (TeO32-) is extremely toxic to bacterial cells. In Rhodobacter capsulatus, tellurite enters the cytosol by means of the high uptake-rate acetate permease RcActP2, encoded by one of the three actP genes present in this species (actP1, actP2 and actP3). Conversely, in Escherichia coli a low rate influx of the oxyanion is measured, which depends mainly on the phosphate transporter EcPitA, even though E. coli contains its own EcActP acetate permease. Here we report that when the actP2 gene from R. capsulatus is expressed in wild-type E. coli HB101 and in E. coli JW3460 ΔpitA mutant, the cellular intake of tellurite increases up to four times, suggesting intrinsic structural differences between EcActP and RcActP2. Indeed, a sequence analysis indicated the presence in RcActP2 of an insert of 15-16 residues, located between trans-membrane (TM) helices 6 and 7, which is absent in both EcActP and RcActP1. Based on this observation, the molecular models of homodimeric RcActP1 and RcActP2 were calculated and analyzed. In the RcActP2 model, the insert induces a perturbation in the conformation of the loop between TM helices 6 and 7, located at the RcActP2 dimerization interface. This perturbation opens a cavity on the periplasmic side that is closed, instead, in the RcActP1 model. This cavity also features an increase of the positive electric potential on the protein surface, an effect ascribed to specific residues Lys261, Lys281 and Arg560. We propose that this positively charged patch in RcActP2 is involved in recognition and translocation of the TeO32- anion, attributing to RcActP2 a greater ability as compared to RcActP1 to transport this inorganic poison inside the cells.