A combined in silico/in vitro approach unveils common molecular requirements for efficient BVDV RdRp binding of linear aromatic N-polycyclic systems.

In this work, we present and discuss a comprehensive set of both newly and previously synthesized compounds belonging to 5 distinct molecular classes of linear aromatic N-polycyclic systems that efficiently inhibits bovine viral diarrhea virus (BVDV) infection. A coupled in silico/in vitro investigation was employed to formulate a molecular rationale explaining the notable affinity of all molecules to BVDV RNA dependent RNA polymerase (RdRp) NS5B. We initially developed a three-dimensional common-feature pharmacophore model according to which two hydrogen bond acceptors and one hydrophobic aromatic feature are shared by all molecular series in binding the viral polymerase. The pharmacophoric information was used to retrieve a putative binding site on the surface of the BVDV RdRp and to guide compound docking within the protein binding site. The affinity of all compounds towards the enzyme was scored via molecular dynamics-based simulations, showing high correlation with in vitro EC50 data. The determination of the interaction spectra of the protein residues involved in inhibitor binding highlighted amino acids R295 and Y674 as the two fundamental H-bond donors, while two hydrophobic cavities HC1 (residues A221, I261, I287, and Y289) and HC2 (residues V216, Y303, V306, K307, P408, and A412) fulfill the third pharmacophoric requirement. Three RdRp (K263, R295 and Y674) residues critical for drug binding were selected and mutagenized, both in silico and in vitro, into alanine, and the affinity of a set of selected compounds towards the mutant RdRp isoforms was determined accordingly. The agreement between predicted and experimental data confirmed the proposed common molecular rationale shared by molecules characterized by different chemical scaffolds in binding to the BVDV RdRp, ultimately yielding compound 6b (EC50 = 0.3 µM; IC50 = 0.48 µM) as a new, potent inhibitor of this Pestivirus.

Cationic carbosilane dendrimers and oligonucleotide binding: an energetic affair.

Generation 2 cationic carbosilane dendrimers hold great promise as internalizing agents for gene therapy as they present low toxicity and retain and internalize the genetic material as an oligonucleotide or siRNA. In this work we carried out complete in silico structural and energetical characterization of the interactions of a set of G2 carbosilane dendrimers, showing different affinity towards two single strand oligonucleotide (ODN) sequences in vitro. Our simulations predict that these four dendrimers and the relevant ODN complexes are characterized by similar size and shape, and that the molecule-specific ODN binding ability can be rationalized only by considering a critical molecular design parameter: the normalized effective binding energy ΔG(bind,eff)/N(eff), i.e. the performance of each active individual dendrimer branch directly involved in a binding interaction.

The sigma enigma: in vitro/in silico site-directed mutagenesis studies unveil σ1 receptor ligand binding.

The σ1 receptor is an integral membrane protein that shares no homology with other receptor systems, has no unequivocally identified natural ligands, but appears to play critical roles in a wide variety of cell functions. While the number of reports of the possible functions of the σ1 receptor is increasing, almost no information about the three-dimensional structure of the receptor and/or possible modes of interaction of the σ1 protein with its ligands have been described. Here we performed an in vitro/in silico investigation to analyze the molecular interactions of the σ1 receptor with its prototypical agonist (+)-pentazocine. Accordingly, 23 mutant σ1 isoforms were generated, and their interactions with (+)-pentazocine were determined experimentally. All direct and/or indirect effects exerted by the mutant residues on the receptor-agonist interactions were reproduced and rationalized in silico, thus shining new light on the three-dimensional structure of the σ1 receptor and its ligand binding site.

Tell me something I do not know. Multiscale molecular modeling of dendrimer/ dendron organization and self-assembly in gene therapy.

Due to the relative easy synthesis and commercial availability, nanovectors based on dendrimers and dendrons are among the most utilized non-viral vectors for gene transfer. Contextually, recent advances in molecular simulations and computer architectures not only allow for accurate predictions of many structural, energetical, and eventual self-assembly features of these nanocarriers per se, but are able to yield vital (and perhaps otherwise unattainable) molecular information about the interactions of these nanovectors with their nucleic acid cargoes. In the present work, we aim at reviewing our own efforts in the field of multiscale molecular modeling of these interesting materials. In particular, our originally developed computational recipes will be presented, and the link between simulations and experiments will be described and discussed in detail. This review is written by computational scientists for experimental scientists, with the specific purpose of illustrating the potentiality of these methodologies and the usefulness of multiscale molecular modeling as an innovative and complementary tool in their current research.

Synthesis and anti-picornaviridae in vitro activity of a new class of helicase inhibitors the N,N'-bis[4-(1H(2H)-benzotriazol-1(2)-yl)phenyl] alkyldicarboxamides.

A series N,N'-bis[4-(1H(2H)-benzotriazol-1(2)-yl)phenyl]alkyldicarboxamides (3a-f and 5a-j) were prepared starting from their already known (1a-d) and (4a-c) or new (4d) amine parents. Because of the antiviral activity of several N-[4-(1H(2H)-benzotriazol-1(2)-yl)phenyl]alkylcarboxamides previously reported, title compounds were evaluated in vitro for cytotoxicity and antiviral activity against viruses representative of Picornaviridae, [i.e. Enterovirus Coxsackie B2 (CVB-2) and Polio (Sb-1)] and of two of the three genera of the Flaviviridae [Bovine Viral Diarrhea Virus (BVDV) and Yellow Fever Virus (YFV)]. Furthermore, because of the in silico activity against the RNA-dependent RNA-helicase of Polio 1 previously reported, title compounds were evaluated against the 3D model of the Sb-1 helicase and against the 2D model of the CVB-2 helicase. As a reference we used the antiviral and in silico activities of an imidazo counterpart of the title compounds, N,N'-bis[4-(2-benzimidazolyl)phenyl]alkyldicarboxamides (III) that other authors reported to be able to inhibit the corresponding enzyme of Hepatitis C Virus (HCV). In cell-based antiviral assays, N,N'-bis[4-(1H-benzotriazol-1-yl)phenyl]alkyldicarboxamides (3a-f) resulted completely inactive whereas the bis-5,6-dimethyl-benzotriazol-2-yl derivatives (5d-f) exhibited good activity against the Enteroviruses, (EC(50)s ranged between 7 and 11 microM against CVB-2 and 19-52 against Sb-1). Interestingly, bis-5,6-dichloro-benzotriazol-2-yl derivatives (5h-j) showed very selective activity against CVB-2 (EC(50)s = 4-11 microM) whereas they resulted completely inactive against all the other viruses screened. In general, all title compounds showed a good cytotoxicity profile in MT-4 cells. Molecular modeling investigations showed that active compounds may interact with the binding site of the Sb-1 helicase and that their free binding energy values are in agreement with their EC(50)s values.

Functional analyses and molecular modeling of two c-Kit mutations responsible for imatinib secondary resistance in GIST patients.

Imatinib-acquired resistance related to the presence of secondary point mutations has become a frequent event in gastrointestinal stromal tumors. Here, transient transfection experiments with plasmids carrying two different KIT-acquired point mutations were performed along with immunoprecipitation of total protein extracts, derived from imatinib-treated and untreated cells. The molecular mechanics/Poisson Boltzmann surface area computational techniques were applied to study the interactions of the wild-type and mutated receptors with imatinib at the molecular level. Biochemical analyses showed KIT phosphorylation in cells transfected with vectors carrying the specific mutant genes. Imatinib treatment demonstrated that T670I was insensitive to the drug at all the applied concentrations, whereas V654A was inhibited by 6 microM of imatinib. The modeling of the mutated receptors revealed that both substitutions affect imatinib-binding site, but to a different extent: T670I substantially modifies the binding pocket, whereas V654A induces only relatively confined structural changes. We demonstrated that T670I and V654A cause indeed imatinib-acquired resistance and that the former is more resistant to imatinib than the latter. The application of molecular simulations allowed us to quantify the interactions between the mutated receptors and imatinib, and to propose a molecular rationale for this type of drug resistance.

Synergistic gelation of xanthan gum with locust bean gum: a rheological investigation.

Many industrial products often include in their formulation more than one polysaccharide to achieve the desired properties during and after processing. Many such mixed systems behave as would be expected from the known properties of the individual polymers. In others, however, their properties are superior to those of either component alone, or may be qualitatively different. In many polysaccharide systems, the combination of a gelling polymer with a nongelling one gives rise to strong synergistic effects, as a consequence of interaction among different chain polymers and formation of mixed junction zones. Probably, the most exploited mixed gels, especially by the food industry, are those involving the microbial polysaccharide xanthan gum (XG) and the plant galactomannans, like locust bean gum (LBG). Concentrated aqueous systems of LBG and XG display quite different rheological properties: the former show the behaviour typical of hyperentangled macromolecular solutions, whereas the flow and viscoelastic properties of XG systems correspond to those of tenuous, weak-gel networks. Interestingly, when mixed together these macromolecules interact to form a firm, thermoreversible gel with synergistic effects. In the present paper we report the results of a thorough investigation of both polymer concentration and temperature effects on the rheological properties of mixed LBG-XG systems in 20 mM KCl under continuous and oscillatory flow conditions. Under continuous shear at 25 degrees C, pure LBG shows the flow properties of a macromolecular solution, with a shear-thinning behaviour and a Newtonian region at low shear rates, whereas the rheological behaviour of XG and all LX mixed systems is that typical of weak-gels. Furthermore, in the mixed systems the viscosity values do not increase monotonically with increasing xanthan concentration, but the synergistic effect has a maximum in accordance with the XG:LBG ratio 1:1. As the temperature is increased from 25 degrees C to 85 degrees C, whilst the LBG system do not show any qualitative change but there is only a parallel, downward shift of viscosity values, in the case of xanthan there is a dramatic change in the corresponding curve profiles, due to the thermally induced helix-coil conformational transition. The differences in the rheological behaviour of the systems examined can be better shown through dynamic tests at 25 degrees C. The strain sweeps performed at constant frequency of oscillation reveal that the mixed systems show higher sensitivity to strain amplitude, and lower strain values must be attained to ensure linear viscoelastic properties. The mechanical spectra clearly show the influence of composition on the viscoelastic properties of these biopolymer systems. All LX systems show the mechanical spectra typical of polysaccharide gels: G' is always much greater than G" and is nearly independent of the applied frequency over a wide frequency range. In addition, the marked gap between the elastic responses of the pure LBG and the LX 1:3 systems demonstrates the strong effect of the initial addition of xanthan to the pure LBG, especially in the low frequency range, whereas the highest synergistic effect is attained for the LX 1:1 system. A comprehensive description of the frequency dependence of both moduli can be suitably obtained through the four-parameter Friedrich model, which belongs to the class of fractional derivative approaches viscoelasticity. The same thermal effect is observed for the XG and all LX mixed systems considered, indicating a progressive change from the behaviour of a typical gel to that of a quasi-solution state, when temperature is increased from 25 degrees C to 85 degrees C. Among all mixed systems, the LX 1:1 has the highest values of the moduli at any temperature considered, and is characterized by the highest gel-sol transition temperature. (ABSTRACT TRUNCATED)

Flow properties of N-(carboxymethyl) chitosan aqueous systems in the sol and gel domains.

The flow behaviour and the viscoelastic properties of N-(carboxymethyl) chitosan aqueous systems in the sol and gel domains have been investigated by means of dynamic, steady and transient shear techniques. For polymer concentrations Cp up to 1%, a typical response of moderately concentrated polymer solutions was observed under continuous and oscillatory shear conditions. No time-dependent properties were detected during transient shear experiments. On the other hand, for all the samples with Cp greater than 1%, the rheological properties were more similar to those of a weak gel system. The continuous shear flow behaviour was of the plastic type and the viscoelastic quantities G' and G" were parallel to each other and slightly dependent on the frequency of oscillation omega. Stress overshoots were observed during transient shear experiments, and the kinetics of the structural breakdown and build-up processes were found to be dependent both on the polymer concentration and the applied shear rate.