Surface electrostatic potentials on macromolecules in a monopole approximation: a computer program and an application to cytochromes

In-Depth Study of Cyclodextrin Complexation with Carotenoids toward the Formation of Enhanced Delivery Systems

The goal of this study was molecular modeling of cyclodextrin (CD) and carotenoid complex formation. Distinction was made between complexes resulting from interactions between carotenoids and either molecularly dispersed CDs or solid crystalline CDs, considering that both cases can occur depending on the complex formation process pathways. First, the formation of complexes from dispersed CD molecules was investigated considering five different CDs (αCD, βCD, methyl-βCD, hydroxypropyl-βCD, and γCD) and lutein, as a model carotenoid molecule. The interactions involved and the stability of the different complexes formed were evaluated according to the CD size and steric hindrance. Second, the formation of complexes between four different crystalline CDs (βCD with three different water contents and methyl-βCD) and three carotenoid molecules (lutein, lycopene, and β-carotene) was studied. The docking/adsorption of the carotenoid molecules was modeled on the different faces of the CD crystals. The findings highlight that all the CD faces, and thus their growth rates, were equally impacted by the adsorption of the carotenoids. This is due to the fact that all the CD faces are exhibiting similar chemical compositions, the three studied carotenoid molecules are rather chemically similar, and last, the water-carotenoid interactions appear to be weak compared to the CD-carotenoid interactions.

Benzylic-type couplings provide an important asymmetric entry to functionalized, non-racemic helicenes

Benzylic-type couplings are key reactions to make non-racemic helicenes.

Prediction of HIV-1 protease inhibitor resistance by Molecular Modeling Protocols (MMPs) using GenMol software

This paper investigates the contribution of Molecular Modeling to (i) predict and (ii) understand more fundamentally HIV drug resistance. Based on a new automated GenMol module, these goals are approached by Molecular Modeling Protocols (MMPs), respectively, (i) the Molecular Modeling Phenotype Protocol (MMPP) and (ii) the Molecular Modeling Phenotype-Genotype Protocol (MMGPP). Section 2 recalls clinical practice with a reference case study and Section 3 presents atomistic simulation tools. Section 4 is the heart of the paper. In Section 4.1, MMPP drug resistance prediction is based on correlations between fold resistances versus binding energies on 2959 HIV-1 complexes with 6 protease inhibitors. Based on a drug sensitivity twofold criterion, modeling prediction is able to replace long and costly phenotype tests. In Section 4.2, MMGPP enlightens drug resistance by investigating steric and energetic residues/inhibitor interaction. Section 5 gives a synthesis on modeling contribution to drug resistance prediction. In conclusion, the most promising trend consists of MMP automats that are able to suggest a real time diagnosis taking into account the history of each patient, to enrich databases and to develop therapy strategy and new drugs.

Resistance of Hepatitis C Virus to Ns3–4A Protease Inhibitors: Mechanisms of Drug Resistance Induced by R155Q, A156T, D168A and D168V Mutations

Background/aims

One of the main issues in the development of antiviral therapy is the emergence of drug-resistant viruses. In the case of hepatitis C virus (HCV), selection of drug-resistant mutants was evidenced by in vitro studies on protease inhibitors (PIs); for example, BILN-2061, VX-950 and SCH-6. Four mutations in the HCV protease (R155Q, A156T, D168A and D168V) have been identified in vitro in the HCV replicon system that confer resistance to BILN-2061 (a reference inhibitor). However, the molecular mechanism of drug resistance is still unknown. The aim of this study is to unravel, using an molecular modelling strategy, the structural basis of such molecular mechanism of HCV resistance to PIs. We focused on protease mutations conferring HCV resistance to BILN-2061 and described for the first time such mechanism at a molecular level.

Methods

The structures of drug-resistant NS3 proteases were obtained by mutation of selected residues (R155Q, A156T, D168A and D168V) and the ternary complexes formed between NS3–4A and BILN-2061 were optimized using GenMol software ( www.3dgenoscience.com ; Genoscience, Marseille, France).

Results

Two mechanisms were evidenced for viral resistance to BILN-2061. A ‘direct’ resistance mechanism is based on contacts between the mutated R155Q and A156T protease residues and its inhibitor. In the ‘indirect’ resistance mechanism, the mutated D168A/V residue is not in close contact with the drug itself but interacts with other residues connected to the drug.

Conclusions

These data provide new insights in the understanding of the mechanisms of HCV drug escape, and may allow predicting potential cross-resistance phenomenon with other PIs. This approach can be used as a basis for future rational PI drug design candidates.

Phases, periphases, and interphases equilibrium by molecular modeling. I. Mass equilibrium by the semianalytical stochastic perturbations method and application to a solution between (120) gypsum faces

The SASP (semianalytical stochastic perturbations) method is an original mixed macro-nano-approach dedicated to the mass equilibrium of multispecies phases, periphases, and interphases. This general method, applied here to the reflexive relation C(k)<=>mu(k) between the concentrations C(k) and the chemical potentials mu(k) of k species within a fluid in equilibrium, leads to the distribution of the particles at the atomic scale. The macroaspects of the method, based on analytical Taylor's developments of chemical potentials, are intimately mixed with the nanoaspects of molecular mechanics computations on stochastically perturbed states. This numerical approach, directly linked to definitions, is universal by comparison with current approaches, DLVO Derjaguin-Landau-Verwey-Overbeek, grand canonical Monte Carlo, etc., without any restriction on the number of species, concentrations, or boundary conditions. The determination of the relation C(k)<=>mu(k) implies in fact two problems: a direct problem C(k)=>mu(k) and an inverse problem mu(k)=>C(k). Validation of the method is demonstrated in case studies A and B which treat, respectively, a direct problem and an inverse problem within a free saturated gypsum solution. The flexibility of the method is illustrated in case study C dealing with an inverse problem within a solution interphase, confined between two (120) gypsum faces, remaining in connection with a reference solution. This last inverse problem leads to the mass equilibrium of ions and water molecules within a 3 A thick gypsum interface. The major unexpected observation is the repulsion of SO(4) (2-) ions towards the reference solution and the attraction of Ca(2+) ions from the reference solution, the concentration being 50 times higher within the interphase as compared to the free solution. The SASP method is today the unique approach able to tackle the simulation of the number and distribution of ions plus water molecules in such extreme confined conditions. This result is of prime importance for all coupled chemical-mechanical problems dealing with interfaces, and more generally for a wide variety of applications such as phase changes, osmotic equilibrium, surface energy, etc., in complex chemical-physics situations.

Mechanistic basis for reduced viral and enzymatic fitness of HIV-1 reverse transcriptase containing both K65R and M184V mutations

HIV-1 drug resistance mutations are often inversely correlated with viral fitness, which remains poorly described at the molecular level. Some resistance mutations can also suppress resistance caused by other resistance mutations. We report the molecular mechanisms by which a virus resistant to lamivudine with the M184V reverse transcriptase mutation shows increased susceptibility to tenofovir and can suppress the effects of the tenofovir resistance mutation K65R. Additionally, we report how the decreased viral replication capacity of resistant viruses is directly linked to their decreased ability to use natural nucleotide substrates and that combination of the K65R and M184V resistance mutations leads to greater decreases in viral replication capacity. All together, these results define at the molecular level how nucleoside-resistant viruses can be driven to reduced viral fitness.

Force field calculations on five membered ring aminoxyl radicals

Two force fields (MM2 and Genmol) have been applied to the modeling of five membered ring aminoxyl radicals. For the six molecules which were investigated the geometry of the conformation with the lowest strain energy was in very good agreement with the X-ray geometry. However owing to the high flexibility of five membered rings other conformations were shown to have a strain energy close to the energy minimum.

Conformational analysis of the amino termini (5 residues) of human glycophorin AM and AN: differentiation of the structural features of the TN and T antigenic determinants in relation to their specificity

The N-terminus of glycophorin A, the main transmembrane erythrocyte glycoprotein responsible for the MN blood-group specificity, has been modelled. As the minimum size of the protein recognised by the antiglycophorin A antibodies is the N-terminal glycopentapeptide, attention was focused on the TN and T antigenic determinants of this size in order to determine wether differences in 3D structure exist and how a specific response with different antibodies is induced.

The computer program MolPot: a useful tool in chemical reactivity analysis

MolPot is a fast program for producing reactivity diagrams of molecular compounds, particularly for drugs. These diagrams are characteristic of the molecule envelope and the Molecular Electrostatic Potential (MEP) of the molecule surface (van der Waals surface or the portion of this surface that is solvent accessible). The input data includes only the atom names and their Cartesian coordinates.