Browsing by Author "Bello, Martiniano"
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- Binding free energy calculations using MMPB/GBSA approaches for PAMAM-G4-drug complexes at neutral, basic and acid pH conditionsPublication . Martínez-Muñoz, Alberto; Bello, Martiniano; Romero-Castro, Aurelio; Rodríguez-Fonseca, Rolando Alberto; Rodrigues, João; Sánchez-Espinosa, Víctor Armando; Correa-Basurto, JoséDendrimers are synthetic macromolecules with a highly-branched structure and high concentration of surface groups. Among dendrimers, Poly(amidoamine) (PAMAM) has received substantial attention as a novel drug carrier and delivery system. Depending on the generation and type of terminal groups, dendrimer toxicity could change and include cytotoxicity. Although PAMAM is water soluble, molecular modeling of the dendrimer-drug complex is considered challenging for exploring the conformational mobility of dendrimers and atomic specific interactions during the dendrimer-drug association. However, conventional protocols for predicting binding affinities have been designed for small protein molecules or protein-protein complexes that can be applied to study the dendrimer-drug association. In this work, we performed docking calculations for a set of 94 previously reported compounds on PAMAM of fourth generation (G4-PAMAM) to select six compounds, cromoglicic acid (CRO) - a mast cell stabilizer, Fusidic acid (FUS) - a bacteriostatic antibiotic, and Methotrexate (MTX) - a chemotherapy agent and immune system suppressant, which have the highest affinities for G4-PAMAM, and Lidocaine (LDC) - used to numb tissue in a specific area and for ventricular tachycardia treatment, Metoprolol (MET) - a β1 receptor blocker, and Pindolol (PIN) - a β blocker, which have the lowest affinities for the G4-PAMAM dendrimer, to perform MD simulations combined with the molecular mechanics generalized/Poisson-Boltzmann surface area MMGBSA/MMPBSA approach to investigate the interactions of generating 4 charge-neutral, charge-basic and charge-acid G4-PAMAM dendrimers. In addition, to validate these theoretical G4-PAMAM-drug complexes, the complexes were experimentally conjugated to determine their stability in aqueous solubility studies immediately and over one year. Our results show that among the different commercial drugs, both charged and neutral PAMAM have the most favorable binding free energies for CRO, MTX, and FUS, which appears to be due to a complex counterbalance of electrostatics and van der Waals interactions. These theoretical and aqueous solubility studies supported the high affinity of methotrexate for the G4-PAMAM-drug due to its carboxyl and aryl moieties that favor its accommodation by noncovalent interactions.
- In silico search, chemical characterization and immunogenic evaluation of amino-terminated G4-PAMAM-HIV peptide complexes using three-dimensional models of the HIV-1 gp120 proteinPublication . Rodríguez-Fonseca, Rolando Alberto; Bello, Martiniano; Muñoz-Fernández, María Ángeles de los; Luis Jiménez, José; Rojas-Hernández, Saúl; Fragoso-Vázquez, M.J.; Gutiérrez-Sánchez, Mara; Rodrigues, João; Cayetano-Castro, N.; Borja-Urby, R.; Rodríguez-Cortés, Octavio; García-Machorro, Jazmín; Correa-Basurto, JoséPeptide epitopes have been widely used to develop synthetic vaccines and immunotherapies. However, peptide epitopes may exhibit poor absorption or immunogenicity due to their low molecular weights. Conversely, fourth-generation polyamidoamine (G4-PAMAM) dendrimers are nonimmunogenic and relatively nontoxic synthetic nanoparticles that have been used as adjuvants and nanocarriers of small peptides and to improve nasal absorption. Based on this information, we hypothesized that the combination of intranasal immunization and G4-PAMAM dendrimers would be useful for enhancing the antibody responses of HIV-1 gp120 peptide epitopes. Therefore, we first used structural data, peptide epitope predictors and docking and MD simulations on MHC-II to identify two peptide epitopes on the CD4 binding site of HIV-1 gp120. The formation of G4-PAMAM-peptide complexes was evaluated in silico (molecular docking studies using different G4-PAMAM conformations retrieved from MD simulations as well as the MMGBSA approach) and validated experimentally (electrophoresis, 1H NMR and cryo-TEM). Next, the G4-PAMAM dendrimer-peptide complexes were administered intranasally to groups of female BALB/cJ mice. The results showed that both peptides were immunogenic at the systemic and mucosal levels (nasal and vaginal), and G4-PAMAM dendrimer-peptide complexes improved IgG and IgA responses in serum and nasal washes. Thus, G4-PAMAM dendrimers have potential for use as adjuvants and nanocarriers of peptides.