RESUMO
Dengue virus (DENV) is a danger to more than 400 million people in the world, and there is no specific treatment. Thus, there is an urgent need to develop an effective method to combat this pathology. NS2B/NS3 protease is an important biological target due it being necessary for viral replication and the fact that it promotes the spread of the infection. Thus, this study aimed to design DENV NS2B/NS3pro allosteric inhibitors from a matrix compound. The search was conducted using the Swiss Similarity tool. The compounds were subjected to molecular docking calculations, molecular dynamics simulations (MD) and free energy calculations. The molecular docking results showed that two compounds, ZINC000001680989 and ZINC000001679427, were promising and performed important hydrogen interactions with the Asn152, Leu149 and Ala164 residues, showing the same interactions obtained in the literature. In the MD, the results indicated that five residues, Lys74, Leu76, Asn152, Leu149 and Ala166, contribute to the stability of the ligand at the allosteric site for all of the simulated systems. Hydrophobic, electrostatic and van der Waals interactions had significant effects on binding affinity. Physicochemical properties, lipophilicity, water solubility, pharmacokinetics, druglikeness and medicinal chemistry were evaluated for four compounds that were more promising, showed negative indices for the potential penetration of the Blood Brain Barrier and expressed high human intestinal absorption, indicating a low risk of central nervous system depression or drowsiness as the the side effects. The compound ZINC000006694490 exhibited an alert with a plausible level of toxicity for the purine base chemical moiety, indicating hepatotoxicity and chromosome damage in vivo in mouse, rat and human organisms. All of the compounds selected in this study showed a synthetic accessibility (SA) score lower than 4, suggesting the ease of new syntheses. The results corroborate with other studies in the literature, and the computational approach used here can contribute to the discovery of new and potent anti-dengue agents.
Assuntos
Vírus da Dengue , Inibidores de Proteases , Proteínas não Estruturais Virais , Animais , Antivirais/química , Antivirais/farmacologia , Vírus da Dengue/efeitos dos fármacos , Vírus da Dengue/enzimologia , Humanos , Camundongos , Simulação de Acoplamento Molecular , Peptídeo Hidrolases/farmacologia , Inibidores de Proteases/química , Inibidores de Proteases/farmacologia , RNA Helicases/antagonistas & inibidores , RNA Helicases/química , Ratos , Serina Endopeptidases/química , Proteínas não Estruturais Virais/antagonistas & inibidores , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismoRESUMO
Identification of allosteric inhibitors of PTPs has attracted great interest as a new strategy to overcome the challenge of discover potent and selective molecules for therapeutic intervention. YopH is a virulence factor of the genus Yersinia, validated as an antimicrobial target. The finding of a second substrate binding site in YopH has revealed a putative allosteric site that could be further exploited. Novel chalcone compounds that inhibit PTPs activity were designed and synthesized. Compound 3j was the most potent inhibitor, interestingly, with different mechanisms of inhibition for the panel of enzymes evaluated. Further, our results showed that compound 3j is an irreversible non-competitive inhibitor of YopH that binds to a site different than the catalytic site, but close to the well-known second binding site of YopH.
Assuntos
Proteínas da Membrana Bacteriana Externa/antagonistas & inibidores , Chalcona/farmacologia , Inibidores Enzimáticos/farmacologia , Proteínas Tirosina Fosfatases/antagonistas & inibidores , Fatores de Virulência/antagonistas & inibidores , Sítio Alostérico/efeitos dos fármacos , Proteínas da Membrana Bacteriana Externa/metabolismo , Chalcona/síntese química , Chalcona/química , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Estrutura Molecular , Proteínas Tirosina Fosfatases/metabolismo , Relação Estrutura-Atividade , Fatores de Virulência/metabolismoRESUMO
Malaria is the world's most widespread protozoan infection, being responsible for more than 445,000 annual deaths. Among the malaria parasites, Plasmodium falciparum is the most prevalent and lethal. In this context, the search for new antimalarial drugs is urgently needed. P. falciparum superoxide dismutase (PfSOD) is an important enzyme involved in the defense mechanism against oxidative stress. The goal of this study was to identify through hierarchical screening on pharmacophore models and molecular dynamics (MD), promising allosteric PfSOD inhibitors that do not show structural requirements for human inhibition. MD simulations of 1000 ps were performed on PfSOD using GROMACS 5.1.2. For this, the AMBER99SB-ILDN force field was adapted to describe the metal-containing system. The simulations indicated stability in the developed system. Therefore, a covariance matrix was generated, in which it was possible to identify residues with correlated and anticorrelated movements with the active site. These results were associated with the results found in the predictor of allosteric sites, AlloSitePro, which affirmed the ability of these residues to delimit an allosteric site. Then, after successive filtering of the Sigma-Aldrich® compounds database for HsSOD1 and PfSOD pharmacophores, 152 compounds were selected, also obeying Lipinski's rule of 5. Further filtering of those compounds based on molecular docking results, toxicity essays, availability, and price filtering led to the selection of a best compound, which was then submitted to MD simulations of 20,000 ps on the allosteric site. The study concludes that the ZINC00626080 compound could be assayed against SODs. Graphical Abstract Plasmodium falciparum superoxide dismutase.
Assuntos
Antimaláricos/química , Inibidores Enzimáticos/química , Simulação de Dinâmica Molecular , Plasmodium falciparum/química , Proteínas de Protozoários/química , Superóxido Dismutase/química , Regulação Alostérica , Sequência de Aminoácidos , Antimaláricos/metabolismo , Bases de Dados de Compostos Químicos , Descoberta de Drogas , Inibidores Enzimáticos/metabolismo , Humanos , Simulação de Acoplamento Molecular , Plasmodium falciparum/enzimologia , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estrutura Secundária de Proteína , Proteínas de Protozoários/antagonistas & inibidores , Proteínas de Protozoários/metabolismo , Homologia de Sequência de Aminoácidos , Especificidade da Espécie , Relação Estrutura-Atividade , Superóxido Dismutase/antagonistas & inibidores , Superóxido Dismutase/metabolismo , Termodinâmica , Interface Usuário-ComputadorRESUMO
To substantiate the functionality of a crystallographically evidenced allosteric site in Bacillus caldovelox arginase (Bewley et al., 1999), we have examined the kinetic consequences of the single mutations of Asp199 and Glu256, which interact with l-arginine in this site. The introduced mutations (Asp199 â Asn, Asp199 â Ala, Glu256 â Gln and Glu256 â Ala) had no effect on the hexameric structure of the enzyme (mol. wt. 195 ± 10 kDa). However, in contrast with the Michaelis-Menten kinetics exhibited by the wild-type species, the D199A, D199N, E256A and E256Q variants exhibited positive cooperativity with respect to l-arginine. The Glu278 â Ala mutation, which compromise interactions at the trimer-trimer interface, yielded trimeric species (mol. wt. 100 ± 5 kDa) exhibiting hyperbolic kinetics that changed to sigmoidal by the additional Glu256 â Ala mutation. In addition to demonstrating the total functionality of the trimer, our results also suggest that B. caldovelox is kinetically cooperative and that the commonly detected hyperbolic behavior results from binding of l-arginine as a typical allosteric activator.