Homology molecular modeling and molecular docking studies of potential therapeutic targets for Chagas Disease

The development of new drugs against Trypanosoma cruzi is still needed since the only drugs used to treat cause serious side effects. Naphthoquinones derivatives β-lapachone and oxiran-alfa-lapachone have high trypanocidal activity and act on different targets in the parasite. With the aim of obtaining parameters that influence the activity profile of these derivatives, computational techniques were used to study the interaction between protease inhibitors and oligopeptidase B and cruzain. In the first part of this work models of oligopeptidase B were built by homology modeling. Due to the low identity with the template 2BKL, models were constructed from alignments performed in ClustalW and 3D-coffee while were used SWISS-MODEL and Modeller programs to obtain three-dimensional structure. After the models validation, the model obtained from SWISS-MODEL and the alignment with ClustalW yielded better results, so it was selected for use in molecular docking studies. In the second part of this work, we studied molecular docking of β- lapachone and oxiran-alfa-lapachone in the active site of cruzain and oligopeptidase B. Studies of molecular docking in the active site of cruzain showed that β-lapachone, E64, a standard cysteine protease inhibitor, are involved in hydrogen bonds and interact hydrophobically with residues of the S1 sub-site, important for the specificity of the enzyme, justifying the inhibitory activity, while the oxiran-alfa lapachone does not participate in important interactions. The results of molecular docking in the active site of oligopeptidase B indicated that the oxiran-alfa-lapachone is located near the catalytic triad of the enzyme. The analysis of the complex showed that it participates in two hydrogen bonds with residues ARG649 and TYR481 corroborate the trypanocidal activity, and guide the oxiran ring with the SER562 the catalytic triad, indicating a possible nucleophilic attack (irreversible inhibition). The oligopeptidase B enzymes do not have homologues in humans, therefore is a potential target in studies of new drugs with trypanocidal activity. Thus, based on tests carried out and jointly with data obtained from the literature of oligopeptidase B inhibitors, 8 new derivatives of oxiran-alfa-lapachone were proposed based on molecular hybridization in order to increase the surface contact with the active site through hydrophobic interactions and salt bridges, as described in the literature as important for the inhibition of serine proteases.Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorO desenvolvimento de novos fármacos contra o Trypanosoma cruzi ainda é necessário uma vez que os únicos fármacos usados no tratamento causam efeitos colaterais graves. Os derivados naftoquinônicos β-lapachona e oxirano-alfa-lapachona possuem alta atividade tripanocida e atuam em diferentes alvos no parasita. Com o objetivo de se obter parâmetros que influenciam no perfil da atividade desses derivados, foram utilizadas técnicas computacionais para o estudo da interação entre os inibidores e as proteases cruzaína e oligopeptidase B do parasita. Na primeira parte deste trabalho construímos modelos por homologia da oligopeptidase B. Devido à baixa identidade com o molde 2BKL, foram construídos modelos a partir de alinhamentos realizados no ClustalW e no 3Dcoffee, enquanto foram utilizados os programas SWISS-MODEL e Modeller para obtenção da estrutura tridimensional. Após a validação dos modelos, aquele obtido no SWISS-MODEL a partir do alinhamento com ClustalW apresentou melhores resultados, assim foi selecionado para o uso no estudo de docking molecular. Na segunda parte desse trabalho foram realizados estudos de docking molecular da β-lapachona e do oxirano-alfa-lapachona no sítio ativo da cruzaína e da oligopeptidase B. Os estudos de docking molecular no sítio ativo da cruzaína mostraram que β-lapachona e E64, um inibidor padrão de cisteinoprotease, participam de ligações de Hidrogênio e interagem hidrofobicamente com resíduos do sub-sítio S1, importantes para a especificidade da enzima, justificando suas atividades inibitórias, enquanto o oxirano-alfa-lapachona não participa de interações importantes. Os resultados de docking molecular no sítio ativo da oligopeptidase B indicaram que o oxirano-alfa-lapachona localiza-se próximo à tríade catalítica da enzima. A análise do complexo mostrou que o mesmo participa de duas ligações de Hidrogênio com os resíduos ARG649 e TYR481 que colaboram com a atividade tripanocida, além de orientarem o anel oxirano com a SER562 da tríade catalítica, indicando um possível ataque nucleofílico (inibição irreversível). A oligopeptidase B não possui enzimas homólogas em humanos, logo é um potencial alvo molecular nos estudos de novos fármacos com atividade tripanocida. Com isso, baseado nas análises realizadas e juntamente com dados obtidos da literatura com relação a inibidores de oligopeptidase B, foram propostos 8 novos derivados do oxirano-alfa-lapachona baseadas em hibridação molecular com a finalidade de aumentar a superfície de contato com o sítio através de interações hidrofóbicas e pontes salinas, descritas na literatura como importantes para a inibição de serino proteases

Computational methods applications on the structure activity relationship and toxicological profile study of new antiparasitic and antimicobacterium compounds

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Profile of pharmaceutical interventions of a pharmacotherapeutic follow-up model for diabetic patients in a community pharmacy

The insertion of Pharmaceutical Care in Primary Health Care (PHC) improves patients’ clinical outcomes and quality of life. Pharmacotherapeutic follow-up can contribute to the management of chronic diseases such as diabetes, promoting better glycemic control and adherence to therapy. This study aimed to assess the Drug-therapy Problems (DTPs) and Pharmacist Interventions (PIs) on the pharmacotherapeutic management in patients with type 2 diabetes mellitus (T2DM) in a community pharmacy. A quantitative, retrospective, and cross-sectional study was conducted in a Pharmaceutical Care Program within the PHC in Juiz de Fora (Minas Gerais, Brazil). Inclusion criteria were patients with T2DM above 18, who attended at least three pharmaceutical consultations between July 2016 and October 2018 and presented two or more glycated hemoglobin tests. The study group (n = 17) was largely composed of women (65%), elderly (76%), sedentary (72%), and obese people (52%). The resolution was achieved in 79% of the DTPs identified (n = 115). Most of DTPs were related to administration and adherence to pharmacotherapy (46%). 60% of the 437 PIs involved the provision of information and counseling. In other words, accessible interventions lead to high resolvability. Therefore, clinical actuation of pharmacists could improve the prognosis in diabetes treatment

Structural insights into the allosteric site of Arabidopsis NADP-malic enzyme 2: role of the second sphere residues in the regulatory signal transmission

Structure–function studies contribute to deciphering how small modifcations in the primary structure could introduce desirable characteristics into enzymes without afecting its overall functioning. Malic enzymes (ME) are ubiquitous and responsible for a wide variety of functions. The availability of a high number of ME crystal structures from diferent species facilitates comparisons between sequence and structure. Specifcally, the structural determinants necessary for fumarate allosteric regulation of ME has been of particular interest. NADP-ME2 from Arabidopsis thaliana exhibits a distinctive and complex regulation by fumarate, acting as an activator or an inhibitor according to substrate and efector concentrations. However, the 3D structure for this enzyme is not yet reported. In this work, we characterized the NADP-ME2 allosteric site by structural modeling, molecular docking, normal mode analysis and mutagenesis. The regulatory site model and its docking analysis suggested that other C4 acids including malate, NADP-ME2 substrate, could also ft into fumarate’s pocket. Besides, a non-conserved cluster of hydrophobic residues in the second sphere of the allosteric site was identifed. The substitution of one of those residues, L62, by a less fexible residue as tryptophan, resulted in a complete loss of fumarate activation and a reduction of substrate afnities for the active site. In addition, normal mode analysis indicated that conformational changes leading to the activation could originate in the region surrounding L62, extending through the allosteric site till the active site. Finally, the results in this work contribute to the understanding of structural determinants necessary for allosteric regulation providing new insights for enzyme optimization.Fil: Gerrard Wheeler, Mariel Claudia. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Argentina.Fil: Arias, Cintia Lucía. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Argentina.Fil: Da Fonseca Rezende e Mello, Juliana. Universidade Federal do Rio de Janeiro. Faculdade de Farmácia. Laboratório de Modelagem Molecular & QSAR (ModMolQSAR); Brazil.Fil: Cirauqui Diaz, Nuria. Universidade Federal do Rio de Janeiro. Faculdade de Farmácia. Laboratório de Modelagem Molecular & QSAR (ModMolQSAR); Brazil.Fil: Rodrigues, Carlos Rangel. Universidade Federal do Rio de Janeiro. Faculdade de Farmácia. Laboratório de Modelagem Molecular & QSAR (ModMolQSAR); Brazil.Fil: Drincovich, María Fabiana. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Argentina.Fil: Mendonça Teles de Souza, Alessandra. Universidade Federal do Rio de Janeiro. Faculdade de Farmácia. Laboratório de Modelagem Molecular & QSAR (ModMolQSAR); Brazil.Fil: Alvarez, Clarisa Ester. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Argentina

Hologram QSAR Models of 4-[(Diethylamino)methyl]-phenol Inhibitors of Acetyl/Butyrylcholinesterase Enzymes as Potential Anti-Alzheimer Agents

Hologram QSAR models were developed for a series of 36 inhibitors (29 training set and seven test set compounds) of acetyl/butyrylcholinesterase (AChE/BChE) enzymes, an attractive molecular target for Alzheimer’s disease (AD) treatment. The HQSAR models (N = 29) exhibited significant cross-validated (AChE, q2 = 0.787; BChE, q2 = 0. 904) and non-cross-validated (AChE, r2 = 0.965; BChE, r2 = 0.952) correlation coefficients. The models were used to predict the inhibitory potencies of the test set compounds, and agreement between the experimental and predicted values was verified, exhibiting a powerful predictive capability. Contribution maps show that structural fragments containing aromatic moieties and long side chains increase potency. Both the HQSAR models and the contribution maps should be useful for the further design of novel, structurally related cholinesterase inhibitors

Antimycobacterial and Anti-Inflammatory Activities of Substituted Chalcones Focusing on an Anti-Tuberculosis Dual Treatment Approach

Tuberculosis (TB) remains a serious public health problem aggravated by the emergence of M. tuberculosis (Mtb) strains resistant to multiple drugs (MDR). Delay in TB treatment, common in the MDR-TB cases, can lead to deleterious life-threatening inflammation in susceptible hyper-reactive individuals, encouraging the discovery of new anti-Mtb drugs and the use of adjunctive therapy based on anti-inflammatory interventions. In this study, a series of forty synthetic chalcones was evaluated in vitro for their anti-inflammatory and antimycobacterial properties and in silico for pharmacokinetic parameters. Seven compounds strongly inhibited NO and PGE2 production by LPS-stimulated macrophages through the specific inhibition of iNOS and COX-2 expression, respectively, with compounds 4 and 5 standing out in this respect. Four of the seven most active compounds were able to inhibit production of TNF-α and IL-1β. Chalcones that were not toxic to cultured macrophages were tested for antimycobacterial activity. Eight compounds were able to inhibit growth of the M. bovis BCG and Mtb H37Rv strains in bacterial cultures and in infected macrophages. Four of them, including compounds 4 and 5, were active against a hypervirulent clinical Mtb isolate as well. In silico analysis of ADMET properties showed that the evaluated chalcones displayed satisfactory pharmacokinetic parameters. In conclusion, the obtained data demonstrate that at least two of the studied chalcones, compounds 4 and 5, are promising antimycobacterial and anti-inflammatory agents, especially focusing on an anti-tuberculosis dual treatment approach

Thieno[2,3-b]pyridine derivatives: a new class of antiviral drugs against Mayaro virus

Mayaro virus (MAYV) is an arthropod-borne virus and a member of the family Togaviridae, genus Alphavirus. Its infection leads to an acute illness accompanied by long-lasting arthralgia. To date, there are no antiviral drugs or vaccines against infection with MAYV and resources for the prevention or treatment of other alphaviruses are very limited. MAYV has served as a model to study the antiviral potential of several substances on alphavirus replication. In this work we evaluated the antiviral effect of seven new derivatives of thieno[2,3-b]pyridine against MAYV replication in a mammalian cell line. All derivatives were able to reduce viral production effectively at concentrations that were non-toxic for Vero cells. Molecular modeling assays predicted low toxicity risk and good oral bioavailability of the substances in humans. One of the molecules, selected for further study, demonstrated a strong anti-MAYV effect at early stages of replication, as it protected pre-treated cells and also during the late stages, affecting virus morphogenesis. This study is the first to demonstrate the antiviral effect of thienopyridine derivatives on MAYV replication in vitro, suggesting the potential application of these substances as antiviral molecules against alphaviruses. Additional in vivo research will be needed to expand the putative therapeutic applications.Fil: Amorim, Raquel. Universidade Federal do Rio de Janeiro; BrasilFil: Meneses, Marcelo Damião Ferreira de. Universidade Federal do Rio de Janeiro; BrasilFil: Borges, Julio Cesar. Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro; BrasilFil: Pinheiro, Luiz Carlos da Silva. Universidade Federal do Rio de Janeiro; BrasilFil: Caldas, Lucio Ayres. Universidade Federal do Rio de Janeiro; BrasilFil: Cirne Santos, Claudio Cesar. Universidade Federal do Rio de Janeiro; BrasilFil: Mello, Marcos Vinícius Palmeira de. Universidade Federal Fluminense; BrasilFil: Souza, Alessandra Mendonça Teles de. Universidade Federal do Rio de Janeiro; BrasilFil: Castro, Helena Carla. Universidade Federal Fluminense; BrasilFil: Paixão, Izabel Christina Nunes de Palmer. Universidade Federal Fluminense; BrasilFil: Campos, Renata de Mendonça. Universidade Federal do Rio de Janeiro; BrasilFil: Bergmann, Ingrid Evelyn. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología ; ArgentinaFil: Malirat, Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología ; ArgentinaFil: Bernardino, Alice Maria Rolim. Universidade Federal Fluminense; BrasilFil: Rebello, Moacyr Alcoforado. Universidade Federal do Rio de Janeiro; BrasilFil: Fernandes Ferreira, Davis. Universidade Federal do Rio de Janeiro; Brasi