Navegando por Assunto "Modelagem molecular"

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Acesso aberto (Open Access)
Atividade antiplasmodial e modelagem molecular de novas chalconas e derivados
(Universidade Federal do Pará, 2008) PEREIRA, Glaécia Aparecida do Nascimento; RIBEIRO, Cláudio Tadeu Daniel; http://lattes.cnpq.br/0814854098256062; NASCIMENTO, José Luiz Martins do; http://lattes.cnpq.br/7216249286784978
Malaria is an infection caused by Plasmodium sp. and It can be serious, if not treated precociously. It affects significant fraction of humanity and has profound health impact worldwide. It is estimated that 3.3 billion people are exposed to the risk of transmission. One of the problems of the infection is the growing emergence of parasite resistance to antimalarial drugs. In this context, studies are needed to develop new alternative chemotherapy. Many substances, such as the chalcones, have had their antiplasmodial activity proven. However, the physicochemical properties of these molecules, which are important for biological actions, are not well established. In this work, molecular modeling was performed and the antiplasmodial activity was evaluated of two chalcones (HBR1, and LH2) and four derivatives of chalcones (GH3, IV4, LCH1, and LCH3). For that, we determined the drug concentration inhibitory of 50% of the growth of P. falciparum in vitro as well as the physicochemical properties of derivatives of chalcones as HOMO, LUMO, electrostatic potential, C log P, hydration energy, polarizability and molecular volume through virtual calculations. The results of the calculated values were correlated with the biological activity in order to identify chemical parameters that can influence the antiplasmodial action. The inhibitory concentrations in 50% of the growth of P. falciparum ranged from 0,2 to 1,7 M, and these values were smaller than described them in the literature. The study of the correlation between the biological activities and the physicochemical properties showed determinating parameters for the biological activity, as LUMO, electrostatic potential, C log P and hydration energy, which may help in the selection of molecules more active against P. falciparum. Thus, these molecular properties can be used in the rational planning of new chalcones and/or derivatives with antiplasmodial activity.
Acesso aberto (Open Access)
Estudo computacional de arilpiperidina e arilpiperazina como inibidores de tirosinase: aplicações cosméticas e terapêuticas
(Universidade Federal do Pará, 2025-04-08) BENTES, Beatriz Alves; SILVA, José Rogério de Araújo; SILVA, Jerônimo Lameira; http://lattes.cnpq.br/7711489635465954
Tyrosinases (TYR) catalyze the oxidation of phenols and catechols, playing a crucial role in melanogenesis, which regulates melanin production and provides protection against UV radiation. However, pigmentation-related disorders drive the search for effective TYR inhibitors. Compounds such as hydroquinone, arbutin, and kojic acid have limitations, highlighting the need for new inhibitors. In this study, arylpiperidine- and arylpiperazine-based compounds demonstrated potent inhibitory activity against TYR. Computational analysis included molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations using the Linear Interaction Energy (LIE) method, revealing a strong correlation with experimental affinity data. To enhance the understanding of structure-activity relationships (SAR), Free Energy Perturbation (FEP) transformations were performed for selected ligand pairs. Additionally, Density Functional Theory (DFT) calculations were applied to inhibitors L04 and L19, enabling the determination of electronic descriptors and frontier molecular orbitals. The inhibitors interact with TYR mainly through electrostatic interactions with the copper ion and van der Waals forces with critical residues such as Phe197, Pro201, Val218, Asn205, and Arg209. These findings are promising for both cosmetic and therapeutic applications, enabling the development of skin-lightening agents to treat melasma and sunspots, as well as potential treatments for hyperpigmentation-related diseases and melanomas. The development of more selective inhibitors with lower toxicity may expand the clinical and cosmetic use of these compounds, offering safer and more effective alternatives for melanin production modulation.
Acesso aberto (Open Access)
Estudo teórico do complexo cefoxitina-proteína 5 de ligação à penicilina da Escherichia Coli por dinâmica molecular com método híbrido de mecânica quântica/ mecânica molecular
(Universidade Federal do Pará, 2014-12-12) SILVA, Thaís Boulhosa Barros da; BARROS, Carlos Augusto Lima; http://lattes.cnpq.br/8902921733540173; MONTEIRO, Marta Chagas; http://lattes.cnpq.br/6710783324317390
The Penicillin Binding Proteins (PBPs) are important for the development of new drugs against bacterial infections biological targets. This study was aimed to understand the interaction between the protein and cefoxitin 5 Penicillin-Binding (PBP5) of Escherichia coli (deposited in the PDB under the code 3MZE) through simulation Molecular Dynamics (MD), using the approach hybrid quantum molecular mechanics (QM/MM) and mechanical. As well as develop a prototype to evaluate, through computer simulation, the susceptibility of Gram negative bacteria against antibiotics. The analysis of antimicrobial susceptibility to antibiotics tested has shown that this strain of E. coli ATCC 8739 was sensitive to 5 antimicrobials study. The strain of E. coli derived from the clinical isolate was resistant to ciprofloxacin 5 μg and gentamicin 10 μg, intermediate sensitivity to cefepime 30 μg and ceftazidime 30 μg, and sensitivity to cefoxitina 30 μg. The difference in susceptibility of E. coli strain ATCC 8739 and strain of E. coli isolated from a clinical can show a molecular immunological memory of the bacteria. We observed no production of β-lactamases by the strain of E. coli derived from clinical isolate, suggested because no observed difference in antimicrobial susceptibility with respect to the presence or absence of EDTA on the disks containing the antibiotics. The analysis has revealed that protonation of the deprotonated His146, His151, His216 and His320 residues. The stabilization of the complex was studied after 0,6 ns of MD simulation. Moreover, a decomposition analysis in terms of energy was performed to determine the contributions of individual amino acid residues for protein-ligand interactions. The results revealed that cefoxitin has a strong interaction with Lis44, Lis210, Ser41, Gli212, His213, Glu246 residue, apart from water, which are important for stabilizing cefoxitin-PBP5 complex. The electrostatic potential map Molecular cefoxitin revealed a highly electrophilic center corresponding to the β-lactam ring, which promotes hydroxyl attack nuceofílico the serine residue of the E. coli PBP5 active site region. These results can give support the planning of new more selective and effective drugs to control bacterial infections. The experimental results were statistically consistent with the theoretical results thus this work can be used as a prototype for computing theoretical evaluate the antimicrobial susceptibility to Gram negative bacteria. This study may find applications in future planning and development of new and potent compounds with antimicrobial activity. Mainly in attempts to modify an inhibitor, particularly of the cephalosporin class in order to improve its selectivity and its activity.
Acesso aberto (Open Access)
Investigação computacional de bromo-ariloxi-2-acetamida etil-benzimidazólicos como inibidores não-peptídicos da proteinase cruzaína de trypanosoma cruzi
(Universidade Federal do Pará, 2017-11-17) FERREIRA, Fábio Jorge de Nazaré; ALENCAR, Nelson Alberto Nascimento de; http://lattes.cnpq.br/3035968396241810; https://orcid.org/ 0000-0002-5763-7024; CARNEIRO, Agnaldo da Silva; http://lattes.cnpq.br/8915348778787525
Chagas’ disease is an infection caused by the Trypanosoma Cruzi flagellated protozoan transmitted by insects (gnat) known in Brazil as “barbeiro” (barber). In the Amazon region, studies have shown that oral contamination has been frequent. The only available drugs for the treatment of Chagas’ disease - Benzonidazole (Rochagan R , Roche) and Nifurtimox (Lampit R , Bayer) - have shown limited efficiency and severe side effects. Cruzain is an enzyme present at all stages of the life cycle of T. cruzi and is the most abundant of the family of papain cysteine proteases found in the parasite, being a promising enzymatic target for the design and development of inhibitors against the disease. Non-peptidic non covalently bound to the enzyme were synthesized and evaluated biologically in vitro and in vivo by Ferreira et al. (2014) analogs of the 8D (or B95) leader compound (crystallographic), yielding a series of active compounds, of which the most powerful are: 8K, 8L and 8R. This work investigated the potential interactions and energies of the cruzain (PDB code: 3KKU) complexed with these four ligands by means of computational tools in order to help elucidate their potential inhibition activity in this enzyme. The computational protocol (parameters, topologies, coordinates, minimizations, thermalizations and productions) was the same for each system. In the final stage of molecular dynamics (MD) production, each system was simulated for a period of 100 ns, to which the mean square deviation (RMSD) stability values of the enzyme and the marked change in 8L ligand conformation were analyzed. The quality of the simulation was also evaluated through potential, kinetic and total energy, volume and temperature graphs. Interactions of hydrogen bonds of the ligands with some amino acid residues belonging to the catalytic site were analyzed. The interaction between the ASP161 and the 8R ligand is emphasized, being ratified by the energy decomposition by residue showing that ASP161 has the best contribution. In terms of binding free energy, the ∆Gtotal follows the experimental trend, pointing the 8R ligand as the most favorable to the reaction having a theoretical value of -30.04kcal.mol−1. This spontaneity is ratified by means of the values obtained with the SIE method, whose theoretical value was -7.54 kcal.mol−1. The results of this work should favor the optimization of compound 8R or development of a series of analogs of this molecule in order to be used as a possible drug for the treatment of Chagas’ disease.
Acesso aberto (Open Access)
Modelagem molecular de inibidores da enzima tirosinase
(Universidade Federal do Pará, 2018-12-21) MARTINS, Lucas de Sousa; SILVA, José Rogério de Araújo; http://lattes.cnpq.br/0925631339396542; https://orcid.org/0000-0003-2310-5107
The enzyme Tyrosinase (TYR), responsible for the catalysis of the early stages of melanogenesis in various organisms, is described in some groups. Among those that stand out: hyperpigmentation, melasma and skin cancer, in not melanoma forms and malignant melanoma. In general, dysfunctions are treated with depigmenting agents, TYR enzyme alerts. However, among them is the kojic acid (KA), marked side effects. Such phenomena make a TYR a model of biological development of drug prototypes. In the meantime, I investigated some TYR enzyme inhibitory genes, in particular AK and analogous plants, as well as a Tropolone and some benzaldehyde derivatives, structurally related to the natural substrates of TYR (L-Tyrosine and L-Dopa), as the Molecular Docking, Molecular Dynamics (MD), and the Linear Interaction Energy (LIE) method, used to calculate the free binding energy of the systems. Specifically application of Molecular Docking defined the mode of binding of the inhibitors in the TYR site, being possible to quantify how interactions occur in the systems. As the MD simulations, they exhibited the effect of the enzyme with different inhibitors and how they act when complexed with a TYR enzyme, using a copper dummy atom model. Thus, the results obtained by LIE were concordant with the experimental results, obtaining an R2 of 0.91 in a linear regression of LIE vs Experimental, and this allowed to analyze how Tropolona, KA, MOL2 and MOL3 interactions with the important to the active site of TYR. Thus, the results achieved at work contributed significantly to the achievement of inhibition of the TYR enzyme, helping to combat the evils caused by a cycle of melanin production in organisms.
Acesso aberto (Open Access)
Planejamento e síntese de novos derivados da associação molecular benzonidazol e metronidazol
(Universidade Federal do Pará, 2018-09-25) COSTA, Fernanda Menezes; BORGES, Rosivaldo dos Santos; http://lattes.cnpq.br/4783661132100859; https://orcid.org/0000-0003-4072-7573
Chagas disease is caused by protozoan Trypanosoma cruzi, still has high contagion rates in present days, especially in the Amazon region. After contamination, the infective cycle of Chagas disease has two phases: acute and chronic. The acute phase is, in majority of cases, asymptomatic and efficiently treated, however the chronic phase is symptomatic and has proved not efficient treatment. There is only one available medicine, the generic benznidazole or Rochagan®, distributed free of charge, and it must be administered for 60 days, approximately. However, benznidazole has low efficiency, being effective only on acute phase (asymptomatic). Besides that, the medicine use to cause severe side effects in clinical patients, producing in many times the treatment rejection. The molecular modeling has become an important tool on new drugs design, using the DFT method to evaluate of the new potent molecules. Thereby, the main goal of this work was to design new derivatives by using molecular modifications of benznidazole and metronidazole aiming to reduce their redox capacity. With this purpose, a theoretical study was performed of two benznidazole derivatives through molecular association and chain increase. From the theoretical study, this molecular association between benznidazole and metronidazole molecules can develop a less toxic new derivative of than benznidazole. Both designed derivatives were synthesized on laboratory using the classics methodologies of electrophilic and nucleophilic substitution, esterification, alkylation and nitration. According to their HOMO, LUMO, ionization potential, and electron affinity values, it was possible observe that the nibendazole 1 and nibendazole 2 compounds have a lower redox capacity when compared to benznidazole. The GAP values showed that the derivatives are less reactive than benznidazole. The HOMO and LUMO graphics, showed that the nitroimidazoles rings have high electron-withdrawing capacity as well as benzyl group has high electron-donating capacity. These properties change in accordance to methyl moiety or nitrogen positions on azolic ring of derivatives compounds.
Acesso aberto (Open Access)
Planejamento e síntese de novos derivados relacionados ao piroxicam
(Universidade Federal do Pará, 2019-12-09) OTA, Sirlene Sayuri Barros; BORGES, Rosivaldo dos Santos; http://lattes.cnpq.br/4783661132100859; https://orcid.org/0000-0003-4072-7573
Piroxicam is a drug belonging to the group of oxicams, derived from phenolic acids, in the class of NSAIDs. Although not the drug of choice in some treatments, the drug is indicated for the treatment of acute musculoskeletal disorders, post-traumatic and postoperative pain, rheumatoid arthritis and osteoarthritis, primary dysmenorrhea, endometriosis and hemorrhagic cyst. Like non-steroidal anti-inflammatory drugs, piroxicam is able to inhibit prostaglandin synthesis from arachidonic acid by competitively reversible inhibition of COX activity, with some predominance to inhibit COX-2 activity. Photosensitivity is one of the adverse effects caused by the drug, being observed in about 1% of patients. In addition, various techniques have been used to improve the stability of piroxicam without diminishing its potential. Thus, the objective of this paper is to plan, synthesize and evaluate more stable derivatives related to the phototoxicity of the study drug. Calculations of electronic properties such as high energy occupied molecular orbital (HOMO), low energy occupied molecular orbital (LUMO) and ionization potential (IP), as well as reactivity index calculations (Mulliken, CHELPG and Fukui) were calculated. performed using the Gaussview and Gaussian 2009 packages. The proposed derivatives have been synthesized through classical reactions such as esterification and nucleophilic substitution and are in the process of purification. The results of the HOMO and LUMO values showed that the D4 molecule has a better electronic distribution, with the second lowest HOMO value and the highest LUMO value, and can be considered the most stable. The D6 molecule proved to be the most reactive derivative and this can be explained by the presence of two hydroxyls in the naphthalene ring of the derivative, influencing the reactivity of the molecule. Based on the GAP values, the nitrated derivative (D2) presented lower value (3.36 eV), indicating high reactivity. The D4 molecule presented the highest GAP value, confirming its stability. In the analysis of Mulliken, CHELPG and Fukui loads of piroxicam, differences in substitution orientation were observed, probably due to the difference in calculations performed for each index. In the theoretical results of the chemical reactivity study using UV-Vis, piroxicam and its naphthalenic derivative showed completely different profiles, referring to its three main peaks, being the most expressive in the C = C system, indicating that in the benzothiazine system it functions as a reactive alkene after energy absorption.Thus, the molecular modification by the naphthalene system presented a compound with higher chemical stability and lower reactivity.
Acesso aberto (Open Access)
Planejamento, Síntese, Avaliação das Propriedades Teóricas de orto-Regioisômeros Substituídos do Paracetamol
(Universidade Federal do Pará, 2018-12-28) MORAIS, Roberto Barbosa de; BORGES, Rosivaldo dos Santos; http://lattes.cnpq.br/4783661132100859; https://orcid.org/0000-0003-4072-7573
Paracetamol is a clinically proven analgesic and antipyretic, which promotes analgesia by elevating the pain threshold and antipyretic through action in the hypothalamic center that regulates the temperature. Currently paracetamol is one of the medicines that is available in all the countries of the world in places related to health and can be acquired without prescription. Considered one of the most widely used drugs in the world as it is cheap and easy to access, it can also be used from birth to the elderly. Like non-steroidal anti-inflammatory drugs (NSAIDs) paracetamol is able to inhibit the synthesis of prostaglandins from arachidonic acid under specific conditions by inhibiting cyclooxygenase (COX). Although it is considered safe at therapeutic doses, Paracetamol has a toxicity attributed to one of its metabolic intermediates called N-acetyl-p-imine-benzoquinone (NAPQI), produced through enzymes present in cytochrome P450 (CYPE21). Thus, the objective of this present work is to plan, synthesize and evaluate possible antinociceptive and antipyretic activities of paracetamol analogues, ortacetamol and its derivatives in order to obtain a less toxic derivative. The calculations of electronic properties such as higher energy occupied molecular orbital (HOMO), lower energy unoccupied molecular orbital (LUMO), ionization potential (PI), phenolic bond dissociation energy (BDEOH) and spin densities were performed using the Gaussview and Gaussian 2009 packages. The values of the average values of BDENH, among others, are those that are observed with the quality of a heating cycle for the high speed with the possibility of a chelation defined by a hydrogen bond of the amide with the phenoxyl radical. Given the results it is possible that BDENH energy compounds may be less potent than hindering the action of CYP on oxidation to form toxic intermediates. A proposed chlorinated derivative was proposed and synthesized. It is in biological evaluation phase. Orthacetamol was more potent antioxidant than paracetamol. Experimental results are in aggrement with theoretical values. We conclude that ortcetamol may be a potentially safer bioactive candidate than paracetamol.
Acesso aberto (Open Access)
Usando a dinâmica molecular para avaliar o impacto que as mutações na protease do HIV-1 produzem na interação da proteína com o antirretroviral darunavir
(Universidade Federal do Pará, 2019-03-29) CUNHA, Karoline Leite; BARROS, Carlos Augusto Lima; http://lattes.cnpq.br/8902921733540173
The emergence of drug-resistant strains used in antiretroviral therapy grows alarmingly on a global scale. Antiretrovirals used in the treatment of first and second line HIV are the ones that most have case reports of resistant strains. Protease inhibitors are a class of antiretroviral drugs that play a key role in AIDS treatment regimens. In addition to the emergence of resistance to IPs used in the usual treatment regimens, Darunavir, a protease inhibitor used in therapeutic rescue treatment, is already reported in patients who already have failed initial treatment and proven resistance. The aim of this work is to evaluate, identify and quantify HIV-1 3UCB protease mutations, as well as to evaluate, through molecular dynamics simulations, the impact that mutations produce on the interaction of 3UCB and its darunavir ligand when compared to the native HIV-1 protease 4LL3 complexed to the same linker.The results obtained in this study showed that the 3UCB multi-resistant HIV-1 protease had a slightly more stable binding profile than the native HIV-1 protease complex 4LL3, with binding free energy results -68.77 and -64.62 kcal / mol, respectively.