Quantum biochemical analysis of the TtgR regulator and effectors.

The recent expansion of multidrug-resistant (MDR) pathogens poses significant challenges in treating healthcare-associated infections. Although antibacterial resistance occurs by numerous mechanisms, active efflux of the drugs is a critical concern. A single species of efflux pump can produce a simultaneous resistance to several drugs. One of the best-studied efflux pumps is the TtgABC: a tripartite resistance-nodulation-division (RND) efflux pump implicated in the intrinsic antibiotic resistance in Pseudomonas putida DOT-T1E. The expression of the TtgABC gene is down-regulated by the HTH-type transcriptional repressor TtgR. In this context, by employing quantum chemistry methods based on the Density Functional Theory (DFT) within the Molecular Fragmentation with Conjugate Caps (MFCC) approach, we investigate the coupling profiles of the transcriptional regulator TtgR in complex with quercetin (QUE), a natural polyphenolic flavonoid, tetracycline (TAC), and chloramphenicol (CLM), two broad-spectrum antimicrobial agents. Our quantum biochemical computational results show the: [i] convergence radius, [ii] total binding energy, [iii] relevance (energetically) of the ligands regions, and [iv] most relevant amino acids residues of the TtgR-QUE/TAC/CLM complexes, pointing out distinctions and similarities among them. These findings improve the understanding of the binding mechanism of effectors and facilitate the development of new chemicals targeting TtgR, helping in the battle against the rise of resistance to antimicrobial drugs. These advances are crucial in the ongoing fight against rising antimicrobial drug resistance, providing hope for a future where healthcare-associated infections can be more beneficially treated.

Quantum Biochemical Investigation of Lys49-PLA2 from Bothrops moojeni.

Envenomation via snakebites occurs largely in areas where it is harder to access the hospital. Its mortality rate and sequelae acquired by the survivors symbolize a big challenge for antivenom therapy. In particular, the homologous phospholipase A2 (Lys49-PLA2) proteins can induce myonecrosis and are not effectively neutralized by current treatments. Thus, by taking advantage of crystallographic structures of Bothrops moojeni Lys49-PLA2 complexed with VRD (varespladib) and AIN (aspirin), a quantum biochemistry study based on the molecular fractionation with conjugate cap scheme within the density functional theory formalism is performed to unveil these complexes' detailed interaction energies. The calculations revealed that important interactions between ligands and the Lys49-PLA2 pocket could occur up to a pocket radius of r = 6.5 (5.0 Å) for VRD (AIN), with the total interaction energy of the VRD ligand being higher than that of the AIN ligand, which is well-correlated with the experimental binding affinity. Furthermore, we have identified the role played by the amino acids LYS0069, LYS0049, LEU0005, ILE0009, CYS0029, GLY0030, HIS0048, PRO0018, ALA0019, CYS0045, TYR0052, TYR0022, PRO0125*, and PHE0126* (LYS0069, LYS0049, GLY0032, LEU0002, and LEU0005) in the VRD↔Lys49-PLA2 (AIN↔Lys49-PLA2) complex. Our simulations are a valuable tool to support the big challenge for neutralizing the damages in victims of snakebites.

New ethionamide boosters and EthR2: structural and energetic analysis.

Ethionamide (ETH) is a high-profile drug for the treatment of patients with multidrug-resistant Mycobacterium tuberculosis and, in order to produce its inhibitory effects, it needs to be bioactivated by monooxygenase EthA. This process is under the control of the transcriptional repressors EthR and EthR2, so that their inhibition results in the boosting of ethionamide activation. Herein, through crystallographic data and computer simulations, we calculated the interaction binding energies of four inhibitors with improved in vitro potency, namely BDM76060 (PDB ID: 6HS1), BDM72201 (PDB ID: 6HRX), BDM76150 (PDB ID: 6HS2) and BDM72719 (PDB ID: 6HRY), in complexes with the transcriptional repressor EthR2, using density functional theory (DFT) within the molecular fractionation with conjugated caps (MFCC) approach. It was observed that these ligands share the same binding site within a 10.0 Å radius of the EthR2 protein; however, their structural particularities have a significant impact on the global energies of systems. The BDM72201 and BDM72719 components are weakly attached to the binding site, while BDM76060 and BDM76150 components produce stronger bonds, corroborating with experimental studies demonstrating that BDM76060 and BDM76150 are more successful in producing inhibitory effects. BDM76060 and BDM76150 have many functional groups that increase the contact surface with the protein and attract a more significant number of amino acid residues, being able to produce polarities that generate stronger interactions. In the current scenario of a growing number of cases of bacterial resistance, the obtained data can be used to guide clinical trials of these inhibitors and other inhibitors that act on the alternative EthR2 pathway, focusing on improving the activity of ethionamide, its effectiveness, a reduction in the treatment time and exposure to cytotoxic effects.

Exploring human porphobilinogen synthase metalloprotein by quantum biochemistry and evolutionary methods.

Previous studies have shown the porphobilinogen synthase (PBGS) zinc-binding mechanism and its conservation among the living cells. However, the precise molecular interaction of zinc with the active center of the enzyme is unknown. In particular, quantum chemistry techniques within the density functional theory (DFT) framework have been the key methodology to describe metalloproteins, when one is looking for a compromise between accuracy and computational feasibility. Considering this, we used DFT-based models within the molecular fractionation with conjugate caps scheme to evaluate the binding energy features of zinc interacting with the human PBGS. Besides, phylogenetic and clustering analyses were successfully employed in extracting useful information from protein sequences to identify groups of conserved residues that build the ions-binding site. Our results also report a conservative assessment of the relevant amino acids, as well as the benchmark analysis of the calculation models used. The most relevant intermolecular interactions in Zn2+-PBGS are due to the amino acids CYS0122, CYS0124, CYS0132, ASP0169, SER0168, ARG0221, HIS0131, ASP0120, GLY0133, VAL0121, ARG0209, and ARG0174. Among these residues, we highlighted ASP0120, GLY0133, HIS0131, SER0168, and ARG0209 by co-occurring in all clusters generated by unsupervised clustering analysis. On the other hand, the triple cysteines at 2.5 Å from zinc (CYS0122, CYS0124, and CYS0132) have the highest energy attraction and are absent in the taxa Viridiplantae, Sar, Rhodophyta, and some Bacteria. Additionally, the performance of the DFT-based models shows that the processing time-dependence is more associated with the choice of the basis set than the exchange-correlation functional.

In silico approach of modified melanoma peptides and their immunotherapeutic potential.

Melanoma is a type of skin cancer with increasing incidence worldwide and high lethality. Conventional forms of treatment are not effective in advanced cancer stages. Hence, immunotherapeutic approaches have been tested to modulate immune response against tumor cells. Some vaccine models using tumor-associated antigens (TAAs) such as glycoprotein 100 (gp100) have been studied, but their expected effectiveness has not been shown until now. Antigen immunogenicity is a crucial point to improve the immune response, and therefore mutations are inserted in peptide sequences. It is possible to understand the interactions which occur between peptides and immune system molecules through computer simulation, and this is essential in order to guide efficient vaccine models. In this work, we have calculated the interaction binding energies of crystallographic data based on modified gp100 peptides and HLA-A*0201 using density functional theory (DFT) and the molecular fractionation with conjugated caps (MFCC) approach. Our results show the most relevant residue-residue interactions, the impact of three mutations in their binding sites, and the main HLA-A*0201 amino acids for peptide-HLA binding.

Leiomioma vulvar em lobo-guará (Chrysocyon brachyurus) - relato de caso / Leiomyoma vulvar in maned wolf (Chrysocyon brachyurus) - case report

Descrição de leiomioma vulvar em lobo-guará (Chrysocyon brachyurus), fêmea, castrada, apresentando 10 anos de idade e mantida em cativeiro. Com base na avaliação clínica, no monitoramento de formação nodular de crescimento lento e progressivo e no diagnóstico preliminar sugestivo de neoplasia, procedeu-se à exérese da massa tumoral e à identificação anatomopatológica do leiomioma. Exames complementares radiográficos e ultrassonográficos não apontaram presença de metástases. A ressecção cirúrgica se mostrou satisfatória como conduta clínica, não havendo recidiva.(AU)

Description of leiomyoma vulvar in a female castrated Chrysocyon brachyurus, , ten years of age, and maintained in captivity. Based on the clinical evaluation, monitoring of nodular formation of slow and progressive growth, and preliminary diagnosis suggestive of neoplasia, the tumor mass was excised and anatomopathological identification of the leiomyoma was done. Complementary radiographic and ultrasound examinations did not indicate the presence of metastases. Surgical resection proved to be satisfactory as a clinical practice, and there was no relapse.(AU)

Aspectos clínicos, cirúrgicos, histológicos e pós-operatórios de oito cadelas com leiomioma vaginal / Clinical, surgical, histological and postoperative aspects in the case of eight bitches with vaginal leiomyoma

O presente trabalho reporta as características clínicas e cirúrgicas de oito casos de cadelas portadoras de leiomioma vaginal, com histórico de aumento de volume na região perineal, aparecimento de massa pela vulva, disquezia, tenesmo e disúria. As pacientes foram submetidas à cirurgia de episiotomia para ressecção da massa neoplásica, e em quatro casos foi necessária a ovariossalpingo-histerectomia. Porém, uma delas apresentou recidiva, e, no segundo procedimento cirúrgico de exérese de neoformação, o histopatológico diagnosticou leiomiossarcoma. A paciente ainda apresentou mais duas recidivas, até o proprietário optar pela eutanásia. Decorridos quatro meses, as sete cadelas diagnosticadas com leiomioma não apresentaram recidiva, e os proprietários relataram ausência de sinais relacionados com a doença descrita. Conclui-se que a episiotomia para ressecção da massa vaginal e a ovariossalpingo-histerectomia nas cadelas inteiras nos casos de tumores vaginais benignos são tratamentos satisfatórios, com bom prognóstico, ao contrário do leiomiossarcoma.

This study reports the clinical and surgical procedures of eight cases of bitches with vaginal leiomyoma. All animals presented increased volume in the perineal region, and exteriorization of the vulva, dyschezia, tenesmus and dysuria. The patients underwent episiotomy surgery for resection of the neoplastic mass, and ovariosalpingohisterectomy in four cases. However, one had recurrence on the second surgical procedure for removal of neoformation, histopathological diagnosed leiomyosarcoma, the patient also had two more relapses, until the owner chose euthanasia. After four months, the seven dogs diagnosed with leiomyoma showed no recurrence and the owners reported no signs of the disease described. We concluded that episiotomy for vaginal mass resection combined with ovariohysterectomy in cases of benign vaginal tumors have shown satisfactory treatment with good prognostic.

Desempenho de alevinos de tilápia do nilo alimentados com folha de mandioca desidratada na dieta / Performance of nile tilapia fingerlings fed dehydrated cassava leaf in the diet

O objetivo foi avaliar o crescimento e a viabilidade econômica de alevinos de tilápia do Nilo (Oreochromis niloticus), alimentados com diferentes níveis de farinha da folha de mandioca desidratada na ração (FFMD). Foram utilizados 80 alevinos distribuídos em 20 recipientes de 18L, constando de sistema de recirculação de água, durante um período de 51 dias. Cem exemplares, alimentados três vezes ao dia até a saciedade, foram distribuídos aleatoriamente em um delineamento experimental inteiramente casualizado, constituindo-se de 4 tratamentos (0, 5, 10 e 15% de adição da FFMD na ração) e 5 repetições cada. Os peixes alimentados com 10% de FFMD apresentaram melhor homogeneidade no crescimento. Entretanto, os indivíduos alimentados com inclusão de 5% de FFMD apresentaram homogeneidade de crescimento similar aos alimentados com 10%. Além disso, os peixes alimentados com 5% de FFMD obtiveram melhor desempenho zootécnico e viabilidade econômica da ração. Dessa maneira, recomenda-se a utilização de 5% da farinha de folha de mandioca desidratada em rações para tilápia do Nilo.

The aim was to evaluate the growth and the economic viability of the Nile tilapia (Oreochromis niloticus) fed with different levels of dehydrated cassava leaf flour in the diet (FFMD). 80 fingerlings were distributed into 20 18L containers, consisting of a water recirculation system over a period of 51 days. 100 copies fed three times a day to satiation were randomly assigned in a completely randomized design, constituting 4 treatments (0%, 5%, 10% and 15% addition of FFMD in diet) with 5 repetitions each. The fishes fed with 10% FFMD had better homogeneity in growth. However, individuals fed with inclusion of 5% FFMD homogeneity grew similarly to those fed with 10% FFMD. In addition, the fish from the 5% had better growth performance and economic viability of the feed. Thus, it is recommended to use 5% of dehydrated cassava leaf meal in diets for Nile tilapia.

Relação proteína: carboidrato no desempenho e metabolismo de juvenis de pacamã (Lophiosilurus alexandri) / Ratio protein: carbohydrate on performance and metabolism of Juvenile (Lophiosilurus alexandri)

Objetivou-se neste estudo verificar o melhor nível de inclusão entre proteína e carboidrato no desempenho e algumas respostas metabólicas em juvenis de pacamã (Lophiosilurus alexandri). Testaram-se quatro dietas com as relações proteína/carboidrato (PB:CHO) 1,24; 0,84; 0,51 e 0,33 durante 60 dias. Foram utilizados 240 juvenis de pacamã pesando inicialmente 1,90g, alimentados duas vezes ao dia (8% da biomassa). Avaliou-se o ganho de peso total, taxa de crescimento específico, consumo de ração aparente, conversão alimentar aparente, rendimento de carcaça e gordura visceral. Glicemia, aminoácidos totais livres no plasma e glicogênio hepático também foram avaliados. A relação PB:CHO influenciou (P<0,05) os parâmetros de desempenho e metabolismo, exceto o glicogênio hepático. Maiores concentrações de glicose e aminoácidos totais livres no plasma foram observadas nos peixes que se alimentaram com a dieta contendo a maior relação PB:CHO (1,24). Além disso, observaram-se melhores médias de ganho de peso, taxa de crescimento específico e conversão alimentar aparente. Maiores percentuais de gordura visceral e menor rendimento de carcaça foram observados nos animais submetidos à dieta composta pela menor relação PB:CHO (0,33). Pode-se concluir que a dieta com a relação PB:CHO de 1,24 promoveu melhor desempenho e respostas metabólicas em juvenis de pacamã...

The aim of this study was to determine the best level of inclusion between protein and carbohydrate on performance and some metabolic responses in juvenile pacamã (Lophiosilurus alexandri). We tested four diets regarding protein/carbohydrate (PB: CHO) 1.24, 0.84, 0.51 and 0.33 for 60 days. The experiment was conducted with 240 juvenile pacamã initially weighing 1.90g, fed twice daily (8% of the biomass). We evaluated the total weight gain, specific growth rate, feed intake, feed conversion, carcass yield and visceral fat. Glucose, total plasma free amino acids and liver glycogen were also evaluated. The relationship PB: CHO influenced (P <0.05) the performance and metabolism parameters except the liver glycogen. Higher concentrations of glucose and total plasma free amino acids were observed in fish that were fed the diet containing the highest ratio PB: CHO (1.24); and we also observed better mean weight gain, specific growth rate and feed conversion. A higher percentage of visceral fat and lower carcass yield were observed in animals treated with diet composed by the lower ratio PB: CHO (0.33). We can conclude that a diet with a ratio PB: CHO of 1.24, promotes better performance and metabolic responses in juvenile pacamã...