In silico investigation of potential inhibitors to main protease and spike protein of SARS-CoV-2 in propolis

Docking analysis of propolis's natural compound was successfully performed against SARS-CoV-2 main protease (Mpro) and spike protein subunit 2 (S2). Initially, the propolis's protein was screened using chromatography analysis and successfully identified 22 compounds in the propolis. Four compounds were further investigated, i.e., neoblavaisoflavone, methylophiopogonone A, 3′-Methoxydaidzin, and genistin. The binding affinity of 3′-Methoxydaidzin was ?7.7 kcal/mol, which is similar to nelfinavir (control), while the others were ?7.6 kcal/mol. However, we found the key residue of Glu A:166 in the methylophiopogonone A and genistin, even though the predicted binding energy slightly higher than nelfinavir. In contrast, the predicted binding affinity of neoblavaisoflavone, methylophiopogonone A, 3′-Methoxydaidzin, and genistin against S2 were ?8.1, ?8.2, ?8.3, and ?8.3 kcal/mol, respectively, which is far below of the control (pravastatin, ?7.3 kcal/mol). Instead of conventional hydrogen bonding, the π bonding influenced the binding affinity against S2. The results reveal that this is the first report about methylophiopogonone A, 3′-Methoxydaidzin, and genistin as candidates for anti-viral agents. Those compounds can then be further explored and used as a parent backbone molecule to develop a new supplementation for preventing SARS-CoV-2 infections during COVID-19 outbreaks.     

Evaluation of data integration strategies based on kernel method of clinical and microarray data

The cancer classification problem is one of the most challenging problems in bioinformatics. The data provided by Netherland Cancer Institute consists of 295 breast cancer patient; 101 patients are with distant metastases and 194 patients are without distant metastases. Combination of features sets based on kernel method to classify the patient who are with or without distant metastases will be investigated. The single data set will be compared with three data integration strategies and also weighted data integration strategies based on kernel method. Least Square Support Vector Machine (LS-SVM) is chosen as the classifier because it can handle very high dimensional features, for instance, microarray data. The experiment result shows that the performance of weighted late integration and the using of only microarray data are almost similar. The data integration strategy is not always better than using single data set in this case. The performance of classification absolutely depends on the features that are used to represent the object.     

An open label,randomized clinical trial to compare the tolerability and efficacy of ivermectin plus diethylcarbamazine and albendazole vs. diethylcarbamazine plus albendazole for treatment of brugian filariasis in Indonesia

Improved treatments for lymphatic filariasis (LF) could accelerate the global elimination program for this disease. A triple drug combination of the anti-filarial drugs ivermectin, diethylcarbamazine (DEC) and albendazole (IDA) has been shown to be safe and effective for achieving sustained clearance of microfilariae (Mf) of the filarial parasite Wuchereria bancrofti from human blood. However, the triple drug combination has not been previously been evaluated for treatment of brugian filariasis, which accounts for about 10% of the global LF burden. This hospital-based clinical trial compared the safety and efficacy of IDA with that of the standard treatment (DEC plus albendazole, DA) in persons with Brugia timori infections on Sumba island, Indonesia. Fifty-five asymptomatic persons with B. timori Mf were treated with either a single oral dose of IDA (28 subjects) or with DEC plus albendazole (DA, 27 subjects). Participants were actively monitored for adverse events (AE) for two days after treatment by nurses and physicians who were masked regarding treatment assignments. Passive monitoring was performed by clinical teams that visited participant’s home villages for an additional five days. Microfilaremia was assessed by membrane filtration of 1 ml night blood at baseline, at 24h and one year after treatment. IDA was more effective than DA for completely clearing Mf at 24 hours (25/28, 89% vs. 8/27, 30%, P < 0.001). By 12 months after treatment, only one of 27 IDA recipients had Mf in their blood (4%) vs. 10 of 25 (40%) in persons treated with DA (P = 0.002). Approximately 90% of participants had antibodies to recombinant filarial antigen BmR1 at baseline. Antibody prevalence decreased to approximately 30% in both treatment groups at 12 months. About 45% of persons in both treatment groups experienced AE such as fever, muscle aches, lower back, joint and abdominal pain. These were mostly mild and most common during the first two days after treatment. No participant experienced a severe or serious AE. This study showed that IDA was well-tolerated and significantly more effective for clearing B. timori Mf from the blood than DA. Larger studies should be performed to further assess the safety and efficacy of IDA as a mass drug administration regimen to eliminate brugian filariasis.Trial Registration: {"type":"clinical-trial","attrs":{"text":"NCT02899936","term_id":"NCT02899936"}}NCT02899936.