Structure-based drug design of novel peptidomimetic cellulose derivatives as HCV-NS3 protease inhibitors

Correlation intensity index-index of ideality of correlation: A hyphenated target function for furtherance of MAO-B inhibitory activity assessment

Monoamine oxidases are the enzymes involved in the management of brain homeostasis through oxidative deamination of monoamines such as neurotransmitters, tyramine etc. The excessive production of monoamine oxidase-B specifically results in numerous neurodegenerative disorders like Alzheimer's and Parkinson's diseases. Inhibitors of monoamine oxidase-B are applied in the management of these disorders. Here in this article we have developed robust hybrid descriptor based QSAR models related to 123 monoamine oxidase-B inhibitors through CORAL software by means of Monte Carlo optimization method. Three target functions were applied to prepare QSAR models and three splits were made for each target function. The most reliable, robust and better predictive QSAR models were developed with TF3 (correlation intensity index -index of ideality of correlation). Correlation intensity index showed positive effect on QSAR models. The structural features obtained from the QSAR modeling were incorporated in newly designed molecules and exhibited positive effect on their endpoint. Significant binding interactions were represented by these molecules in docking studies. Molecule B5 displayed prominent pIC50 (8.3) and binding affinity (-11.5 kcal mol-1) towards monoamine oxidase-B.

In-silico study: docking simulation and molecular dynamics of peptidomimetic fullerene-based derivatives against SARS-CoV-2 Mpro

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, has become a global pandemic resulting in significant morbidity and mortality. This study presents 12 new peptidomimetic fullerene-based derivatives in three groups that are investigated theoretically as SARS-CoV-2 Mpro inhibitors to increase the chance of treating COVID-19. Studied compounds are designed and optimized at B88-LYP/DZVP method. Molecular descriptors results show the stability and reactivity of the compounds with Mpro, especially in the 3rd group (Ser compounds). However, Lipinski's Rule of Five values indicates that the compounds are not suitable as oral drugs. Furthermore, molecular docking simulations are carried out to investigate the binding affinity and interaction modes of the top five compounds (compounds 1, 9, 11, 2, and 10) with the Mpro protein, which have the lowest binding energy. Molecular dynamics simulations are also performed to evaluate the stability of the protein-ligand complexes with compounds 1 and 9 and compare them with natural substrate interaction. The analysis of RMSD, H-bonds, Rg, and SASA indicates that both compounds 1 (Gly-α acid) and 9 (Ser-α acid) have good stability and strong binding affinity with the Mpro protein. However, compound 9 shows slightly better stability and binding affinity compared to compound 1.

Molecular dynamics simulation of docking structures of SARS-CoV-2 main protease and HIV protease inhibitors

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We consider possible repurposed-drugs candidates against SARS-CoV-2.

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10 different HIV protease inhibitors were investigated.

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In silico simulations were used to study protease inhibitors for SARS-CoV-2.

In this paper we investigate 10 different HIV protease inhibitors (HPIs) as possible repurposed-drugs candidates against SARS-CoV-2. To this end, we execute molecular docking and molecular dynamics simulations. The in silico data demonstrated that, despite their molecular differences, all HPIs presented a similar behavior for the parameters analyzed, with the exception of Nelfinavir that showed better results for most of the molecular dynamics parameters in comparison with the N3 inhibitor.

Computational Drug Design against Ebola Virus Targeting Viral Matrix Protein VP30

Ebola viral disease (EVD) is a deadly infectious hemorrhagic viral fever caused by the Ebola virus with a high mortality rate. Until date, there is no effective drug or vaccination available to combat this condition. This study focuses on designing an effective antiviral drug for Ebola viral disease targeting viral protein 30 (VP30) of Ebola virus, highly required for transcription initiation. The lead molecules were screened for Lipinski rule of five, ADMET study following which molecular docking and bioactivity prediction was carried out. The compounds with the least binding energy were analyzed using interaction software. The results revealed that 6-Hydroxyluteolin and (-)-Arctigenin represent active lead compounds that inhibit the activity of VP30 protein and exhibits efficient pharmacokinetics. Both these compounds are plant-derived flavonoids and possess no known adverse effects on human health. In addition, they bind strongly to the predicted binding site centered on Lys180, suggesting that these two lead molecules can be imperative in designing a potential drug for EVD.

Novel inhibitors against wild-type and mutated HCV NS3 serine protease: an in silico study

In 2011, the FDA approved boceprevir as a hepatitis C virus (HCV) NS3 serine protease inhibitor. The sustained virological response rate for treatment with this approved compound is considerably low. Patients have not responded as much as expected to boceprevir therapy. In this in silico study, modified boceprevir compounds are suggested and tested on wild-type HCV NS3 protease and 19 mutated HCV NS3 proteases using molecular docking. Results reveal the superiority of two of the proposed modified compounds to boceprevir. One of which appears to be more potent than boceprevir itself concerning activity against wild-type NS3 and most of the examined mutated NS3 proteases.

Review on chemogenomic approaches towards hepatitis C viral targets

Hepatitis C virus (HCV) is the most prevalent viral pathogen that infects more than 185 million people worldwide. HCV infection leads to chronic liver diseases such as liver cirrhosis and hepatocellular carcinoma. Direct-acting antivirals (DAAs) are the recent combination therapy for HCV infection with reduced side effects than prior therapies. Sustained virological response (SVR) acts as a gold standard marker to monitor the success of antiviral treatment. Older treatment therapies attain 50-55% of SVR compared with DAAs which attain around 90-95%. The current review emphasizes the recent chemogenomic updates that have been unfolded through structure-based drug design of HCV drug target proteins (NS3/4A, NS5A, and NS5B) and ligand-based drug design of DAAs in achieving a stable HCV viral treatment strategies.