Molecular docking and ADME properties of bioactive molecules against human acid-beta-glucosidase enzyme, cause of Gaucher's disease

(R)-(+)-Rosmarinic Acid as an Inhibitor of Herpes and Dengue Virus Replication: an In Silico Assessment

Since ancient times, viruses such as dengue, herpes, Ebola, AIDS, influenza, chicken meat, and SARS have been roaming around causing great health burdens. Currently, the prescribed antiviral drugs have not cured the complications caused by viruses, whereas viral replication was not controlled by them. The treatments suggested are not only ineffectual, but also sometimes inefficient against viruses at all stages of the viral cycle as well. To fight against these contagious viruses, people rely heavily on medicinal plants to enhance their innate and adaptive immune systems. In this research, the preparation of ligands and proteins was performed using the Maestro V.13.2 module tool. This software, consisting of LigPrep, Grid Generation, SiteMap, and Glide XP, has each contributed significantly to the preparation of ligands and proteins. Ultimately, the research found that (R)-(+)-rosmarinic acid was found to have significant docking scores of - 10.847 for herpes virus, of - 10.033 for NS5, and - 7.259 for NS1. In addition, the Prediction of Activity Spectra for Substances (PASS) server indicates that rosmarinic acid possesses a diverse spectrum of enzymatic activities, as probability active (Pa) values start at > 0.751, whereas it has fewer adverse effects than the drugs prescribed for viruses. Accordingly, it was found the rate of acute toxicity values of (R)-(+)-rosmarinic acid at doses LD50 log10 (mmol/g) and LD50 (mg/g) in different routes of administration, such as intraperitoneal, intravenous, oral, and subcutaneous. Ultimately, the present study concluded that (R)-(+)-rosmarinic acid would expose significant antiviral effects in in vitro and in vivo experiments, and this research would be a valuable asset for the future, especially for those who wish to discover a drug molecule for a variety of viruses.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s43450-023-00381-y.

Uncovering of Anti-dengue Molecules from Plants Prescribed for Dengue: A Computational Investigation

Dengue fever is a tropical disease spread worldwide, transmitted by the mosquito Aedes aegypti. It affects 100 million people worldwide every year and half a million cases of dengue hemorrhagic fever are registered. At present, it poses sever health burden as combined infections of COVID-19. Currently, as a combined infection with COVID-19, it is becoming a serious health burden. To identify the active molecule, Maestro V12.7 was used with different tools including LigPrep, Grid Generation, SiteMap, Glide XP Docking, Pharmachophores and MM-GBSA. The UNRESS tool was also used to assess the protein stability with this dengue protein. The docking result showed that all examined phytocomponents except berberine and -(+)-l-alliin had good docking scores of -8.577 (azadirachtin), -8.112 (curcumin), -7.348 (apigenin) and -6.028 (andrographolide). However, berberine and -(+)-l-alliin possessed good hydrogen-bonding interactions with RdRp. In addition, molecular dynamic simulations demonstrate that the complex of azadirachtin and dengue protein has a solid understanding of the precise interactions. As per the research results, the present research suggests that this is the first statement of azadirachtin against NS5 RNA-dependent RNA polymerase domain (RdRp), despite extensive research on this molecule in previous investigations. Furthermore, we anticipate that molecules such as curcumin, apigenin, and andrographolide would show beneficial effects while in vitro and in vivo studies are conducted on virally related objects. Since we performed ADMET and pharmacokinetic properties in this research, we feel that the phytochemicals of the screened anti-dengue molecules may not need to be evaluated for toxicological effects.

Discovery of novel natural products as rhodesain inhibitors for human African trypanosomiasis using in silico techniques

Human African Trypanosomiasis (HAT) or sleeping sickness is caused by the Trypanosoma brucei rhodesiense, a subspecies of the Trypanosomatide family. The parasite is associated with high morbidity and mortality rate in both animals and humans, claimed to be more fatal than other vector-transmitted diseases such as malaria. The majority of existing medications are highly toxic, not effective in the late chronic phase of the disease, and require maximum dosages to fully eradicate the parasite. In this study, we used computational methods to find out natural products that inhibit the Rhodesain, a parasitic enzyme that plays an important role in the parasite's pathogenicity, multiplication, and ability to pass through the host's blood-brain barrier. A library of 270540 natural products from ZINC databases was processed by using e-pharmacophore hypnosis and screening procedures, molecular docking, ADMET processes, and MM-GBSA calculations. This led to the identification of 3 compounds (ZINC000096269390, ZINC000035485292, and ZINC000035485242) which were then subjected to molecular dynamics. The findings of this study showed excellent binding affinity and stability toward the Rhodesain and suggest they may be a hopeful treatment for HAT in the future if further clinical trials were performed.Communicated by Ramaswamy H. Sarma.

Anti-dengue Potential of Mangiferin: Intricate Network of Dengue to Human Genes

Dengue fever has become one of the deadliest infectious diseases and requires the development of effective antiviral therapies. It is caused by members of the Flaviviridae family, which also cause various infections in humans, including dengue fever, tick-borne encephalitis, West Nile fever, and yellow fever. In addition, since 2019, dengue-endemic regions have been grappling with the public health and socio-economic impact of the ongoing coronavirus disease 19. Co-infections of coronavirus and dengue fever cause serious health complications for people who also have difficulty managing them. To identify the potentials of mangiferin, a molecular docking with various dengue virus proteins was performed. In addition, to understand the gene interactions between human and dengue genes, Cytoscape was used in this research. The Kyoto Encyclopedia of Genes and Genomes software was used to find the paths of Flaviviridae. The Kyoto Encyclopedia of Genes and Genomes and the Reactome Pathway Library were used to understand the biochemical processes involved. The present results show that mangiferin shows efficient docking scores and that it has good binding affinities with all docked proteins. The exact biological functions of type I interferon, such as interferon-α and interferon-β, were also shown in detail through the enrichment analysis of the signaling pathway. According to the docking results, it was concluded that mangiferin could be an effective drug against the complications of dengue virus 1, dengue virus 3, and non-structural protein 5. In addition, computational biological studies lead to the discovery of a new antiviral bioactive molecule and also to a deeper understanding of viral replication in the human body. Ultimately, the current research will be an important resource for those looking to use mangiferin as an anti-dengue drug.

A scientific pharmacognosy on Gaucher's disease: an in silico analysis

From ancient times, studies on herbal medicine and pharmacognosy have increased gradually worldwide, due to the increased side effects, adverse drug reactions, and charge lines of modern medicines. Plants are well known for their medicinal effects and nutritional values. They contain bioactive compounds which display a wide spectrum of therapeutic effects. Gaucher's disease (GD) is a rare autosomal recessively inherited metabolic disorder caused due to the defect in Glucosylceramidase beta gene coding for the enzyme acid-β-glucosidase in humans. We revealed the profound binding efficiency of five selected bioactive compounds from different plants against the main enzyme acid-β-glucosidase responsible for GD through molecular docking. An in silico approach along with the ADMET profiles of phytocompounds was done using the Schrodinger software. The preventive measure of GD leads to side effects, inaccessible and unaffordable which put forth the emergence of phytocompounds which have fewer toxic effects, and one such compound is β-D-Glucopyranose with the best docking score (-10.28 kcal/mol) and an excellent binding affinity than other ligands, which could be further analyzed for stability using molecular dynamics study and in vitro. Being a dietary supplement, these compounds could be prepared in any form of formulation as a drug.

Cyanobacterial metabolites as novel drug candidates in corona viral therapies: A review

Most of the medical and nonmedical research labs, all around the world, are racing against time to produce an effective vaccine or an antiviral medicine for coronavirus disease 2019 (COVID‐19). Conventional medicines and novel nano‐materials including chemical and herbal‐based compounds are all into positive trials toward coronaviruses and other pandemic infections. Among them, natural immune boosters have attracted physicians because of their longevity and reliability for fewer side effects. This is a review article with a detailed picture of an unexplored antiviral source with maximum potency in curing viral infections. Cyanobacteriae have been known for centuries and are rich in secondary metabolites of proteins, biopeptides, and polysaccharides for prominent antiviral action against chest infections. But detailed exploratory research is required to purify, scale‐up, and commercialize the pharmacologically active agents from these drug reserves.

Virtual Screening of Natural Chemical Databases to Search for Potential ACE2 Inhibitors

The angiotensin-converting enzyme II (ACE2) is a multifunctional protein in both health and disease conditions, which serves as a counterregulatory component of RAS function in a cardioprotective role. ACE2 modulation may also have relevance to ovarian cancer, diabetes, acute lung injury, fibrotic diseases, etc. Furthermore, since the outbreak of the coronavirus disease in 2019 (COVID-19), ACE2 has been recognized as the host receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The receptor binding domain of the SARS-CoV-2 S-protein has a strong interaction with ACE2, so ACE2 may be a potent drug target to prevent the virus from invading host cells for anti-COVID-19 drug discovery. In this study, structure- and property-based virtual screening methods were combined to filter natural product databases from ChemDiv, TargetMol, and InterBioScreen to find potential ACE2 inhibitors. The binding affinity between protein and ligands was predicted using both Glide SP and XP scoring functions and the MM-GBSA method. ADME properties were also calculated to evaluate chemical drug-likeness. Then, molecular dynamics (MD) simulations were performed to further explore the binding modes between the highest-potential compounds and ACE2. Results showed that the compounds 154-23-4 and STOCK1N-07141 possess potential ACE2 inhibition activities and deserve further study.

Effectiveness of Bioactive Compound as Antibacterial and Anti-Quorum Sensing Agent from Myrmecodia pendans: An In Silico Study

Background: antibiotic resistance encourages the development of new therapies, or the discovery of novel antibacterial agents. Previous research revealed that Myrmecodia pendans (Sarang Semut) contain potential antibacterial agents. However, specific proteins inhibited by them have not yet been identified as either proteins targeted by antibiotics or proteins that have a role in the quorum-sensing system. This study aims to investigate and predict the action mode of antibacterial compounds with specific proteins by following the molecular docking approach. Methods: butein (1), biflavonoid (2), 3″-methoxyepicatechin-3-O-epicatechin (3), 2-dodecyl-4-hydroxylbenzaldehyde (4), 2-dodecyl-4-hydroxylbenzaldehyde (5), pomolic acid (6), betulin (7), and sitosterol-(6′-O-tridecanoil)-3-O-β-D-glucopyranoside (8) from M. pendans act as the ligand. Antibiotics or substrates in each protein were used as a positive control. To screen the bioactivity of compounds, ligands were analyzed by Prediction of Activity Spectra for Substances (PASS) program. They were docked with 12 proteins by AutoDock Vina in the PyRx 0.8 software application. Those proteins are penicillin-binding protein (PBP), MurB, Sortase A (SrtA), deoxyribonucleic acid (DNA) gyrase, ribonucleic acid (RNA) polymerase, ribosomal protein, Cytolysin M (ClyM), FsrB, gelatinase binding-activating pheromone (GBAP), and PgrX retrieved from UniProt. The docking results were analyzed by the ProteinsPlus and Discovery Studio software applications. Results: most compounds have Pa value over 0.5 against proteins in the cell wall. In nearly all proteins, biflavonoid (2) has the strongest binding affinity. However, compound 2 binds only three residues, so that 2 is the non-competitive inhibitor. Conclusion: compound 2 can be a lead compound for an antibacterial agent in each pathway.