Structural basis for the inhibition of SARS-CoV2 main protease by Indian medicinal plant-derived antiviral compounds.

A novel coronavirus (SARS-CoV2) has caused a major outbreak in humans around the globe, and it became a severe threat to human healthcare than all other infectious diseases. Researchers were urged to discover and test various approaches to control and prevent such a deadly disease. Considering the emergency and necessity, we screened reported antiviral compounds present in the traditional Indian medicinal plants for the inhibition of SARS-CoV2 main protease. In this study, we used molecular docking to screen 41 reported antiviral compounds that exist in Indian medicinal plants and shown amentoflavone from the plant Torreyanucifera with a higher docking score. Furthermore, we performed a 40 ns atomic molecular dynamics simulation and free binding energy calculations to explore the stability of the top five protein-ligand complexes. Through the article, we insist that the amentoflavone, hypericin and Torvoside H from the traditional Indian medicinal plants may be used as a potential inhibitor of SARS-CoV2 main protease and further biochemical experiments could shed light on understanding the mechanism of inhibition by these plant-derived antiviral compounds.Communicated by Ramaswamy H. Sarma.

A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus poses serious threats to the global public health and leads to worldwide crisis. No effective drug or vaccine is readily available. The viral RNA-dependent RNA polymerase (RdRp) is a promising therapeutic target. A hybrid drug screening procedure was proposed and applied to identify potential drug candidates targeting RdRp from 1906 approved drugs. Among the four selected market available drug candidates, Pralatrexate and Azithromycin were confirmed to effectively inhibit SARS-CoV-2 replication in vitro with EC50 values of 0.008µM and 9.453 µM, respectively. For the first time, our study discovered that Pralatrexate is able to potently inhibit SARS-CoV-2 replication with a stronger inhibitory activity than Remdesivir within the same experimental conditions. The paper demonstrates the feasibility of fast and accurate anti-viral drug screening for inhibitors of SARS-CoV-2 and provides potential therapeutic agents against COVID-19.

Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov.

A novel coronavirus, called 2019-nCoV, was recently found in Wuhan, Hubei Province of China, and now is spreading across China and other parts of the world. Although there are some drugs to treat 2019-nCoV, there is no proper scientific evidence about its activity on the virus. It is of high significance to develop a drug that can combat the virus effectively to save valuable human lives. It usually takes a much longer time to develop a drug using traditional methods. For 2019-nCoV, it is now better to rely on some alternative methods such as deep learning to develop drugs that can combat such a disease effectively since 2019-nCoV is highly homologous to SARS-CoV. In the present work, we first collected virus RNA sequences of 18 patients reported to have 2019-nCoV from the public domain database, translated the RNA into protein sequences, and performed multiple sequence alignment. After a careful literature survey and sequence analysis, 3C-like protease is considered to be a major therapeutic target and we built a protein 3D model of 3C-like protease using homology modeling. Relying on the structural model, we used a pipeline to perform large scale virtual screening by using a deep learning based method to accurately rank/identify protein-ligand interacting pairs developed recently in our group. Our model identified potential drugs for 2019-nCoV 3C-like protease by performing drug screening against four chemical compound databases (Chimdiv, Targetmol-Approved_Drug_Library, Targetmol-Natural_Compound_Library, and Targetmol-Bioactive_Compound_Library) and a database of tripeptides. Through this paper, we provided the list of possible chemical ligands (Meglumine, Vidarabine, Adenosine, D-Sorbitol, D-Mannitol, Sodium_gluconate, Ganciclovir and Chlorobutanol) and peptide drugs (combination of isoleucine, lysine and proline) from the databases to guide the experimental scientists and validate the molecules which can combat the virus in a shorter time.

Large-Scale Target Identification of Herbal Medicine Using a Reverse Docking Approach.

Herbal medicine has been used to countermine various diseases for centuries. However, most of the therapeutic targets underlying herbal therapy remain unclear, which largely slow down the novel drug discovery process from natural products. In this study, we developed a novel computational pipeline for assisting de novo identification of protein targets for herbal ingredients. The pipeline involves pharmacophore comparison and reverse ligand-protein docking simulation in a high throughput manner. We evaluated the pipeline using three traditional Chinese medicine ingredients such as acteoside, quercetin, and epigallocatechin gallate as examples. A majority of current known targets of these ingredients were successfully identified by the pipeline. Structural comparative analyses confirmed that the predicted ligand-target interactions used the same binding pockets and binding modes as those of known ligand-target interactions. Furthermore, we illustrated the mechanism of actions of the ingredients by constructing the pharmacological networks on the basis of the predicted target profiles. In summary, we proposed an efficient and economic option for large-scale target exploration in the herb study. This pipeline will be particularly valuable in aiding precise drug discovery and drug repurposing from natural products.

Inhibitory effects of essential oil from rhizomes of Ligusticum chuanxiong on hypertrophic scarring in the rabbit ear model.

CONTEXT: Hypertrophic scarring, a common proliferative disorder of dermal fibroblasts, results from an overproduction of collagen and excessive deposition of extracellular matrix. Although the treatment with surgical excisions or steroid hormones can modify the symptoms, numerous treatment-related complications have also been established. OBJECTIVE: To investigate the effects of essential oil (EO) from rhizomes of Ligusticum chuanxiong Hort. (Umbelliferae) on hypertrophic scarring in a rabbit ear model. MATERIALS AND METHODS: A rabbit ear model of hypertrophic scarring was established. EO (5, 10, and 20%) was applied once daily to the scars for 22 days. After 28 days of post-wounding, excision of scars was respectively performed for both histological examination and assays of the levels of collagen I, collagen III, matrix metalloproteinase-1 (MMP-1), and transforming growth factor beta 1 (TGF-ß1). The scar elevation index (SEI) was also determined. RESULTS: After 22 days of treatment with indicated concentrations of EO, hypertrophic scarring was significantly inhibited in the rabbit ears. The levels of TGF-ß1, collagen I, and collagen III evidently decreased and MMP-1 level markedly increased in the scar tissue. SEI was also significantly reduced. Immunohistochemical findings exhibited significant amelioration of the scar tissue. DISCUSSION AND CONCLUSION: EO suppresses hypertrophic scarring in the rabbit ear model and is a probably effective cure for human hypertrophic scarring.

Establishment of a luciferase assay-based screening system for detecting estrogen receptor agonists in plant extracts.

In order to effectively treat osteoporosis and other bone-loss disorders, small compounds that could induce bone formation are needed. The present study attempted to establish a screening system for detecting estrogenic activity of compounds, which probably have anti-osteoporosis effects. For this purpose, we established osteoblastic-like MG63 cells stably transfected with the PGL3 reporter gene driven by a promoter consisting of three estrogen response elements (EREs). Using this system, we screened numerous plant extracts, and found several which displayed bioactivity. We conclude that the MG63 cells with estrogen-specific reporter plasmids (MG63-pERE) are useful for high-throughput screening of estrogen receptor agonists from plants which may have favorable potency and could be developed into novel anti-osteoporosis drugs.

Essential oil from rhizomes of Ligusticum chuanxiong induces apoptosis in hypertrophic scar fibroblasts.

CONTEXT: Hypertrophic scarring following surgical procedures, trauma and especially burns can lead to severe functional and cosmetic impairment, causing a decrease in the quality of life. Although a wide choice of treatments is offered, few therapeutic methods are universally accepted because of their side effects. OBJECTIVE: The effects of the essential oil (EO) extracted from rhizomes of Ligusticum chuanxiong Hort. (Umbelliferae) in human hypertrophic scar fibroblasts (HSFs) are investigated for the first time. MATERIALS AND METHODS: Chemical composition of hydrodistilled EO obtained from rhizomes of Ligusticum chuanxiong was analyzed by gas chromatography-mass spectrometry (GC-MS). The effects of EO on cell viability, apoptosis rate, mitochondrial membrane potential (MMP), lactate dehydrogenase (LDH), reactive oxygen species (ROS) and caspase-3 in HSFs were investigated. RESULTS: The experimental results showed that EO significantly inhibited cell viability, elicited morphological changes and induced apoptosis in HSFs. EO also evidently increased the loss of MMP, the levels of LDH release and cellular ROS production, and the activity of caspase-3. DISCUSSION AND CONCLUSION: EO-induced apoptosis was at least partially carried out via destruction of the intracellular antioxidant system and elicitation of excessive ROS accumulation in HSFs, which impaired mitochondrial membranes and elicited caspase-3 activation. EO could be an effective cure for human hypertrophic scar.

Characteristics of aerobic granule and nitrogen and phosphorus removal in a SBR.

The performance of a sequencing batch reactor (SBR) seeded with aerobic granular sludge was studied. The lab-scale SBR treating domestic wastewater operated at a volumetric loading rate (VLR) of 0.75-3.41 kg COD/(m(3)d). The granule stability was related to the organic loading, and high loading would be favorable for granule stability. Analysis of typical cycle showed that granular sludge had good ability to simultaneously remove nitrogen and phosphorus. Most organic substances were removed at the anaerobic stage. At the aerobic stage, simultaneous nitrification and denitrification (SND) happened with phosphorus absorption. The SBR had good removal performance for organic matter and phosphate. However, the total nitrogen (TN) removal performance was ordinary, with average removal efficiency of about 52%. Batch experiments indicated that increases of influent C/N ratio and a large percentage of granule in the sludge were conducive for SND in SBR.

[Simultaneous phosphorus and nitrogen removal of domestic sewage with aerobic granular sludge SBR].

By seeding aerobic granular sludge cultivated from artificial wastewater, an anaerobic/aerobic SBR was applied to treat domestic sewage of high COD, TN and SS. The stability of granular sludge and the removal of organic pollutants, nitrogen and phosphorus of domestic sewage were investigated. After one month incubation, the reactor had good pollutant removal performances and run stably. The ratio of granular sludge to total suspended solids was over 68% all along. The sludge concentration was 5 000 - 6 000 mg/L and SVI value was 20 - 35 mL/g. After three months operation, most of the granules were over 1.25 mm instead of 0.6 - 0.9 mm in the beginning. During the stable operation phase of the granular sludge SBR, the average removal efficiencies of COD, TOC, phosphate, ammonium nitrogen, total nitrogen, SS were 83.04%, 70.41%, 94.30%, 86.51%, 41.82% and 85.89%, respectively. Analysis of the pollutant removal in typical cycle showed that the granular sludge had good simultaneous phosphorus and nitrogen removal performance.