Ginger ring compounds as an inhibitor of spike binding protein of alpha, beta, gamma and delta variants of SARS-CoV-2: An in-silico study

In silico identification of five binding sites on the SARS-CoV-2 spike protein and selection of seven ligands for such sites

To contribute to the development of products capable of complexing with the SARS-CoV-2 spike protein, and thus preventing the virus from entering the host cell, this work aimed at discovering binding sites in the whole protein structure, as well as selecting substances capable of binding efficiently to such sites. Initially, the three-dimensional structure of the protein, with all receptor binding domains in the closed state, underwent blind docking with 38 substances potentially capable of binding to this protein according to the literature. This allowed the identification of five binding sites. Then, those substances with more affinities for these sites underwent pharmacophoric search in the ZINC15 database. The 14,329 substances selected from ZINC15 were subjected to docking to the five selected sites of the spike protein. The ligands with more affinities for the protein sites, as well as the selected sites themselves, were used in the de novo design of new ligands that were also docked to the binding sites of the protein. The best ligands, regardless of their origins, were used to form complexes with the spike protein, which were subsequently used in molecular dynamics simulations and calculations of ligands affinities to the protein through the molecular mechanics/Poisson-Boltzmann surface area method (MMPBSA). Seven substances with good affinities to the spike protein (-12.9 to -20.6 kcal/mol), satisfactory druggability (Bioavailability score: 0.17 to 0.55), and low acute toxicity to mice (LD50: 751 to 1421 mg/kg) were selected as potentially useful for the future development of new products to manage COVID-19 infections.Communicated by Ramaswamy H. Sarma.

Lactate dehydrogenase contribution to symptom persistence in long COVID: A pooled analysis

There's critical need for risk predictors in long COVID. This meta-analysis evaluates the evidence for an association between plasma lactate dehydrogenase (LDH) and long COVID and explores the contribution of LDH to symptoms persistent across the distinct post-acute sequelae of COVID-19 (PASC) domains. PubMed, EMBASE, Web of Science, and Google Scholar were searched for articles published up to 20 March 2023 for studies that reported data on LDH levels in COVID-19 survivors with and without PASC. Random-effect meta-analysis was employed to estimate the standardized mean difference (SMD) with corresponding 95% confidence interval of each outcome. There were a total of 8289 study participants (3338 PASC vs. 4951 controls) from 46 studies. Our meta-analysis compared to the controls showed a significant association between LDH elevation and Resp-PASC [SMD = 1.07, 95%CI = 0.72, 1.41, p = 0.01] but not Cardio-PASC [SMD = 1.79, 95%CI = -0.02, 3.61, p = 0.05], Neuro-PASC [SMD = 0.19, 95%CI = -0.24, 0.61, p = 0.40], and Gastrointestinal-PASC [SMD = 0.45, 95%CI = -1.08, 1.98, p = 0.56]. This meta-analysis suggests elevated LDH can be used for predicting Resp-PASC, but not Cardio-PASC, Neuro-PASC or gastrointestinal-PASC. Thus, elevated plasma LDH following COVID infection may be considered as a disease biomarker.

Strongyloides coinfection in COVID-19 patients treated with corticosteroids: A systematic review

The COVID-19 pandemic linked to the virus SARS-CoV-2, which began in China, affected ∼765 million people as of 30 April 2023. The widespread use of corticosteroids for the symptomatic treatment of COVID-19 could lead to the reactivation of infections of opportunistic pathogens, including Strongyloides. We sought to determine the clinical symptoms and demographic characteristics of SARS-CoV-2-Strongyloides co-infection, particularly in patients with severe disease and being treated with immunosuppressive drugs. To do this, we undertook a systematic review of the literature, and searched public accessible scientific databases-the Web of Science, Scopus, PubMed/Medline and Embase -for eligible studies (1 December 2019 to 30 August 2022). The review protocol is registered in PROSPERO (CRD42022377062). Descriptive statistical analyses were used to present the clinical and laboratory parameters of the co-infection; for this, we calculated prevalence using the following formula: positive cases/total number of cases × 100. Of a total of 593 studies identified, 17 studies reporting 26 co-infected patients met the criteria for inclusion in this review. The median age of these patients was 55.14 years. Most of cases (53.8%) were treated with dexamethasone, followed by methylprednisolone (26.9%). Eighteen of 26 patients were immigrants living in European countries or the USA; most of these immigrants originated from Latin America (58%) and South-East Asia (11%). The commonest symptoms of co-infection were abdominal pain (50%), fever (46.1%), dyspnoea (30.7%) and cough (30.7%), and frequently reported laboratory findings were high absolute eosinophil count (38.4%), high white blood cell count (30.7%), high C-reactive protein (23.0%) and high neutrophil count (19.2%). Two of the 26 patients (7.7%) had fatal outcomes. Most of the SARS-CoV-2-Strongyloides coinfected cases were immigrants living in developed countries, emphasising the need for clinicians in these countries to be aware of clinical and laboratory parameters associated with such co-infections, as well as the key importance of rapid and accurate diagnostic tests for timely and effective diagnosis and patient management.

Natural Product-Based Screening for Lead Compounds Targeting SARS CoV-2 Mpro

Drugs that cure COVID-19 have been marketed; however, this disease continues to ravage the world without becoming extinct, and thus, drug discoveries are still relevant. Since Mpro has known advantages as a drug target, such as the conserved nature of the active site and the absence of homologous proteins in the body, it receives the attention of many researchers. Meanwhile, the role of traditional Chinese medicine (TCM) in the control of epidemics in China has also led to a focus on natural products, with the hope of finding some promising lead molecules through screening. In this study, we selected a commercial library of 2526 natural products from plants, animals and microorganisms with known biological activity for drug discovery, which had previously been reported for compound screening of the SARS CoV-2 S protein, but had not been tested on Mpro. This library contains compounds from a variety of Chinese herbs, including Lonicerae Japonicae Flos, Forsythiae Fructus and Scutellariae Radix, which are derived from traditional Chinese medicine prescriptions that have been shown to be effective against COVID-19. We used the conventional FRET method for the initial screening. After two rounds of selection, the remaining 86 compounds were divided into flavonoids, lipids, phenylpropanoids, phenols, quinones, alkaloids, terpenoids and steroids according to the skeleton structures, with inhibition rates greater than 70%. The top compounds in each group were selected to test the effective concentration ranges; the IC50 values were as follows: (-)-gallocatechin gallate (1.522 ± 0.126 μM), ginkgolic acid C15:1 (9.352 ± 0.531 μM), hematoxylin (1.025 ± 0.042 μM), fraxetin (2.486 ± 0.178 μM), wedelolactone (1.003 ± 0.238 μM), hydroxytyrosol acetate (3.850 ± 0.576 μM), vanitiolide (2.837 ± 0.225 μM), β,β-dimethylacrylalkannin (2.731 ± 0.308 μM), melanin (7.373 ± 0.368 μM) and cholesteryl sodium sulfate (2.741 ± 0.234μM). In the next step, we employed two biophysical techniques, SPR and nanoDSF, to obtain KD/Kobs values: hematoxylin (0.7 μM), (-)-gallocatechin gallate (126 μM), ginkgolic acid C15:1 (227 μM), wedelolactone (0.9770 μM), β,β-dimethylacrylalkannin (1.9004 μM,), cholesteryl sodium sulfate (7.5950 μM) and melanin (11.5667 μM), which allowed better assessments of the binding levels. Here, seven compounds were the winners. Then, molecular docking experiments were specially performed by AutoDock Vina to analyze the mode of interactions within Mpro and ligands. We finally formulated the present in silico study to predict pharmacokinetic parameters as well as drug-like properties, which is presumably the step that tells humans whether the compounds are drug-like or not. Moreover, hematoxylin, melanin, wedelolactone, β,β-dimethylacrylalkannin and cholesteryl sodium sulfate are in full compliance with the "Lipinski" principle and possess reasonable ADME/T properties, they have a greater potential of being lead compounds. The proposed five compounds are also the first to be found to have potential inhibitory effects on SARS CoV-2 Mpro. We hope that the results in this manuscript may serve as benchmarks for the above potentials.