Correction: Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations

[This corrects the article DOI: 10.1039/D0RA06212J.].

Assessing potential inhibitors of SARS-CoV-2 main protease from available drugs using free energy perturbation simulations

The main protease (Mpro) of the novel coronavirus SARS-CoV-2, which has caused the COVID-19 pandemic, is responsible for the maturation of its key proteins. Thus, inhibiting SARS-CoV-2 Mpro could prevent SARS-CoV-2 from multiplying. Because new inhibitors require thorough validation, repurposing current drugs could help reduce the validation process. Many recent studies used molecular docking to screen large databases for potential inhibitors of SARS-CoV-2 Mpro. However, molecular docking does not consider molecular dynamics and thus can be prone to error. In this work, we developed a protocol using free energy perturbation (FEP) to assess the potential inhibitors of SARS-CoV-2 Mpro. First, we validated both molecular docking and FEP on a set of 11 inhibitors of SARS-CoV-2 Mpro with experimentally determined inhibitory data. The experimentally deduced binding free energy exhibits significantly stronger correlation with that predicted by FEP (R = 0.94 ± 0.04) than with that predicted by molecular docking (R = 0.82 ± 0.08). This result clearly shows that FEP is the most accurate method available to predict the binding affinity of SARS-CoV-2 Mpro + ligand complexes. We subsequently used FEP to validate the top 33 compounds screened with molecular docking from the ZINC15 database. Thirteen of these compounds were predicted to bind strongly to SARS-CoV-2 Mpro, most of which are currently used as drugs for various diseases in humans. Notably, delamanid, an anti-tuberculosis drug, was predicted to inhibit SARS-CoV-2 Mpro in the nanomolar range. Because both COVID-19 and tuberculosis are lung diseases, delamanid has higher probability to be suitable for treating COVID-19 than other predicted compounds. Analysis of the complexes of SARS-CoV-2 Mpro and the top inhibitors revealed the key residues involved in the binding, including the catalytic dyad His14 and Cys145, which is consistent with the structural studies reported recently.

Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations

Originating for the first time in Wuhan, China, the outbreak of SARS-CoV-2 has caused a serious global health issue. An effective treatment for SARS-CoV-2 is still unavailable. Therefore, in this study, we have tried to predict a list of potential inhibitors for SARS-CoV-2 main protease (Mpro) using a combination of molecular docking and fast pulling of ligand (FPL) simulations. The approaches were initially validated over a set of eleven available inhibitors. Both Autodock Vina and FPL calculations produced consistent results with the experiments with correlation coefficients of R Dock = 0.72 ± 0.14 and R W = -0.76 ± 0.10, respectively. The combined approaches were then utilized to predict possible inhibitors that were selected from a ZINC15 sub-database for SARS-CoV-2 Mpro. Twenty compounds were suggested to be able to bind well to SARS-CoV-2 Mpro. Among them, five top-leads are periandrin V, penimocycline, cis-p-Coumaroylcorosolic acid, glycyrrhizin, and uralsaponin B. The obtained results could probably lead to enhance the COVID-19 therapy.

Fish-borne trematode metacercariae detected in fish commonly used for raw consumption in Ninh Binh Province, Vietnam

Raw or undercooked fish dishes are the major sources of human infection of fishborne trematodes (FBT) and the situation of metacercarial infection in fish greatly affect the prevalence in humans, especially those fish that are commonly used for raw consumption. To investigate the situation of infection with metacercaria of FBT in fish often used to prepare raw fish dishes by local people to assess the risk of infection to humans in Ninh Binh province, Vietnam. 345 fish belonging to five species of freshwater and one species of brackish water fish were collected from fishermen or small-scale fish dealers in Kim Son and Yen Khanh districts, Ninh Binh province between May 2017 and May 2018. Metacercaria of FBT was discovered by pepsin and hydrochloric acid digestion techniques and identified by the morphological and molecular analysis. Among examined fish, 44.06% infected with FBT metacercaria and the highest prevalence was in Cyprinus carpio (86.54%), Ctenopharyngodon idellus (78.43%) and Hypophthalmichthys molitrix (66.67%) while Konosirus punctatus - the brackish water fish - were free from infection. Three species of FBT were found; namely Haplorchis pumilio (accounting for 99.84% of collected metacercariae), Haplorchis taichui and Clonorchis sinensis. The average density was 1.06 metacercariae per gram of freshwater fish and the highest number was of C. idellus (6.38 cysts/gram) followed by Cirrhinus molitorella and C. carpio. Results of the study show the high prevalence of infection of FBT metacercariae among freshwater fish often used to prepare raw fish dishes in Ninh Binh province. These findings suggest the need for greater awareness of the risk from raw fish dishes among public health authorities and people.