ABSTRACT
The COVID-19 pandemic, caused by SARS-CoV-2, has become a global public health crisis. The entry of SARS-CoV-2 into host cells is facilitated by the binding of its spike protein (S1-RBD) to the host receptor hACE2. Small molecule compounds targeting S1-RBD-hACE2 interaction could provide an alternative therapeutic strategy sensitive to viral mutations. In this study, we identified G7a as a hit compound that targets the S1-RBD-hACE2 interaction, using high-throughput screening in the SARS2-S pseudovirus model. To enhance the antiviral activity of G7a, we designed and synthesized a series of novel 7-azaindole derivatives that bind to the S1-RBD-hACE2 interface. Surprisingly, ASM-7 showed excellent antiviral activity and low cytotoxicity, as confirmed by pseudovirus and native virus assays. Molecular docking and molecular dynamics simulations revealed that ASM-7 could stably bind to the binding interface of S1-RBD-hACE2, forming strong non-covalent interactions with key residues. Furthermore, the binding of ASM-7 caused alterations in the structural dynamics of both S1-RBD and hACE2, resulting in a decrease in their binding affinity and ultimately impeding the viral invasion of host cells. Our findings demonstrate that ASM-7 is a promising lead compound for developing novel therapeutics against SARS-CoV-2.
Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/metabolism , Molecular Docking Simulation , Spike Glycoprotein, Coronavirus/chemistry , Pandemics , Angiotensin-Converting Enzyme 2/metabolism , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , Protein BindingABSTRACT
On December 15, 2020, four dock workers tested positive for severe acute respiratory syndrome-coronavirus 2 (SARS-COV-2) nucleic acids and were reported by Dalian. Up until then, Dalian City had not reported local cases for 136 consecutive days. In this coronavirus disease 2019 (COVID-19) outbreak (referred to as the "Dalian COVID-19 outbreak"), samples from all infected persons (83) and part from the ship cargoes in contact With them during December 15, 2020 to January 8, 2021 were collected. Confirmed cases accounted for 61.45% (51/83) and asymptomatic infections accounted for 38.55% (32/83). Through high-throughput sequencing, 76 SARS-CoV-2 whole-genome sequences were obtained, of which 72 (86.75%) were from clinical samples, and 4 from cold-chain food packaging surface samples on cargo ship A of country R. Refer to Wuhan reference strain (NC_045512), genome analysis revealed 12-16 nucleotide mutations in 76 whole genomes sharing 12 nucleotide mutations and belong to the SARS-CoV-2 branch of B.1.1. Viral genomics and field epidemiological investigations showed that the Dalian COVID-19 outbreak was a local epidemic caused by dock workers infected with imported cold - chain products contaminated with SARS - CoV - 2. During transmission, 3 Virus generations and three relatively independent transmission chains were formed.
ABSTRACT
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-ß levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-ß responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.