B38 for COVID-19

The high-frequency mutation characteristics of SARS-CoV-2 have posed formidable challenges to the development of vaccines and therapeutic agents. Neutralizing antibodies, which serve as effective tools for prevention and control, have undergone continuous updates and iterations in response to viral mutations. This article provides a comprehensive review of researchers’ efforts to achieve both high neutralizing potency and high mutation tolerance in SARS-CoV-2–targeting neutralizing antibodies. Building on the characteristics of conventional antibodies directed against distinct epitopes on the S protein, it further discusses the research on nanobodies, antibody cocktails, multi-specific antibodies, and other antibody formats and engineering approaches, including artificial intelligence–enabled optimization. Each antibody-based strategy targeting SARS-CoV-2 has its own distinctive advantages and potential applications, providing an integrated perspective to support the continued development of antiviral neutralizing antibodies.

Abstract Summary Since the emergence of SARS-CoV-2, numerous studies have investigated antibody interactions with viral variants in vitro, and several datasets have been curated to compile available protein structures and experimental measurements. However, existing data remain fragmented, limiting their utility for the development and validation of machine learning models for antibody–antigen interaction prediction. Here, we present CoV-UniBind, a unified database comprising over 75 000 entries of SARS-CoV-2 antibody–antigen sequence, binding, and structural data, integrated and standardized from three public sources and multiple peer-reviewed publications. To demonstrate its utility, we benchmarked multiple protein folding, inverse folding, and language models across tasks relevant to antibody design and vaccine development. We expect CoV-UniBind to facilitate future computational efforts in antibody and vaccine development against SARS-CoV-2. Availability and implementation The curated datasets, model scores and antibody synonyms are free to download at https://huggingface.co/datasets/InstaDeepAI/cov-unibind. Folded structures are available upon request.

Despite all currently available anti-pandemic monoclonal-antibodies (mAbs) and vaccines, subsequently emerging pandemic-infections will likely become more pan-resistant-, -transmissible and/or -lethal. We have created HEDGES generation-2, a significantly more-combinatorial, -synergistic version of our generation-1 HEDGES DNA vector-based platform. We previously published that one safe intravenous injection of a HEDGES generation-1 DNA vector encoding one of three different FDA-approved mAbs produced durable therapeutic serum mAb levels as well as critical therapeutic endpoints in immunocompetent mice. Here we show one safe, intravenous administration of a 2 nd -generation HEDGES DNA vector co-encoding four different anti-SARS-CoV-2 mAbs rapidly then durably co-produces high anti-SARS-CoV-2 mAb serum levels that effectively block SARS-CoV-2 virus binding to the ACE-2 spike protein in immunocompetent mice. In addition, four weekly intravenous HEDGES generation-2 DNA vector administrations co-encoding a total of ten-different anti-SARS-CoV-2 mAbs, 5J8, plus an anti-1918 pandemic influenza mAb and mepolizumab, an FDA-approved anti-IL-5 mAb, durably co-produce highly-neutralizing 5J8 anti-pandemic influenza mAb serum levels, as well as durably block SARS-CoV-2 virus-ACE-2 receptor binding in mice. Furthermore, unlike vaccines and mAbs, HEDGES does not require an intact cold chain and is readily freeze dried, enabling its prolonged storage at ambient temperatures worldwide, even in equatorial regions. Also, HEDGES can create, then deploy novel, more effective anti-pandemic mAbs ~three weeks after their identification. Conversely, vaccines require ~three months to deploy, recombinant-mAbs ~nine months. By rapidly then durably co-producing many different highly-neutralizing, highly-synergistic anti-pandemic mAbs, HEDGES may effectively co-prevent both SARS-CoV-2 and pandemic-influenza infections. HEDGES may also prevent even more-transmissible, -pan-resistant and/or -lethal pandemic diseases that subsequently-emerge.

Abstract The ongoing COVID-19 pandemic caused by SARS-CoV-2 has raised global concern for public health and the economy. The development of therapeutics and vaccines to combat this virus are continuously progressing. Multi-omics approaches, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and metallomics, have helped understand the structural and molecular features of the virus, thereby assisting in the design of potential therapeutics and accelerating vaccine development for COVID-19. Here, we provide an up-to-date overview of the latest applications of multi-omics technologies in strategies addressing COVID-19, in order to provide suggestions towards the development of highly effective knowledge-based therapeutics and vaccines.