Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies

AbstractThe purpose of this work is to provide an in silico molecular rationale of the role eventually played by currently circulating mutations in the receptor binding domain of the SARS-CoV-2 spike protein (S-RBDCoV‑2) in evading the immune surveillance effects elicited by the two Eli Lilly LY-CoV555/bamlanivimab and LY-CoV016/etesevimab monoclonal antibodies. The main findings from this study show that, compared to the wild-type SARS-CoV-2 spike protein, mutations E484A/G/K/Q/R/V, Q493K/L/R, S494A/P/R, L452R and F490S are predicted to be markedly resistant to neutralization by LY-CoV555, while mutations K417E/N/T, D420A/G/N, N460I/K/S/T, T415P, and Y489C/S are predicted to confer LY-CoV016 escaping advantage to the viral protein. A challenge of our global in silico results against relevant experimental data resulted in an overall 90% agreement. Thus, the results presented provide a molecular-based rationale for all relative experimental findings, constitute a fast and reliable tool for identifying and prioritizing all present and newly reported circulating spike SARS-CoV-2 variants with respect to antibody neutralization, and yield substantial structural information for the development of next-generation vaccines and monoclonal antibodies more resilient to viral evolution.

Download Full-text

In Silico Molecular-Based Rationale for SARS-CoV-2 Spike Circulating Mutations Able to Escape Bamlanivimab and Etesevimab Monoclonal Antibodies

10.1101/2021.05.18.444605 ◽

2021 ◽

Author(s):

Erik Laurini ◽

Domenico Marson ◽

Suzana Aulic ◽

Alice Fermeglia ◽

Sabrina PRICL

Keyword(s):

Monoclonal Antibodies ◽

In Silico ◽

Protective Efficacy ◽

Protein A ◽

Immune Surveillance ◽

Spike Protein ◽

Wild Type ◽

Computer Based ◽

New Challenges ◽

Experimental Findings

The purpose of this work was to provide an in silico molecular rationale of the role eventually played by currently circulating S-RBDCoV‑2 mutations in evading the immune surveillance effects elicited by the two Eli Lilly LY-CoV555/bamlanivimab and LY-CoV016/etesevimab monoclonal antibodies. The main findings from this study and shows that, compared to the wild-type SARS-CoV-2 spike protein, mutations E484A/G/K/Q/R/V, Q493K/L/R, S494A/P/R, L452R and F490S are predicted to be markedly resistant to neutralization by LY-CoV555, while mutations K417E/N/T, D420A/G/N, N460I/K/S/T, T415P, and Y489C/S are predicted to confer LY-CoV016 escaping advantage to the viral protein. A challenge of our global in silico results against the relevant experimental data resulted in an overall 90% agreement. This achievement not only constitutes a further, robust validation of our computer-based approach but also yields a molecular-based rationale for all relative experimental findings, and leads us to conclude that the current circulating SARS-CoV-2 and all possible emergent variants carrying these mutations in the spike protein can present new challenges for mAb-based therapies and ultimately threaten the fully-protective efficacy of currently available vaccines.

Download Full-text

SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies

10.1101/2021.01.19.21249840 ◽

2021 ◽

Cited By ~ 4

Author(s):

Dami A. Collier ◽

Anna De Marco ◽

Isabella A.T.M. Ferreira ◽

Bo Meng ◽

Rawlings Datir ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Immune Responses ◽

Antibody Responses ◽

Spike Protein ◽

Binding Motif ◽

Wild Type ◽

Emerging Viruses ◽

Transmission Potential ◽

Amino Acid Mutations ◽

The Uk

AbstractSevere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission is uncontrolled in many parts of the world, compounded in some areas by higher transmission potential of the B1.1.7 variant now seen in 50 countries. It is unclear whether responses to SARS-CoV-2 vaccines based on the prototypic strain will be impacted by mutations found in B.1.1.7. Here we assessed immune responses following vaccination with mRNA-based vaccine BNT162b2. We measured neutralising antibody responses following a single immunization using pseudoviruses expressing the wild-type Spike protein or the 8 amino acid mutations found in the B.1.1.7 spike protein. The vaccine sera exhibited a broad range of neutralising titres against the wild-type pseudoviruses that were modestly reduced against B.1.1.7 variant. This reduction was also evident in sera from some convalescent patients. Decreased B.1.1.7 neutralisation was also observed with monoclonal antibodies targeting the N-terminal domain (9 out of 10), the Receptor Binding Motif (RBM) (5 out of 31), but not in neutralising mAbs binding outside the RBM. Introduction of the E484K mutation in a B.1.1.7 background to reflect newly emerging viruses in the UK led to a more substantial loss of neutralising activity by vaccine-elicited antibodies and mAbs (19 out of 31) over that conferred by the B.1.1.7 mutations alone. E484K emergence on a B.1.1.7 background represents a threat to the vaccine BNT162b.

Download Full-text

Cross-Neutralizing Activity of Monoclonal Antibodies Against N501Y Mutant Strain of SARS-CoV-2

Journal of Applied Virology ◽

10.21092/jav.v9i4.90 ◽

2020 ◽

Vol 9 (4) ◽

pp. 41-45

Author(s):

Ruxia Ding ◽

Haixin Wang ◽

Yi Yang ◽

Liangshu Xie ◽

Li Zhang ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Mutant Strain ◽

Wild Type Strain ◽

Neutralization Assay ◽

Spike Protein ◽

Wild Type ◽

Neutralizing Activity ◽

Theory Result ◽

Global Concern ◽

The Uk

The dominant N501Y mutation in the spike protein that SARS-CoV-2 virus uses to bind to the human ACE2 receptor were found in the UK, which has aroused global concern and worried. Mutations in spike protein may, in theory, result in more infectious and spreading more easily. In order to evaluate the broad-spectrum protective effect of the monoclonal antibodies(mAbs), we compared the neutralization activities of six prepared mAbs against SARS-CoV-2 with pseudovirus neutralization assay. Only one of them showed a decrease of 6 folds in neutralizing activity to N501Y mutant strain, compared with the wild type strain. We should continue to monitor emergence of new variants in different regions to study their infectivity and neutralization effect.

Download Full-text

Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19

Scientific Reports ◽

10.1038/s41598-020-77077-z ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 3

Author(s):

Tsun-Yung Kuo ◽

Meei-Yun Lin ◽

Robert L. Coffman ◽

John D. Campbell ◽

Paula Traquina ◽

...

Keyword(s):

Neutralizing Antibodies ◽

High Titer ◽

Protein S ◽

Spike Protein ◽

Toll Like Receptor ◽

Wild Type ◽

Applied Technology ◽

A Subunit ◽

Dose Ranging ◽

Potential Vaccine

AbstractThe COVID-19 pandemic is a worldwide health emergency which calls for an unprecedented race for vaccines and treatment. In developing a COVID-19 vaccine, we applied technology previously used for MERS-CoV to produce a prefusion-stabilized SARS-CoV-2 spike protein, S-2P. To enhance immunogenicity and mitigate the potential vaccine-induced immunopathology, CpG 1018, a Th1-biasing synthetic toll-like receptor 9 (TLR9) agonist was selected as an adjuvant candidate. S-2P in combination with CpG 1018 and aluminum hydroxide (alum) was found to be the most potent immunogen and induced high titer of neutralizing antibodies in sera of immunized mice against pseudotyped lentivirus reporter or live wild-type SARS-CoV-2. In addition, the antibodies elicited were able to cross-neutralize pseudovirus containing the spike protein of the D614G variant, indicating the potential for broad spectrum protection. A marked Th1 dominant response was noted from cytokines secreted by splenocytes of mice immunized with CpG 1018 and alum. No vaccine-related serious adverse effects were found in the dose-ranging study in rats administered single- or two-dose regimens of S-2P combined with CpG 1018 alone or CpG 1018 with alum. These data support continued development of CHO-derived S-2P formulated with CpG 1018 and alum as a candidate vaccine to prevent COVID-19 disease.

Download Full-text

EDTA-DEPENDENT MONOCLONAL ANTIBODIES TO HUMAN PROTEIN S

10.1055/s-0038-1644294 ◽

1987 ◽

Author(s):

S Marcovina ◽

R Coppola ◽

M P Protti ◽

C Gelfi ◽

P M Mannucci

Keyword(s):

Monoclonal Antibodies ◽

Ascitic Fluid ◽

Solid Phase ◽

Protein A ◽

Fluid Phase ◽

Protein S ◽

The Other ◽

Human Protein ◽

Sephadex Column ◽

Plot Analysis

Splenocytes from a Balb/c mouse immunized with purified human protein S (PS) were fused with murine hybridoma cell line SP2/0-Agl4 and cultured in Iscove's medium without addition of fetal bovine serum. Hybrid supernatants were screened for the presence of specific antibodies by solid-phase ELISA and cloned by the limiting dilution technique. Pour clones, named S2, S3, S8, and S10, were selected, recloned several times, and injected intraperitoneally into Balb/c mice for the production of antibody-rich ascitic fluid. The monoclonal antibodies (Mabs), all of IgGl subclass with k light chain, were purified from ascitic fluid by Protein-A chromatography. The specificity of Mabs was controlled by the immunoblotting technique: the Mabs appeared to react only with two plasma proteins, one with a MW of about 70.000 dal tons comigrating with purified PS, and the other with a MW >300.000 da that is likely to be the C4b-binding protein-PS complex. No interaction has been observed with PS-depleted plasma. As tested by a fluid phase radio immunoassay, the binding of Mabs to PS was significantly higher in the presence of EDTA while was totally inhibited in the presence of Ca2+. Scatchard plot analysis of the binding between 125I-PS and Mabs showed that the binding affinity of the antibodies ranged from 108 to 109 1/mol. Each EDTA-dependent Mab was then immobilized on Sepharose 4B-CNBr and used to purify PS from barium precipitation of citrated plasma. The fraction eluted with 2 mmol of CaCl2 from the immunoadsorbent appeared to contain only two proteins when stained with Cocmassie Blue. By immuno blotting, all Mabs reacted with both proteins, one comigrating with purified PS and the other with a MW >300.000. Essentially homogeneous PS, free from the high MW component, was obtained when the barium citrate adsorbate was applied to a DEAE-Sephadex column and the protein peack containing the balk of PS was sussequently applied to the immunoadsorbent and eluted with 2 mmol CaCl2.In summary, we have described an unusual set of EDTA-dependent monoclonal antibodies to PS and their use for the purification of homogeneous protein S from human plasma.

Download Full-text

The SARS-CoV-2 B.1.1.529 Omicron virus causes attenuated infection and disease in mice and hamsters

10.21203/rs.3.rs-1211792/v1 ◽

2021 ◽

Author(s):

Michael Diamond ◽

Peter Halfmann ◽

Tadashi Maemura ◽

Kiyoko Iwatsuki-Horimoto ◽

Shun Iida ◽

...

Keyword(s):

Viral Evolution ◽

Lung Infection ◽

Spike Protein ◽

Rodent Models ◽

Respiratory Tract Disease ◽

Wild Type ◽

Antigenic Sites ◽

Binding Data ◽

Recent Emergence ◽

Tract Disease

Abstract Despite the development and deployment of antibody and vaccine countermeasures, rapidly-spreading SARS-CoV-2 variants with mutations at key antigenic sites in the spike protein jeopardize their efficacy. The recent emergence of B.1.1.529, the Omicron variant1,2, which has more than 30 mutations in the spike protein, has raised concerns for escape from protection by vaccines and therapeutic antibodies. A key test for potential countermeasures against B.1.1.529 is their activity in pre-clinical rodent models of respiratory tract disease. Here, using the collaborative network of the SARS-CoV-2 Assessment of Viral Evolution (SAVE) program of the National Institute of Allergy and Infectious Diseases (NIAID), we evaluated the ability of multiple B.1.1.529 Omicron isolates to cause infection and disease in immunocompetent and human ACE2 (hACE2) expressing mice and hamsters. Despite modeling and binding data suggesting that B.1.1.529 spike can bind more avidly to murine ACE2, we observed attenuation of infection in 129, C57BL/6, and BALB/c mice as compared with previous SARS-CoV-2 variants, with limited weight loss and lower viral burden in the upper and lower respiratory tracts. Although K18-hACE2 transgenic mice sustained infection in the lungs, these animals did not lose weight. In wild-type and hACE2 transgenic hamsters, lung infection, clinical disease, and pathology with B.1.1.529 also were milder compared to historical isolates or other SARS-CoV-2 variants of concern. Overall, experiments from multiple independent laboratories of the SAVE/NIAID network with several different B.1.1.529 isolates demonstrate attenuated lung disease in rodents, which parallels preliminary human clinical data.

Download Full-text

In silico Antibody Mutagenesis for Optimizing its Binding to the Spike Protein of SARS-CoV-2

10.26434/chemrxiv.12967832 ◽

2020 ◽

Author(s):

Binquan Luan ◽

Tien Huynh

Keyword(s):

Clinical Trials ◽

Monoclonal Antibodies ◽

Drug Discovery ◽

In Silico ◽

Spike Protein ◽

Computing Power ◽

Atomic Structures ◽

Protein Mutagenesis ◽

Small Molecule Drugs ◽

Global Pandemic

Coronavirus disease 2019 (COVID-19) is an ongoing global pandemic and there are currently no FDA approved medicines for treatment or prevention. Inspired by promising outcomes for convalescent plasma treatment, developing antibody drugs (biologics) to block SARS-CoV-2 infection has been the focus of drug discovery, along with tremendous efforts in repurposing small-molecule drugs. In the last several months, experimentally, many human neutralizing monoclonal antibodies (mAbs) were successfully extracted from plasma of recovered COVID-19 patients. Currently, several mAbs targeting the SARS-CoV-2's spike protein (Spro) are in clinical trials. With known atomic structures of mAb-Spro complex, it becomes possible to in silico investigate the molecular mechanism of mAb's binding with Spro and design more potent mAbs through protein mutagenesis studies, complementary to existing experimental efforts. Leveraging superb computing power nowadays, we propose a fully automated in silico protocol for quickly identifying possible mutations in a mAb (e.g.~CB6) to enhance its binding affinity with Spro for the design of more efficacious therapeutic mAbs.

Download Full-text

Compounds of Citrus medica and Zingiber officinale for COVID-19 inhibition: in silico evidence for cues from Ayurveda

Future Journal of Pharmaceutical Sciences ◽

10.1186/s43094-020-00171-6 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

M. Haridas ◽

Vijith Sasidhar ◽

Prajeesh Nath ◽

J. Abhithaj ◽

A. Sabu ◽

...

Keyword(s):

In Silico ◽

Active Sites ◽

Protein S ◽

Zingiber Officinale ◽

Nasal Carriage ◽

Docking Studies ◽

Spike Protein ◽

Viral Shedding ◽

In Silico Studies ◽

Citrus Medica

Abstract Background The nasal carriage of SARS-CoV-2 has been reported as the key factor transmitting COVID-19. Interventions that can reduce viral shedding from the nasopharynx could potentially mitigate the severity of the disease and its contagiousness. Herbal formulation of Citrus medica and Zingiber officinale is recommended in an Ayurvedic text as a nasal rinse in the management of contagious fevers. These herbs are also indicated in the management of respiratory illnesses and have been attributed with activity against pathogenic organisms in other texts. Molecular docking studies of the phytocompounds of C. medica and Z. officinale were done to find out whether these compounds could inhibit the receptor binding of SARS-CoV-2 spike protein (S protein) as well as the angiotensin-converting enzyme 2 (ACE-2), as evidenced from their docking into binding/active sites. Results The proteins of SARS-CoV-2, essential for its entry into human cells and highly expressed in the goblet and ciliated cells of nasal epithelium, play a significant role in contagiousness of the virus. Docking studies indicated that the specific compounds present in C. medica and Z. officinale have significant affinity in silico to spike protein of virus and ACE-2 receptor in the host. Conclusion In silico studies suggest that the phytochemical compounds in C. medica and Z. officinale may have good potential in reducing viral load and shedding of SARS-CoV-2 in the nasal passages. Further studies are recommended to test its efficacy in humans for mitigating the transmission of COVID-19.

Download Full-text

Sea Urchin Pigments as Potential Therapeutic Agents Against the Spike Protein of SARS-CoV-2 Based on in Silico Analysis

10.26434/chemrxiv.12568595.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Elena Susana Barbieri ◽

Tamara Rubilar ◽

Ayelén Gázquez ◽

Marisa Avaro ◽

Erina Noé Seiler ◽

...

Keyword(s):

Sea Urchin ◽

In Silico ◽

In Silico Analysis ◽

Protein S ◽

Host Cells ◽

Spike Protein ◽

Therapeutic Drug ◽

The Novel ◽

Novel Coronavirus ◽

Silico Analysis

Several studies have been published regarding the interaction between the spike protein of the novel coronavirus SARS-CoV-2 and ACE2 receptor in the host cells. In the presente work, we evaluated the in silico properties of two sea urchin pigments, Echinochrome A (EchA) and Spinochromes (SpinA) against the Spike protein (S) towards finding a potential therapeutic drug against the disease caused by the novel coronavirus (COVID-19). The best ensemble docking pose of EchaA and SpinA showed a binding affinity of -5.9 and -6.7 kcal mol-1, respectively. The linked aminoacids (T505, G496 and Y449 for EchA and Y449, Q493 and G496 for SpinA) are in positions involved in ACE2 binding in both RBDs frim SARS-CoV and SARS-CoV-2 suggesting that EchA and SpinA may interact with Spike proteins drom both viruses. The results suggest that these pigments could act as inhibitors of S protein, pointing them as antiviral drugs for SARS-CoV-2.

Download Full-text

Characterizing flexibility and mobility in the natural mutations of the SARS-CoV-2 spikes

10.1101/2021.09.14.460264 ◽

2021 ◽

Author(s):

James Panayis ◽

Navodya S. Römer ◽

Dom Bellini ◽

A. Katrine Wallis ◽

Rudolf A. Römer

Keyword(s):

In Silico ◽

Geometric Modeling ◽

Protein Structures ◽

Data Bank ◽

Spike Protein ◽

Wild Type ◽

Drug Molecules ◽

Elastic Modes ◽

Novel Drug ◽

Combining Methods

AbstractWe use in silico modelling of the SARS-CoV-2 spike protein and its mutations, as deposited on the Protein Data Bank (PDB), to ascertain their dynamics, flexibility and rigidity. Identifying the precise nature of the dynamics for the spike proteins enables, in principle, the use of further in silico design methods to quickly screen for existing and novel drug molecules that might prohibit the natural protein dynamics. We employ a recent protein flexibility modeling approach, combining methods for deconstructing a protein structure into a network of rigid and flexible units with a method that explores the elastic modes of motion of this network, and a geometric modeling of flexible motion. Our results thus far indicate that the overall motion of wild-type and mutated spike protein structures remains largely the same.

Download Full-text