Receptor-binding Domains of SARS-CoV-2, LT5578, Cited by Nature

A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2, LT5578, was cited by Nature (Potently neutralizing and protective human antibodies against SARS-CoV-2, volume 584, pages443–449(2020)). This peptide was synthesized in 6 days. This is part of the receptor-binding domain (RBD). It is a critical determinant of virus-receptor interaction and thus of viral host range and tropism. The RBD also includes important viral-neutralizing epitopes (21–23), and it may be sufficient to raise a protective antibody response in inoculated animals.

Two potently neutralizing monoclonal antibodies, COV2-2196 and COV2-2130, which recognize non-overlapping sites, bound simultaneously to the S protein and neutralized wild-type SARS-CoV-2 virus in a synergistic manner.

Lately, a recombinant SARS-CoV-2 Spike S (S1+S2) Protein was produced by LifeTein. The amino acid sequences of recombinant protein was derived from (Q14 – Q1208) of accession# YP009724390.1. The SARS-CoV-2 spike (S) protein is composed of two subunits; the S1 subunit contains a receptor-binding domain that engages with the host cell receptor angiotensin-converting enzyme 2 and the S2 subunit mediates fusion between the viral and host cell membranes. The S RBD protein plays key parts in the induction of neutralizing-antibody and T-cell responses, as well as protective immunity, during infection with SARS-CoV-2 (2019-nCoV) as in recent COVID-19 outbreak.

SARS-CoV-2 receptor binding domain structure
Schematic of the SARS-CoV-2 structure; the illustration of the virus is available at doi:

Aureocin A53 is an antimicrobial peptide produced by Staphylococcus aureus A53

LifeTein successfully synthesized Aureocin A53, a highly cationic 51-residue peptide containing ten lysine and five tryptophan residues,   Formyl-MSWLNFLKYIAKYGKKAVSAAWKYKGKVLEWLNVGPTLEWVWQKLKKIAGL, using solid-phase peptide synthesis approach. A53 is a Class II bacteriocins. It was originally isolated from Staphylococcus aureus A53 and is active against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus. The mode of action was proposed as insertion into lipid bilayer and consequent membrane leakage. The solid-phase peptide synthesis provide an inexpensive alternative to isolation from bacteria culture or recombinant expression.

Aureocin A53 Peptide

Aviptadil Fast-Tracked for Respiratory Distress in COVID-19

It was found that RLF-100 (Aviptadil) is associated with rapid respiratory failure recovery among COVID-19 Patients. The clinical findings may be based on evidence that VIP inhibits the replication of the SARS-CoV-2 virus in human lung cells and immune cells (monocytes). No other antiviral agent has demonstrated rapid recovery from viral infection and demonstrated laboratory inhibition of viral replication. It is a patented formulation of aviptadil (synthetic human Vasoactive Intestinal Polypeptide, VIP), which has been granted FDA fast track designation, FDA emergency use IND authorization, and an expanded access protocol. Aviptadil is an injectable formulation of the vasoactive intestinal polypeptide (VIP) in combination with the adrenergic drug phentolamine.

Aviptadil (Senatek), Vasoactive intestinal polypeptide

Peptide Library: SARS-CoV-2 Receptor Binding Domains

Coronavirus receptor binding domain. The key receptor binding domain (residues 319-541) is highlighted in yellow. Variable amino acid residues between SARS-CoV-2 and SARS-CoV are highlighted in cyan. Tyr 489, Asn 487, Gln 493, Tyr 505 are important for ACE2 binding.

LifeTein can help in your research with custom peptide synthesis of the following specific proteins: SARS-CoV-2 Receptor Binding Domains, SARS-CoV-2 Nucleocapsid Fragments, T-cell and B-cell Epitopes of SARS-CoV-2, Fusion Inhibitors Targeting HR1 Domain of the SARS-CoV-2 Spike Proteins, Inhibitors of SARS-CoV-2 Mpro/3CLpro/C30 Endopeptidase, ACE2 Inhibitors and Substrates, and AT2 Receptor Agonists and Antagonists.

Pool of 22 peptides derived from a peptide design (15mers with 5 aa overlap) through the receptor binding domain of S1 protein.

Modifications: N-Terminal: Biotin Labeling

Amount: 1mg per peptide

Purity: 95%

Delivery Format: Freeze dried powder

Application(s): Antibody screening, T-cell assays, Immune monitoring, Antigen specific T-cell stimulation, Cellular immune response

Indication(s)/Topic(s): Covid-19, Infection, Respiratory infection

Delivery Time: 2 weeks

SARS-CoV-2 Receptor Binding Domains Overlapping Peptide Pools:


The Cationic Host Defense Peptides Could Be Used To Kill Enveloped Novel Coronavirus SARS-CoV-2

Direct antimicrobial mechanisms of cationic host defense peptides

The cationic host defense peptides (CHDP), also known as antimicrobial peptides, could be used to kill enveloped viruses such as the 2019 Novel Coronavirus SARS-CoV-2. The peptides have the potential to destabilize the viral envelope on contact, damaging the virions and inhibiting infectivity. The specific antiviral peptide may bind to cellular receptors involved in viral infection or peptide-mediated aggregation of viral particles. The antiviral peptides could create an ‘antiviral shield’ at mucosal surfaces and prevent replication and spread of the Coronavirus if upregulated after the initial infection.

During pandemics, where there is insufficient time to produce vaccines (such as the outbreak of respiratory illness Covid-19 first detected in Wuhan, China), the cationic host defense peptides could be the first-line antiviral treatments.

Some of the antimicrobial peptides are the human cathelicidin LL-37 and β-defensins. Cathelicidins are immunomodulatory antimicrobials with an important role in the regulation of the inflammatory response. The only human cathelicidin, LL-37, is the most well-studied peptide in this family. LL-37 is an α-helical peptide. While defensins have a common β-sheet core stabilized with three disulfide bridges between six conserved cysteine residues.

Direct antimicrobial mechanisms of cationic host defense peptides can be mediated by membrane translocation of the peptides followed by binding to intracellular targets such as nucleic acids and/or proteins to kill bacteria. Proline-rich antimicrobial peptides use inner membrane transporters as Trojan horses to gain entry and bind to intracellular targets such as nucleic acids or nascent proteins. And subsequently affect cell processes such as replication, transcription, translation, protein folding, and cell wall synthesis.

At this stage, only a few peptide-derived treatments have made it to market such as PAC-113, a histatin analog, and dalbavancin, a semisynthetic lipoglycopeptide.

Despite the limited understanding of structure-function relationships, the potential of peptide-based therapies remains a promising new clinical direction for the Coronavirus.

2019-nCoV Coronavirus Receptor -Binding Motif Directly Contacts ACE2 Receptor

2019-nCoV Coronavirus Receptor -Binding Motif Directly Contacts ACE2 Receptor
2019-nCoV Coronavirus Receptor -Binding Motif

The extensive structural analyses have revealed that interactions between SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV.

Studies showed that the sequence of 2019-nCoV coronavirus RBD, including its receptor -binding motif (RBM) that directly contacts ACE2 and uses ACE2 as its receptor with much higher affinity (10-20 times higher!) than SARS.

Several critical residues in 2019-nCoV RBM may provide favorable interactions with human ACE2 such as Gln493 and Asn501.

A total of nine cysteine residues are found in the RBD, six of which forming three pairs of disulfide bonds. Among these three pairs, two are in the core (Cys336-Cys361 and Cys379-Cys432) to help stabilize the β sheet structure while the remaining one (Cys480-Cys488) connects loops in the distal end of the RBM.

LifeTein synthesized a 69 amino acid spike glycoprotein in 6 days

Coronavirus SARS-CoV-2
Coronavirus SARS-CoV-2

2019 Novel Coronavirus SARS-CoV-2 is a virus identified as the cause of an outbreak of respiratory illness Covid-19 first detected in Wuhan, China.

To help expedite Covid-19 research, LifeTein synthesized a 69 amino acid spike glycoprotein with one disulfide bond in 6 days. This effort is a partnership with a biotech company for drug development.

Cyclic peptides as broad-spectrum antiviral agents

Cyclic peptides as broad-spectrum antiviral agent

Cyclic peptides as broad-spectrum antiviral agents

Antiviral drugs and vaccines are the most powerful tools to combat viral diseases. Most drugs and vaccines only target a single virus. However, the broad-spectrum antivirals can be used for rapid management of new or drug-resistant viral strains. Cyclized peptides and peptide analogs are excellent examples of broad-spectrum antivirals.

An artificial peptide molecule was found to neutralize a broad range of group 1 influenza A viruses, including H5N1. The peptide design was based on complementarity determining region (CDR) loops have been reported for other viral targets. The optimized peptides bind to the highly conserved stem epitope and block the low pH-induced conformational rearrangements associated with membrane fusion.

These peptidic compounds and their advantageous biological properties should accelerate development of novel small molecule and peptide-based therapeutics against influenza virus.

The linear peptide is Suc-SQLRSLEYFEWLSQ-NH2. Three cyclization strategies were used: head to tail, side chain to side chain and side chain to tail. An ornithine (Orn) side chain was fused with the carboxyl terminus of β-alanine for lactam formation.

Check here for more details: Potent peptidic fusion inhibitors of influenza virus, Science 28 Sep 2017, DOI: 10.1126/science.aan0516

Lately, more broad-spectrum antiviral agents were found to target viruses. It was found that 55 compounds can target eight different RNA and DNA viruses. Dalbavancin is a novel lipo-glycopeptide antibiotic. The lipoglycopeptide disrupts bacterial cell wall formation by binding to
the terminal d-alanyl-d-alanine peptidoglycan sequence in Gram-positive bacteria in a linear, concentration-dependent manner. The dalbavancin has effects on echovirus 1, ezetimibe against HIV1 and Zika virus.

More details:

Tips for Working with Magnetic Beads

Magnetic beads

Protein purification with magnetic beads is an excellent choice for high-throughput microscale purification, pull-down/CoIP, and protein/protein or protein/DNA interaction studies. Magnetic beads can be coated with specific affinity ligands for antigens, antibodies, proteins, or nucleic acids.

Magnetic beads have a defined diameter and non-porous. There are no hidden surfaces for the molecules to stick to. So the background, purification, and washing steps are all reduced. Separation using magnetic beads is the quickest, cleanest, and most efficient technique out of all the bead separation methods using agarose, sepharose, or silica beads.

Here are some tips for new users.

  1. Resuspend your beads thoroughly to ensure consistency between the aliquots

Magnetic beads need to have enough magnetic contents to allow simple pull-down by a magnet. Our Magnetic Beads are nano-superparamagnetic beads covalently coated with highly functional groups. The increased beads surface area results in increased binding capacity and improved dispersion. Magnetic beads are massive particles comprised of iron oxide, so they sediment over time. It is crucial to vortex and thoroughly resuspend the magnetic beads before use to redisperse the beads.

2. Wash your beads to reduce non-specific binding

Increase the number of washing steps helps to reduce non-specific binding to the beads. When washing the magnetic beads with either ethanol or recommended wash buffer, use enough wash solution to cover the pellet. Understand the functional groups of your beads
Our beads covalently coated with maleimide, primary amine, NHS, carboxylic acid, purified streptavidin, protein A, reduced glutathione, nickel-charged nitrilotriacetic acid, or groups for DNA/RNA purification. The coatings, buffer conditions, and functional groups will affect the properties of the beads. It is essential to understand the necessary information about the beads to handle them better.

3. Capture the beads to ensure all beads are recovered

Generally, the magnetic beads are attracted to the magnet and form a pellet within a minute. Prolong the attraction of the magnetic beads to the magnet helps.

4. Do not disturb the bead pellet when removing the wash solution

Angle the pipette tip when removing the wash solution or supernatant. Do not let the tip touch the pellet of magnetic beads.

New Publication: Cell Cited LifeTein Biotinylated Peptide Products

Pull-down assay using biotinylated peptides

Giantin, a novel conserved Golgi membrane protein, is a disulfide-linked homodimer. It was found that BFA-induced Golgi disorganization is associated with the monomerization of giantin.

The pull-down experiment was performed. The control peptide biotin-GHGTGSTGSGSMLRTLLRRRL synthesized by LifeTein was incubated with lysate and Dynabeads, as well as the lysate incubated with Dynabeads only served as a control. Dynabeads carrying MGAT1 peptide were able to pull-down giantin from the lysate of HeLa cells, however, giantin was not detected in the pull-down fraction from the lysate exposed to the Dynabeads or in combination with control peptide. It is logical to hypothesize that the MGAT1 binding domain of giantin lies within its N-terminal non-coiled-coil area.

The Dynabeads function similarly to LifeTein magnetic beads:

Cells 2019, 8(12), 1631;