Scientists from St Petersburg University are investigating a peptide that could potentially block coronavirus

Complex of spike protein and ACE2 according to x-ray diffraction data (PDB ID 6M0J). The ACE2-binding domain of the spike protein is grey; ACE2 is red; and the ACE2 fragment corresponding to SBP1 is blue.

To enter the cells of the human body, coronaviruses, including SARS-CoV-2, use the so-called ‘spikes’. With the help of these spikes, formed by certain specific protein on the surface of the virus, the virus docks to a human cell. To this end, virus uses one of the many types of receptor proteins on the surface of a human cell. In the case of SARS-CoV-2, it is angiotensin-converting enzyme 2 (ACE2).

At the end of March, Chinese scientists published the crystal structure of this enzyme in complex with the receptor-binding domain of the viral spike protein. This allowed researchers from Massachusetts Institute of Technology (USA) to identify the ACE2 fragment which is involved in the virus binding. This is a peptide consisting of 23 amino acid residues (IEEQAKTFLDKFNHEAEDLFYQS). According to the developers of the peptide, it should block the binding site of the spike protein, thereby abrogating the binding of the virus to ACE2 and preventing its entry into the cells of the human body. With this idea in mind, the authors named their peptide ‘spike-binding peptide 1’ (SBP1). Recently this peptide became the subject of the investigation by the scientists from St Petersburg University together with colleagues from Tsinghua University and the Institute of Cytology of the Russian Academy of Sciences.

The idea of such a peptide became possible only after the structure of the ACE2 complex with the coronavirus spike protein has been reported. Only by seeing the structure of the complex between the two proteins, it is possible to identify a small fragment within one protein that could bind to the other protein.

Olga Rogacheva, Ph.D., researcher at the Department of Biochemistry and the Laboratory of Biomolecular NMR in the Institute of Translational Biomedicine, St Petersburg University

When designing peptides, it is not always possible to predict their physico-chemical properties. Therefore, it often turns out that the proposed peptide can bind non-specifically to other human proteins or lipids of cell membranes; that is, do something other than intended in the human body. ‘A peptide with such properties is at best useless, since it is unlikely to reach its target. Hydrophobic peptides tend to behave in such a way. SBP1 is not hydrophobic. But we will certainly test it for non-specific binding using a battery of bait proteins. It is unlikely that SBP1 would fit (like a key to a lock) to a receptor other than ACE2, thereby triggering some unexpected processes in the cell. Nevertheless, it cannot be completely ruled out. These effects are usually apparent at the stages of cell-line experiments and animal experiments,’ said Olga Rogacheva.

The studies are being carried out by researchers from the Laboratory of Biomolecular NMR at St Petersburg State University: Olga Rogacheva; Dmitrii Luzik; and Irina Tyuryaeva. NMR experiments are conducted at the Resource Centre for Magnetic Resonance in the Research Park of St Petersburg State University, while cell line experiments are pursued in the Institute of Cytology of the Russian Academy of Sciences. Some of the computer modelling is done in the laboratory of Prof. Yi Xue at Tsinghua University in China as a part of the international collaborative effort. The project is led by the head of the Bio-NMR Laboratory Prof. Nikolai Skrynnikov.

 ‘Our laboratory already has experience with protein-peptide complexes, so we are well-equipped to solve such problems. First, we study the binding of a peptide to its protein target in vitro, using NMR spectroscopy, as well as in silico, using Molecular Dynamics  modelling. The main objective of these experiments is to prove that the peptide binds to the desired site on the surface of the protein, and that the binding is sufficiently strong. Also, at this stage, we test the peptide’s propensity to interact non-specifically with other proteins. If the peptide passes these tests, we move to studies on cell cultures. Unfortunately, from the entire range of methods, only computer simulations are currently available to us. At present, work in the laboratory is suspended due to the lockdown,’ said Olga Rogacheva.

At this stage, the researchers launched Molecular Dynamics simulations seeking to model SBP1 binding to the ACE2 receptor; they have also ordered everything necessary for in vitro experiments.

If the SBP1 virus-blocking properties are confirmed and no off-target binding is detected, this peptide can potentially be used to create a medicine for COVID-19. Moreover, according to scientists, possible future mutations of the virus should not undermine its efficiency. ‘Blocking viral proteins is not the most popular strategy because viruses are constantly mutating. At some point, the drug molecule may stop binding to the viral protein. However, SBP1 is cut out of human ACE2. If due to certain mutations the spike protein fails to bind SBP1, it will also likely fail to bind ACE2. Thus, such mutated SARS-CoV-2 strain will no longer be a danger to humans. On the other hand, if one day a new coronavirus emerges that also uses ACE2 to enter the cells, SBP1 will also be effective against it,’ noted Olga Rogacheva.

In most cases, coronaviruses enter the human body through the respiratory system. However, preliminary evidence suggests the ACE2 gene is only weakly expressed in the lungs. ‘This might be the reason why most people are not susceptible to SARS-CoV-2. If we look more closely at the parts of the respiratory system, the highest level of expression of the ACE2 gene is found in the nasal cavity, and the lowest in the pulmonary alveoli. This means that most patients will only suffer from a runny nose, as SARS-CoV-2 simply cannot replicate in their lungs. However, severe cases of COVID-19 indicate that, under certain conditions, the expression of ACE2 gene in the lungs jumps to a high level. In such cases, the proliferation of SARS-CoV-2 in the lungs can cause pneumonia. If the immune system ‘overreacts’ to the viral assault, this can lead to the acute respiratory distress syndrome, which can be lethal. Blocking the interaction of the SARS-CoV-2 with ACE2 spike protein at the early stages of the disease could protect such patients and reduce their vulnerability to the virus, preventing the severe form of the disease,’ explained Olga Rogacheva.

Since the virus invades the respiratory system and does not enter the bloodstream (until possibly very late in the game), scientists favour inhalational or intranasal delivery for perspective SBP1 therapy.

Whether SBP1 is beneficial at the stage of acute respiratory distress syndrome remains to be seen. In my opinion, regulators of immune response should be the key to treat this condition.

Olga Rogacheva, Ph.D., researcher at the Department of Biochemistry and the Laboratory of Biomolecular NMR in the Institute of Translational Biomedicine, St Petersburg University

In Olga Rogacheva’s opinion, SBP1 has a potential to become a medicine, but it is too early to speak about it with a 100% confidence. Nevertheless, the ongoing clinical trials of the recombinant non-membrane form of ACE2 to treat COVID-19 offer some grounds for optimism. ‘SBP1, according to its originators, is only slightly inferior to ACE2 in binding the spike protein. At the same time, unlike ACE2, it should not become involved in any unrelated process in the human body. Ideally, if all of this is confirmed, SBP1 has a chance of reaching clinical trials as an inexpensive and safe medication against all coronaviruses that use ACE2 to enter the cell. Unfortunately, in reality, only few of all promising molecules manage to complete the journey from the laboratory bench to the pharmacy shelf, and this journey takes a lot of time. Our experiments should tell us whether it is worthwhile to initiate SBP1 studies on animals. At this moment, there is a real need for an answer,’ concluded Olga Rogacheva.