For the infamous SARS-CoV-2 spike protein to bind to human cells, it must initially attach itself to carbohydrate molecules known as heparan sulphate proteoglycans. Studying this interaction is the basis of a project led by Rebecca Wade of Heidelberg Institute for Theoretical Studies (HITS) and Heidelberg University, which will also investigate the potential antiviral properties of heparin, a drug first discovered over 100 years ago.
Rebecca Wade is the head of a computational research group that investigates how proteins interact with other molecules. They have developed computational methods that they apply to many major research questions in the areas of structure-based drug design and protein engineering.
Although the group has previously done work related to viruses and anti-infectives, coronaviruses were not something they had previously explored. “If you had asked me a year ago whether we had considered doing any work in this area, I would have told you that I had not even thought about it once!” she says. “However, when it was clear how serious the pandemic was, we, like many people, asked ourselves what we could do to help.”
Rebecca Wade and Giulia Paiardi
Having investigated the influenza virus in the past, research into the SARS-CoV-19 virus is not entirely removed from the experience of Wade’s group at HITS. As well as carrying out some work on structure-based drug design, for which they are now awaiting experimental data to provide validation, the group has also set out to investigate the role of glycans in the spike protein system. Giulia Paiardi, a visiting scientist in Wade’s group from the University of Brescia, Italy, has combined her expertise in modelling glycans with Wade’s experience in simulating proteins to provide the basis for a PRACE project entitled “DyCoVin – Interactions and dynamics of SARS-CoV-2 spike-heparin complex”. PRACE awarded the project with 3 520 000 core hours on Marconi100, hosted by CINECA in Italy. Before joining Wade’s group, Paiardi had been studying the HIV virus under the supervision of Prof. Marco Rusnati in Brescia, specifically the mechanism it uses to interact with host cells. “The HIV virus, as well as a number of other viruses, use heparan sulphate proteoglycans (HSPGs) as the first attachment site,” explains Paiardi. “Many papers are being written on how the spike protein interacts with these HSPGs, but most of these are based on experimental work. None of them explain the mechanistic effect of the HSPGs on the spike protein, and so the idea of this project is to better understand this interaction.”
As well as this, the project is also exploring the anti-infective properties of heparin on SARS-CoV-2. Previous experimental work has shown that heparin can effectively prevent the coronavirus strain HSR1 from binding. Heparin, a very old drug discovered over 100 years ago in 1916, is an anticoagulant, preventing the formation of blood clots and growth of existing clots. It is used in the treatment of lung diseases such as pulmonary fibrosis, bronchial asthma and asthma-induced airway hypersensitivity, and recent clinical trials suggest that inhaled heparin for lung diseases is beneficial and safe.
Close-up view of the spike glycoprotein-heparin interaction. The surface of the spike glycoprotein is shown coloured by its electrostatic properties with red indicating negatively charged and blue indicating positively charged regions. The N-glycans of the spike glycoprotein are shown by grey spheres. Heparin is shown coloured by element (carbon in yellow, oxygen in red, nitrogen in blue, hydrogen in white). Heparin is strongly anionic and therefore it mainly binds to positive regions of the spike glycoprotein.
The overall objective of the project is to pinpoint the role of HSPGs in SARS-CoV-2 spike infection using realistic computer simulations. This knowledge will allow for the characterisation of the structure and dynamics of putative binding patches for heparin-like compounds on the spike receptor, which needs to adopt the open form to bind ACE2. For that reason, the team aims to stabilise the receptor using different heparin chains to shield binding sites and to decrease the flexibility of the spike. “Thanks to the resources provided by PRACE, we have been able to investigate HSPGs and heparin and how they both interact with the spike protein and with each other,” says Paiardi. “Although heparin itself would probably not be used as an antiviral due to its anticoagulant properties, we hope that by understanding its antiviral mechanisms we might be able to suggest some modifications to it that would make it more suitable for therapeutic use.”
Schematic illustration of the DyCoVin PRACE project. (A) Recent findings suggest that the process of SARS-CoV-2 infection depends on the interaction of the mechanism by which heparin could hinder the spike/HSPG interaction spike protein with both the glycan chains of the heparan sulphate proteoglycans (HSPGs) and the angiotensin Converting enzyme 2 (ACE2) receptor on the human host cell and that heparin might interfere with these interactions. In the DyCoVin project, we are studying the mechanism by which heparin could hinder the spike/HSPG interaction. (B) View of the atomic-detail model of one of the simulated systems consisting of the spike glycoprotein trimer (grey), with one monomer in an open conformation suitable for binding ACE2, interacting with 3 heparin chains (pink), each composed of 31 monosaccharides. (C) The use of high-performance computers (HPC) enables such systems to be simulated about 25 times faster than on a workstation and 5 times faster than on a typical in-house compute-cluster.
The allocation provided by PRACE has allowed Paiardi and Wade to look at five different models of the spike protein, both with closed and open conformations. They have also been able to improve the stochastic evaluation of their data by carrying out four different independent replicas for each model. Although Wade’s group do have some in-house computing resources at their disposal, the spike protein’s size along with the long-chain molecule of heparin meant that larger computational power was needed to fully investigate the matter. Having finished the simulations, the team is now finalising the analysis of the data they have produced and hoping to publish a paper shortly. “At the end of the project, we will have a better understanding of heparin’s possible antiviral properties against SARS-CoV-2, as well as a basis for coming up with other related molecules that can be used against it,” says Wade. The first results on the binding of heparin to the spike glycoprotein are available as a preprint.
The researchers believe that the impact of this approach for treating the viral infection could be high because the FDA has already approved heparin for therapeutics use. Aerosol drug administration could provide the advantage of directly delivering heparin to the site of the SARS-CoV-2 infection and thereby stopping the interaction between the virus and the receptor.
G. Paiardi, St. Richter, M. Rusnati, R.C. Wade: Mechanism of inhibition of SARS-CoV-2 infection by the interaction of the spike glycoprotein with heparin (2021). Preprint
3.52 million core hours on Marconi100, hosted by CINECA in Italy