Periodic Reporting for period 1 - MAT4COVID (Interaction of SARS-CoV-2 virus with materials: a multi computational simulation study.)
Período documentado: 2021-10-01 hasta 2023-09-30
The SARS-CoV-2 virus can remain infectious over horus or even days over certain surfaces, whereas it is rapidly inactivated over other surfaces. The underlying reasons for this observed behaviour are unknown. The goal of this project was to study the interaction between the SARS-CoV-2 virus and surfaces of different materials with atomistic detail. The methods used were advanced computational chemistry methods like Molecular Dynamics simulation that utilize the known molecular structure of the virus. The objective of the simulations was to show the atomistic and molecular scale details of the interactions between the most external feature of the virus (the Spike protein) and different materials. The specific objectives were (1) Perform atomistic simulations of the interaction between the Spike protein of the virus and common materials such as metals (which could be virucidal) and common plastics (which are susceptible to spread the virus), (2) Classify the materials based on the interaction identified between these materials and the S protein. The results show which factors stabilize the virus on the surface of materials or which factors may affect/destroy/modify the structure of the virus or its components during the interaction with materials.This information would be critical to identify which common materials may contribute to spread the virus and also how to design a new generation of materials with anti viral activity.
To achieve the main goal we studied different systems. Indeed, the fellowship was productive at a period of 11 months with 2 journal publications and 4 presentations at international workshops and conferences. The studied systems were the following:
1. Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface
Polystyrene is a commonly used plastic found in electronics, toys, and many other common objects.Our results show that the main driving forces for the adsorption of the S protein over polystyrene were hydrophobic and π–π interactions with S amino acids and glycans.
These results were published in the following article in Open Access format:
Mehdi Sahihi and Jordi Faraudo, "Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface" J. Chem. Inf. Model. 2022, 62, 16, 3814–3824. (IF=6.16)
2. Computer Simulation of the interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals
Coinage metals like silver, gold and copper are historically known as materials with anti-infective properties; but the mechanism behind these properties is not yet clear. Our results revealed that spike protein is adsorbed onto the surface of these metals, being the Cu metal with the highest interaction with the spike and Au, the metal which induces bigger structural changes in the spike.
The scientific article describing these results is currently under review in the journal Langmuir (2nd round of revisions, minor changes).
The article was also posted as preprint at BioRxive: Mehdi Saihi and Jordi Faraudo "Computer Simulation of the interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals " https://doi.org/10.1101/2022.07.28.501856.
The project results were also presented at the following international conferences and workshops:
-Oral presentation by Jordi Faraudo at NanoSpain2022 conference, May 17-22, 2022. Madrid (Spain) https://www.nanospainconf.org/2022/
-Oral presentation by Mehdi Sahihi at Regional Biophysics Conference; RBC2022 (Pécs, Hungary, August 22-26, 2022). https://www.rbc2022.hu/
-Poster presentation by Mehdi Sahihi at CECAM workshop (Present and Future of Hybrid Quantum Chemical and Molecular Mechanical Simulations June 20, 2022 - June 23, 2022, CECAM-IT-SIMUL, Politecnico di Milano, Italy) .https://www.cecam.org/workshop-details/1152
-Oral presentation by Jordi Faraudo at the EMLG/JMLG European/Japanese Molecular Liquids conference, September 12-16, 2022 (Barcelona, Spain) https://www.emlg2022.com/2022/
1. Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface
Polystyrene is a commonly used plastic found in electronics, toys, and many other common objects.Our results show that the main driving forces for the adsorption of the S protein over polystyrene were hydrophobic and π–π interactions with S amino acids and glycans.
These results were published in the following article in Open Access format:
Mehdi Sahihi and Jordi Faraudo, "Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface" J. Chem. Inf. Model. 2022, 62, 16, 3814–3824. (IF=6.16)
2. Computer Simulation of the interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals
Coinage metals like silver, gold and copper are historically known as materials with anti-infective properties; but the mechanism behind these properties is not yet clear. Our results revealed that spike protein is adsorbed onto the surface of these metals, being the Cu metal with the highest interaction with the spike and Au, the metal which induces bigger structural changes in the spike.
The scientific article describing these results is currently under review in the journal Langmuir (2nd round of revisions, minor changes).
The article was also posted as preprint at BioRxive: Mehdi Saihi and Jordi Faraudo "Computer Simulation of the interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals " https://doi.org/10.1101/2022.07.28.501856.
The project results were also presented at the following international conferences and workshops:
-Oral presentation by Jordi Faraudo at NanoSpain2022 conference, May 17-22, 2022. Madrid (Spain) https://www.nanospainconf.org/2022/
-Oral presentation by Mehdi Sahihi at Regional Biophysics Conference; RBC2022 (Pécs, Hungary, August 22-26, 2022). https://www.rbc2022.hu/
-Poster presentation by Mehdi Sahihi at CECAM workshop (Present and Future of Hybrid Quantum Chemical and Molecular Mechanical Simulations June 20, 2022 - June 23, 2022, CECAM-IT-SIMUL, Politecnico di Milano, Italy) .https://www.cecam.org/workshop-details/1152
-Oral presentation by Jordi Faraudo at the EMLG/JMLG European/Japanese Molecular Liquids conference, September 12-16, 2022 (Barcelona, Spain) https://www.emlg2022.com/2022/
The lack of fundamental, physico-chemical knowledge of the virus-surface interaction was in contrast with the wealth of atomistically detailed information available about the virus and its molecular interactions. So far, these advanced atomistic simulation studies have focused in elucidating the molecular interactions of interest for drug or vaccine development but have ignored questions related to disease propagation such as the virus interaction with materials.
Therefore, the vision of this research project was to use advanced computational chemistry tools to predict the interaction of SARS-CoV-2 with surfaces and determine the impact of the different properties of the surfaces in their interactions with the virus and all atom MD simulation technique was used in this regard. The study that we proposed in this project focused on an essential aspect of the pandemic not being studied by other research groups. It involved a multi- and interdisciplinary study by bringing together concepts and tools from the fields of chemistry, molecular biology, physics and material science.
In the case of the studied systems in this project, which had several millions of atoms, we employed GROMACS package which has been optimised for large system simulations in supercomputing facilities.
For the calculation of interactions in the MD simulations, our method of choice was the CHARMM36 classical force field, since it has a consistent parametrization for biomolecules, small molecules, organic polymers and many inorganic materials. Moreover, for the first time, we compared the affinity of the up and down conformations of the spike protein for the interaction with the surface of materials. On the other hand, fully glycosylated form of the S protein was considered in our calculation to investigate the effect of glycan groups on the stability of the S protein-material complexes.
It was a new strategy to design new anti-viral materials and breakdown the transmission chain of COVID-19. Its results could be of great interest for the design of measures to overcome and control COVID-19 disease. The results promise strong potential for dissemination, communication and exploitation impacting across academic and private/public sector groups in Spain, the EU and worldwide.
Results triggered new debates and analytical strategies within hitherto isolated fields of research, impacting new interdisciplinary perspectives and comparative approaches to the studies of SARS-CoV-2 virus and the recent pandemic situation.
In addition of the above mentioned open access publications and presentations, we also organised several meeting with other research groups around EU and one industry in the field (Solesis), emphasising the role of investigation of interactions between viruses and materials to design new anti-viral materials. It provided an opportunity for different communities and specialists to come together, in particular boosting connections theoretical and experimental researchers in physics, chemistry and biology.
Due to the recent COVID-19 pandemic situation, the results of the present project could be used by companies to make new materials with anti-viral properties and chemical companies to produce chemicals that can be used to shorten the life time of the virus on the surfaces.
Finally, we hope the results of this study might pave the way for developing a new generation of virucidal materials/coatings based on metals.
Therefore, the vision of this research project was to use advanced computational chemistry tools to predict the interaction of SARS-CoV-2 with surfaces and determine the impact of the different properties of the surfaces in their interactions with the virus and all atom MD simulation technique was used in this regard. The study that we proposed in this project focused on an essential aspect of the pandemic not being studied by other research groups. It involved a multi- and interdisciplinary study by bringing together concepts and tools from the fields of chemistry, molecular biology, physics and material science.
In the case of the studied systems in this project, which had several millions of atoms, we employed GROMACS package which has been optimised for large system simulations in supercomputing facilities.
For the calculation of interactions in the MD simulations, our method of choice was the CHARMM36 classical force field, since it has a consistent parametrization for biomolecules, small molecules, organic polymers and many inorganic materials. Moreover, for the first time, we compared the affinity of the up and down conformations of the spike protein for the interaction with the surface of materials. On the other hand, fully glycosylated form of the S protein was considered in our calculation to investigate the effect of glycan groups on the stability of the S protein-material complexes.
It was a new strategy to design new anti-viral materials and breakdown the transmission chain of COVID-19. Its results could be of great interest for the design of measures to overcome and control COVID-19 disease. The results promise strong potential for dissemination, communication and exploitation impacting across academic and private/public sector groups in Spain, the EU and worldwide.
Results triggered new debates and analytical strategies within hitherto isolated fields of research, impacting new interdisciplinary perspectives and comparative approaches to the studies of SARS-CoV-2 virus and the recent pandemic situation.
In addition of the above mentioned open access publications and presentations, we also organised several meeting with other research groups around EU and one industry in the field (Solesis), emphasising the role of investigation of interactions between viruses and materials to design new anti-viral materials. It provided an opportunity for different communities and specialists to come together, in particular boosting connections theoretical and experimental researchers in physics, chemistry and biology.
Due to the recent COVID-19 pandemic situation, the results of the present project could be used by companies to make new materials with anti-viral properties and chemical companies to produce chemicals that can be used to shorten the life time of the virus on the surfaces.
Finally, we hope the results of this study might pave the way for developing a new generation of virucidal materials/coatings based on metals.