 So, go ahead, Elgar. Thank you, Uriel. I just want to ask you if you see my screen, and if you see importantly, give me a second. If you see my laser pointer, will you see? Yes. Okay. There is something asking me for stop sharing, but okay, let me go ahead. Thank you. So, it is a pleasure to be here today and to present the most recent work, my group done in collaboration with all these people here. Many of them are in this workshop, especially when this is in collaboration with a group of Ali, in which we study the blocking of spike protein of coronavirus, which is this structure, with legacy molecules, which are these ones. This is a molecular dynamics study, which we combine with some fancy data analysis and statistical physics techniques. So, before starting, I just introduce you to my current group. We work on studying non-eclarean fluctuations in physics and biology. We think the emerging field of stochastic thermodynamics, so for more information, you can go to my website and check our main interest. So, here in this conference we have Roman, who will give a talk about first-party sites. We have also Gianaro, who will talk about stochastic resetting. As we will discuss active matter, also Rita is my student working on the same topic, and Fajat, who is also present in the conference, is working on biophysics of receptors. We are theorists. We do data analysis. We do numerical simulations, but we also collaborate with many experimental labs on different topics from bullfrogs, optical twisters, quantum dots, so we are very broad, and also very recently with molecular dynamic simulation groups, as in the project that I will discuss now. So, you've seen a lot of this about coronavirus, its structure. So, this is our target study. So, coronavirus has this structure with a lipid membrane and a protein shell that I can highlight here, which is made of spike proteins protecting its RNA, its genetic information inside this membrane. The spike proteins have this structure of a trimer, and here I'm just highlighting the monomer, so one of these three units of the protein, which has two parts called S1 and S2 by the biologist. In particular, we are here focused on S1, which is the most exposed part of the protein, which is also the one that interacts with the human cells, which is what I will explain later. So, in particular, we will discuss in the monomer what happens and what are the dynamics and the fluctuations of the loop dominant receptor binding domain, which is called RBD, which is the one that ultimately interacts with the human cell, as I'm showing in this figure here. This is a sketch, and you can see that the coronavirus targets the H2 human receptor, and this is like the entry gate for the virus to be able to infect a human cell. So, in the last month, there has been a lot of research on trying to block the entry of the coronavirus in the cell, and there are two very promising lines. One is to use H2 receptor solvable in water, so put a lot of H2 in a solution, and this, let's say, cheats the virus to think that it has infected the cell that it doesn't, because it's bound to H2 that is out of the cell. With this, there is a beautiful paper in cells, experiments which have shown that using solvable H2, you can reduce the viral load in a human cell. Moreover, there is another research line which is using antibodies, as I show here in the illustration, which have been also very effective to stop or to reduce the viral load in human cells, and this recent work in nature is showing that the crystal structure of the receptor binding domain bound to the antibody shows prominent hydrogen bonds, so this motivates us to study this junction very much because we see that water may have an important role in the infection of the cells by the coronavirus. In particular, we have a different approach, which is illustrated here with a movie in which we are inspired by the action of soap on virus. This is a typical soap molecule. Well, soap is an amphiphilic molecule which has a polar head and a non-polar lipid tail, and because of this dual action, it is able to both disrupt the membrane deep in the middle of the virus, take out, for example, oil residues in the skin by doing this type of structures which are called micelles. So, molecules are interacting with their non-polar tails with the oily parts of these molecules and taking them out of the skin, but also, they are very effective in interacting with the coronavirus because of what I'm going to show in this movie. What they do mainly is, okay, this is the liquid bilayer. It's an illustration. This is not molecular dynamics, and what the amphiphilic molecules do is they internalize the membrane, and then you think to the action of water penetrating in the membrane, they can form this type of structures called micelles and both take out parts of the membrane but also trap the protein of the virus. In particular, we are more interested in the second part, which has been taking little attention until now, which is the interaction between the viral protein and sulfractal molecules. So, this is our goal. So, we want to understand the molecular interactions of the RBM in coronavirus with non-toxic surfactants because be careful not to think that soap is toxic, so you cannot put soap molecules in ourselves. You want to look for biodegradable natural amphiphilic molecules that may be putative blockers of the coronavirus, the single molecule that... In particular, this is our system. So, we are looking at the RBD, this protein structure shown here, that binds to the ACE2 via some hotspot residues. So, there are some amino acids that have been shown to form bonds, like hydrogen bonds with the ACE2 human receptor. And for convenience, we have introduced this nomenclature of different regions in this RBD protein, which I will discuss later. The most important part here is this red part, the RBM, which is the zone that is most exposed to the human receptor ACE2. So, this is the molecule that we want to target, and this is, like, the weapon we use to target. It is called lechithin in chemical nomenclature. Its name is POPC, and it's a biodegradable amphiphilic phospholine. It's present in cells, in the members of cells, in soybean, so you can get it in soya, in eggs, you can also go to the supermarket and buy it. So, I bought it myself. It's not that I'm eating this, but it means that it's something you can take and don't die when you eat it. So, our body is able to metabolize it. And it's also, not importantly, present in the lung, alveolar are surfactant. So, in the lung, we have surfactant liquid, and this has, in one of its components, is this lechithin POPC. This structure is as follows. It has a non-polar hydrocarbon chain and then a polar head, as I'm showing here. So now, what I'm going to show you is molecular dynamic simulations that we did while this was done mainly by Nawazquez Rani during the lockdown. So, this is the RBD in water. I'm not showing the water molecules in the presence of lechithin molecules. And you will see how lechithin attacks the RBD and binds into some specific hotspots in this RBM zone and in this zone as well. So, here are some details. We are using the MBT ensemble at room temperature. This is a box and it has pretty boundary conditions. And we can repeat these simulations for a larger number of lechithin molecules. And we were very excited to see this. We did this simulation for different concentrations, so different values of number of lechithin molecules and for different initial conditions. So, we built a lot of data. And what we did next was we tried to analyze the data from these simulations. We have here an orthodox approach. We get holistic because we look at three phases of the problem. First, what happened with the protein, where lechithin comes. Second, where do lechithin molecules bind in the RBD? Where do they bind? And third, what is the role of water in all this story? I'm going to talk mainly about these two, but only at the end, I will explain a little bit about this. For this, we use a combination of HPC molecular dynamics. We do very exhausted data analysis in my group and insights from chemistry because chemistry plays also a very important role in this process. All right. So first, I will go to the second question, which is where and how long do lechithin molecules bind to the RBD? What you see here is a snapshot for the case of 15 lechithin molecules. You see the lechithin are attached in this region and in this region mainly. What I brought here is a contact map. So it's like an interaction matrix. What it's showing is the lechithin molecules, which are shown in these slides, interact with different residues of the protein. What we see is that there are dark spots here, meaning the distance is small. So there are dark spots in the distance between the molecule and this region of the protein. So this is what I highlighted here. So the RBM at this amino acid shown here from 439507 are having these marked spots here, which means that there are many lechithin molecules. So you see there is long interaction times and small distance. So lechithin molecules are close to these parts of the protein and this happens in two parts, the RBM and some two. The RBM we know it's important because it's exposed to water and some two, it is the part, this is not exposed to water, but it's inside. So it could be accessible to molecules when there is an opening and closing of the triangle, which we know it can happen in real experiments. So this would be less accessible. But this is very relevant for the problem of infection. Edgar? Yes. One question. Why do you see that this happens only in these particular sections of the protein? Because I see a lot of black spots outside of those regions. Yes, it is. There are also black spots here. So maybe with this I want to say that you see patterns, so you see one here, one here, one here. It's the same structure and also here you see patterns. In the other ones it's not so clear. Okay, I would say the other sounds have also contacts because the lechithin molecules are long. So you combine the sound from here and then stretch a little bit and get close to another song. I'm giving a, let's say, close to the picture that you combine mostly to these ones, but you also combine them. Sure. A bit weaker. Sorry, may I ask a question? Yes. And it seems that the concentration of the lechithin is very high in your simulation. This is really huge, actually. And the question is that in the higher concentration that you have, what about the other micro molecules? So I think lechithin could decorate any micro molecule that you have, any protein and everything that you have in this space. That's right? Yeah, sure. This is proof of concept simulations where we are looking at, let's say, the simplest scenario where there's only lechithin, but of course if there would be other proteins, we cannot destroy lechithin. We find also two other proteins. Then one question could be that how if you compare the affinity of the lechithin to the different proteins that you are, you can find in their environment, does lechithin prefer to connect the RBD spike protein or something else, for example? Yeah, this is a great question and I must say I don't know the answer by now, but I mean, which protein do you think would be interested to compare with? I think any protein in this space, because the proteins have very similar parts, a similar residue. And if the lechithin is very attractive to some kind of the residue in this protein, RBD, why it doesn't attract to other helices or better sheets in the other proteins, similar proteins or something like that? Yeah, sure, sure, sure. The question is that is the lechithin affinity to RBD is higher than other proteins or not? Is there some kind of comparison needed here, or something like that? Yeah, I agree. This is a very important feature to look at, which we haven't done yet, but we must do. Because if in the end you say, okay, I would like that a molecule of lechithin reaches the virus, in the end you would say, for example, like a nanoparticle with H2 that then joins with the virus and then brings the lechithin. In that case, you could do. This is something we are kind of discussing, but of course it's far from what we can do in situations by now. One could use lechithin as a carrier, which others have used in recent therapy for COVID, for example. But yeah, by now we are in the ideal world, but there's water, the spike, and lechithin. Okay, that's good. Great, thank you. Yes, okay. Sorry, I had another question. In the picture you are showing at the left side, at the top. A problem I have is that the population of the lechithins around H2 seems to be, seems for me that there are a lot of them because in the cell, H2 is a transmembrane domain and if you rotate your conformation now for 180 degrees, then the stucco sits within the membrane and if there is no membrane in your simulations, then this interaction matrices you are presenting at least may not be very accurate for the ACE part. I totally agree, and by now this is what we could achieve. So these are a lot of atoms and that is a very high result. Yeah, I know, I know. But it is, actually I will say this in the open questions. So our next goal is to try to repeat this in contact with the ACE2 and see if lechithin can enter. In contact with the membrane, right? Yes, yes, yes. Okay, the membrane is one thing. With the H2 is another thing. With the membrane H2 is an even more complicated problem. So you are at the atoms and it is even more complicated. But that would be our kind of our final goal and this would be, of course, beautiful to do it. Yeah, thank you. Thanks. Thanks, thanks. All right, so may I continue? Okay, so this is what I show here is the distance between the center of mass of the residue and the protein. But now what I will show you is this entangling of this interaction between polar and non-polar center of mass. So I'll show you the same contact maps but broken into two parts. One for the polar, the other for non-polar. What we see is that the polar contacts are much weaker than the non-polar contacts of residue. So we are seeing that mostly is this part which is binding closely to the protein both in sum 2 and REM. The signature is very clear so we can conclude that the contacts between residue and REM are really dominated by either of the interactions. The distance is more than 100 meters and the time scales are ordered of 100 nanoseconds, 300 nanoseconds binding. That's why these simulations have to be done for a long time because this thing can be there for hundreds of nanoseconds. So you need very powerful computing resources or wait a lot of time. So you see that hydrophobic contacts are dominating this interaction but then the question that comes to our minds is, do you have an hydrophobic contact? What does it do with hydrophobic? What is happening with the water near this contact? It's really dehydrating the protein and this is what we tried to answer by doing an analysis on the water density near the RBM H2 hotspots. So we have the RBM and we know there are 16 hotspots. In each of the hotspots we take the alpha carbon in the amino acid and we draw a sphere of radius R and we count the water density with this relative to the bulk density of water. So when you increase and increase the radius of these spheres you see more and more water at the end for very large radius you will see the bulk density. But very importantly we compare here for two amino acids the real distribution without and with density. So what we see is with density this density is moving out. So for any value of R we are having less water molecules when we add the density. And what is very striking for us is that we look at the 16 hotspots and in the 16 we have a displacement of the Gibbs dividing interface positive displacement. So we have the wetting near all the 16 amino acids in the hotspot. And this we can show with a snapshot. So this is without density water is moving very happily near the RBM so this is the phenylalanine this residue and now when we put less density it comes here with its non-polar groups and it takes water out of it. But there is really a depletion of water near the hotspot. So this is a very clear effect of depletion of water near all amino acids and we also see that this is a concentration dependent. So the more less density Excuse me Erdogan isn't that just excluded volume effect that recetin occupies space that water cannot reach to the residue or is that effect of the because recetin is the oily molecule and this hydrogen bond can make with the water. Which one is more important here the extra volume effect or having an oily molecule in the neighborhood? We think this because it's an oily molecule but yet we don't have a very clear I mean we haven't quantified this effect. We don't know yet. I think of both which is what I think but we have to quantify or it's only because of scuba boiling or because of an oily. Surely what we have tried is with other molecules and it wasn't that clear this effect. It wasn't that strong the bond. So we know the oily part of the recetin is spending an important role because we try with other antiphilic molecules and it wasn't that clear of this effect. But we have to order this. Of course somewhere. Some kind of hydrophobic effect around the residue that you have a corona of the hydrophobic particles around your particle and then no water can come inside. Yes, but it's not so clear because some residues you don't see so I mean I'm showing here extreme case which seems okay because it has to go somewhere. In this one you see water all around so it's not that clear. But yeah it's a great question we have to investigate this. Thank you for your suggestion. Erdogan, we need to wrap up. Yes, I just these are the conclusions just okay this thing has a big problem blocking the spike protein and it's done thanks to hydrophobic interactions which is a combination of wetting as we just discussed there are open problems that have been discussed also during the monami kinetics of these simulations or simulate the virus so the lecithin near liquid envelopes this is something we would like to get some feedback from you and that's it. I want to acknowledge the work of many people and you see we were meeting we did all this work during the quarantine so we were meeting on the street sitting on the ground in the mollo and this is ICDP is a unidirectional collaboration it's something very in common with also industry we all work with our chemists and yeah I just finished with this movie thank you for your attention and please check what happens here because you will see the naturalism of the protein at some point thank you for your attention you see, thank you. Thanks a lot Erdogan that was a really nice talk unfortunately we don't have time for more questions but we have now a break of five minutes and if you want you can stick around