Science

NNadir

(33,523 posts) Fri Mar 27, 2020, 10:30 PM Mar 2020

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2

The paper I'll discuss in this post is this one: Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 (Yaning Li et al., Science (2020) Vol. 367, Issue 6485, pp. 1444-1448)

Although I downloaded the full paper using my subscription, it probably is open sourced: The world's scientific publications are making all Covid related paper open sourced free of charge.

While the paper is technical, interested readers with only a modicum of scientific training should be able to get the basic idea, which sketches out a pathway for the development of antiviral drugs, if not for this particular epidemic, then for similar outbreaks which may occur in the future. (These SARS type viruses seem to be pretty facile in carrying out evolution, which is not entirely surprising given that they are RNA viruses with low accuracy replication machinery, prone to errors, and thus quick to evolve.)

The paper focuses on how the virus binds to cells as the first step to entering them. As I've discussed in other posts here, this is an effect of the binding of the "S" (for Spike) protein to the ACE2 protein on the surface of lung (and other types of cells). ACE2 is "Angiotensin Converting Enzyme 2" which is responsible for the control of blood pressure.

From the text:

Severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) is a positive-strand RNA virus that causes severe respiratory syndrome in humans. The resulting outbreak of coronavirus disease 2019 (COVID-19) has emerged as a severe epidemic, claiming more than 2000 lives worldwide between December 2019 and February 2020 (1, 2). The genome of SARS-CoV-2 shares about 80% identity with that of SARS-CoV and is about 96% identical to the bat coronavirus BatCoV RaTG13 (2).

In the case of SARS-CoV, the spike glycoprotein (S protein) on the virion surface mediates receptor recognition and membrane fusion (3, 4). During viral infection, the trimeric S protein is cleaved into S1 and S2 subunits and S1 subunits are released in the transition to the postfusion conformation (4–7). S1 contains the receptor binding domain (RBD), which directly binds to the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) (8), whereas S2 is responsible for membrane fusion. When S1 binds to the host receptor ACE2, another cleavage site on S2 is exposed and is cleaved by host proteases, a process that is critical for viral infection (5, 9, 10). The S protein of SARS-CoV-2 may also exploit ACE2 for host infection (2, 11–13). A recent publication reported the structure of the S protein of SARS-CoV-2 and showed that the ectodomain of the SARS-CoV-2 S protein binds to the PD of ACE2 with a dissociation constant (Kd) of ~15 nM (14).

Although ACE2 is hijacked by some coronaviruses, its primary physiological role is in the maturation of angiotensin (Ang), a peptide hormone that controls vasoconstriction and blood pressure...

The authors have studied the structure of the ACE2 protein.

A picture:

The caption:

(A) Representative size exclusion chromatography purification profile of full-length human ACE2 in complex with B0AT1. UV, ultraviolet; mAU, milli–absorbance units; MWM, molecular weight marker. (B) Cryo-EM map of the ACE2-B0AT1 complex. The map is generated by merging the focused refined maps shown in fig. S2. Protomer A of ACE2 (cyan), protomer B of ACE2 (blue), protomer A of B0AT1 (pink) and protomer B of B0AT1 (gray) are shown. (C) Cartoon representation of the atomic model of the ACE2-B0AT1 complex. The glycosylation moieties are shown as sticks. The complex is colored by subunits, with the PD and CLD in one ACE2 protomer colored cyan and blue, respectively. (D) An open conformation of the ACE2-B0AT1 complex. The two PDs, which contact each other in the closed conformation, are separated in the open conformation.

Other figures in the paper detail protein interactions leading to the behavior of the ACE2 protein itself, and more importantly, it's interaction with the S protein of the virus.

It doesn't, apparently take all that much evolution to change the nature of the virus. Apparently, according to this paper, comparison of the interaction of the SARS-COV-RBD (an older coronavirus) (RBD = receptor binding domain, i.e. the points at which the ACE2 protein interfaces with the viral "S" protein) varies only slightly from the far more pernicious SARS-COV-2-RBD, although the variations over 139 amino acid residues show an RMS deviation of about 0.7 Angstroms. An interesting comparison is noted where an interaction in the SARS-COV-RBD which involves a "greasy" amino acid, valine, at residue 404 is displaced by a hydrophilic residue, lysine, at residue 417 in SARS-COV-2-RBD.

The pictures are in the full paper. They should be open for perusal.

All of this is notable, according to the authors, because:

...Our structural work reveals the high-resolution structure of full-length ACE2 in a dimeric assembly. Docking the S protein trimer onto the structure of the ACE2 dimer with the RBD of the S protein bound suggests simultaneous binding of two S protein trimers to an ACE2 dimer. Structure-based rational design of binders with enhanced affinities to either ACE2 or the S protein of the coronaviruses may facilitate development of decoy ligands or neutralizing antibodies for suppression of viral infection.

Regrettably there is a long way from these kinds of findings to a real drug. We should be aware that any agent interfering in this system may have severe hypotensive or hypertensive consequences, something only a careful clinical trial can reveal.

I wish that in this emergency, this weekend you will find some joy in the reflections that this unexpected change to your life may bring, the tragedy of it all notwithstanding.

Be safe; be healthy.

4 replies

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Highlight:

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 (Original Post) NNadir Mar 2020 OP

Thanks for posting this intrepidity Mar 2020 #1

I looked ACE2 up on Uniprot. Often the text... NNadir Mar 2020 #2

Finally getting back over here... intrepidity Apr 2020 #3

I didn't tolerate lisinopril myself. If your side effect is that you cough... NNadir Apr 2020 #4

intrepidity

(7,302 posts)

1. Thanks for posting this

Reply to NNadir (Original post)

Fri Mar 27, 2020, 11:12 PM

Mar 2020

I read this paper quickly a few days ago, and have a question that I haven't had time yet to look up, so maybe you'll have a quick answer. If so, thanks in advance.

Is there the suggestion that ACE2 needs to homodimerize in order for the virus to bind or otherwise proceed to infection?

If so, is this a normal behavior of ACE2, or just a property that the virus exploits, perhaps especially in those with overexpressed ACE2? That is, is dimerization something that's physiologically required of ACE2? I'm wondering whether preventing dimerization is a therapeutic target. And I wonder if the dimerization could play a role in the heightened risk factors (high blood pressure, diabetes ==> increased ACE2, more available to dimerize). I could easily be way off base here.

There's just so much to read...!

NNadir

(33,523 posts)

2. I looked ACE2 up on Uniprot. Often the text...

Reply to intrepidity (Reply #1)

Sat Mar 28, 2020, 07:14 AM

Mar 2020

therein refers to a normally dimeric protein if it usually exists as a dimer, but it doesn't in this case. This does not mean that the virus induces dimerization however, nor does it mean that the protein does not dimerize naturally. It's not always clear how these dynamics work, since often these things are connected with crystal structures, which may not reflect physiological states. Recently I became aware of mass spec based approaches to the nature of protein dynamics, which may improve the understanding of physiological states.

To be perfectly frank, this is not a protein with which I have much familiarity in terms of its action or dynamics, which reflects a certain amount of laziness on my part, since the mechanism of this protein should be of interest to me, since I have high blood pressure, probably from my youthful stupidity in seeking to engage anti-nukes whose intellectual flexibility is the equivalent of Trump or Sanders. (The ignore key here is a wonderful thing.)

I thought about a related question to the one you asked, since I take an ABR inhibitor, the much maligned valsartan, the core of which is a valine. It's a very long shot, and probably extremely naive to say, but in the context of the paper cited in the OP, maybe having hydrophobic valine type molecules around in one's lung tissue is not an entirely bad thing.

When I first realized I had high blood pressure, I took an ACE inhibitor, lisinopril, a pseudopeptide with the sequence FKP, where the F (Phe) and K (Lys) are not connected with a peptide bond but rather share the alpha nitrogen. I had a terrible cough, however, a well known side effect of ACE inhibitors. You inspired me to look into it, and it appears that this side effect is related to an ACE polymorphism: Association between genetic polymorphisms and angiotensin-converting enzyme inhibitor-induced cough: a systematic review and meta-analysis This is not a journal to which I have access, even in normal times. I doubt my son's university library has this journal either.

Right now, having an ACE polymorphism is a good thing, I'd guess, or at least a hopeful thing.

While looking through Uniprot - which you inspired me to do - (Thank you!) I did see a report of an ACE polymorphism that is suspected to block the SARS/ACE complex from forming, implying immunity to SARS-CoV-2.

I'll download that paper, and if it's interesting, I'll post something here about it.

intrepidity

(7,302 posts)

3. Finally getting back over here...

Reply to NNadir (Reply #2)

Thu Apr 9, 2020, 06:20 PM

Apr 2020

Curious if you've got further insights into this ACE2 polymorphism issue.

I was reading about ACE2 yesterday - I never realized that Lisinopril was the fake dipeptide. There was a paper recently about FP being used to lower cholesterol. And I thought: hey, that peptide might fit nicely onto ACE2, blocking the virus binding site

https://www.nature.com/articles/s41598-019-56031-8

I was also reading a paper comparing Lisinopril to losartan with respect to ACE2 levels, and they seemed to find that, with losartan, there was higher ACE2 activity *in cardiac tissue*. (I think I went down that rabbit hole when I saw a SciAm article about heart damage in covid19 patient

https://www.ahajournals.org/doi/full/10.1161/CIRCULATIONAHA.104.510461

The reason I'm interested is that I need to be on BP meds, but I don't tolerate Lisinopril, and since covid, am now concerned about mechanisms. I'm going to ask my doc for losartan. I just think that I'd rather be on an ARB. Do you have an opinion on losartan vs valsartan?

BTW, also saw that there's a clinical trial using soluble ACE2, competitive binding strategy.

Sorry, a bit jumbled... too much to absorb...

NNadir

(33,523 posts)

4. I didn't tolerate lisinopril myself. If your side effect is that you cough...

Reply to intrepidity (Reply #3)

Thu Apr 9, 2020, 08:52 PM

Apr 2020

...which is the side effect I experience, I learned in all of this that this means I have an ACE2 mutation.

I take valsartan, which works great, and no, I'm not losing sleep over nitrosamines. (They're in bacon, and I don't eat bacon, but not because of nitrosamines. They can also arise in chlorinated pool water.)

I've been driving my family nuts with mutant jokes, a point I made over in the Lounge:

Trapped in the house with me, I feel for my wife and sons listening to me brag about my ACE2.

I have the paper somewhere in my files describing this fact, but I'm too lazy to dig it out right now.

There is no evidence that this mutation confers immunity to Covid-19, but hey, you never know.

The sartan you propose to try, losartan, is going to be subject of a clinical trial at the University of Minnesota as a Covid-treatment.

There is also going to be an ACE inhibitor in another trial at that institution. I ran across these at Clinical Trials.gov

I mentioned this in this post: A "Cryptic Epitope" to SARS-COV-1 Also Binds to SARS-COV-2: A Key to Vaccine Design.

I was motivated to look into the use of the "Sartans" as treatment when I saw a paper in one of the journals discussing the advisability of keeping Covid-19 patients on their blood pressure medicines. Again, as I've been distracted by other things, I haven't organized my Covid-19 papers very well, and won't have too much time to look it up.

On some level this make sense, although I would imagine that this study could be done by a meta-analysis. High blood pressure is supposedly a risk factor and I would imagine that a retrospective analysis of people being treated with ACE inhibitors or ARBs is possible and may be enlightening.

I've become even more insufferable to my family by telling them I'm on Valsartan.

They remind me of all the assholes who pretended Covid-19 wasn't a worry to them and died from it. They have a point.

If you are on a BP medication, and are having problems with ACE inhibitors, my experience is that the sartans are very effective. My blood pressure is completely normal now, because of Sartans, and because of using the ignore list here to avoid the dumbest of the anti-nukes.

Stay safe and be healthy.

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