Haitchpeasauce | 9 points | Oct 29 2020 14:54:46

Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin - direct antiviral activity identified

https://www.tandfonline.com/doi/full/10.1080/07391102.2020.1839564

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[-] Haitchpeasauce | 10 points | Oct 29 2020 14:55:44

Not sure if this has been posted before, but this molecular docking study has been published today with good findings:

https://www.tandfonline.com/doi/full/10.1080/07391102.2020.1839564

Parth Sarthi Sen Gupta , Satyaranjan Biswal , Saroj Kumar Panda , Abhik Kumar Ray & Malay Kumar Rana

Received 13 Jun 2020, Accepted 08 Oct 2020, Published online: 28 Oct 2020

Abstract (bold for emphasis):

While an FDA approved drug Ivermectin was reported to dramatically reduce the cell line of SARS-CoV-2 by \~5000 folds within 48?h, the precise mechanism of action and the COVID-19 molecular target involved in interaction with this in-vitro effective drug are unknown yet. Among 12 different COVID-19 targets along with Importin-a studied here, the RNA dependent RNA polymerase (RdRp) with RNA and Helicase NCB site show the strongest affinity to Ivermectin amounting -10.4?kcal/mol and -9.6?kcal/mol, respectively, followed by Importin-a with -9.0?kcal/mol. Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site and Importin-a, with MM/PBSA free energy of -187.3?kJ/mol, almost twice that of Helicase (-94.6?kJ/mol) and even lower than that of Importin-a (-156.7?kJ/mol). The selectivity of Ivermectin to RdRp is triggered by a cooperative interaction of RNA-RdRp by ternary complex formation. Identification of the target and its interaction profile with Ivermectin can lead to more powerful drug designs for COVID-19 and experimental exploration.

We might comment on the limitations of docking studies, but there is value in identifying potential targets for drugs and drug interactions. They highlight that they modelled the Importin-α protein at the highest resolution; efforts were made to get accurate results. To my untrained eye the study looks thorough and well put together.

The study repeats results found in other docking studies, and reaffirms the understanding that IVM prevents the formation of the Importin α/β dimer complex and thus transport of various proteins into the nucleus. This mechanism we are familiar with.

Of greater interest is that the Ivermectin molecule has higher binding affinity with RdRP which is the machinery RNA viruses use to make copies of their genome. The binding affinity is even stronger again when the RdRP has RNA (i.e. is in the process of replicating the RNA). This is huge, because it means Ivermectin is acting directly against viral replication mechanisms.

Lastly Ivermectin has binding affinity with NSP13 Helicase which further inhibits viral replication.

Together this study further demonstrates Ivermectin as a potent antiviral.

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[-] TrumpLyftAlles | 2 points | Nov 01 2020 19:43:51

Great post, Haitch!

From your link:

Helicase unwinds the DNA

Helicases are enzymes that bind and may even remodel nucleic acid or nucleic acid protein complexes. There are DNA and RNA helicases. [COVID-19 is a RNA virus.] DNA helicases are essential during DNA replication because they separate double-stranded DNA into single strands allowing each strand to be copied. During DNA replication, DNA helicases unwind DNA at positions called origins where synthesis will be initiated. DNA helicase continues to unwind the DNA forming a structure called the replication fork, which is named for the forked appearance of the two strands of DNA as they are unzipped apart.

The process of breaking the hydrogen bonds between the nucleotide base pairs in double-stranded DNA requires energy. To break the bonds, helicases use the energy stored in a molecule called ATP, which serves as the energy currency of cells. DNA helicases also function in other cellular processes where double-stranded DNA must be separated, including DNA repair and transcription. RNA helicases are involved in shaping the form of RNA molecules, during all processes involving RNA, such as transcription, splicing, and translation.

This article doesn't mention ivermectin, but it elucidates NSP13 (which is new to me):

Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13)

SARS-CoV helicase named as Nsp13 in superfamily 1 helicase family with the activity of 5′-3′ RNA/DNA helicase RTPase and the enzyme is known to be a part of the replication and translation complex which is required for life cycle of SARS-CoV [10,13,[15], [16], [17]]. SARS-CoV Nsp13 has five domains which are zinc-binding domain, stalk domain, 1B domain, 1A domain and 2A domain [18,19]. The 1B, 1A and 2A domains have been studied for SARS-CoV and demonstrated that they are involved in the dsDNA unwinding process [18,20]. Also, the substrate, transition and product states of SARS-CoV Nsp13 observations showed the coordination between the 1A and 2A domains during translocation.

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[-] No-Sandwich-777 | 1 points | Nov 02 2020 02:03:00

[COVID-19 is a DNA virus.]

Your understanding is truly limited. Sars-CoV-2 is an RNA virus! The Nsp13 helicase is used on the duplex RNA.

https://www.sciencedirect.com/science/article/pii/S0188440920308638

https://content.sciendo.com/configurable/contentpage/journals$002facph$002f70$002f2$002farticle-p145.xml

" Its substrates are double-stranded RNAs (dsRNA). The main mode of action is the unwinding of a substrate in a process depending mainly on ATP gradient in a 5’-to-3’ direction. Length of the 5’ loading strand of the partially duplex RNA substrate is another factor playing a crucial role affecting the efficiency of the unwinding reaction (13). "

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271831/

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[-] TrumpLyftAlles | 1 points | Nov 02 2020 02:09:57

Just a glitch. I've made that mistake several times. Always get corrected.

By YOU, actually! This is your thing!

Thanks for the correction. I'll check the links! Always appreciate links.

Also, my understanding is truly limited. My brain is 67 years old. Doing the best I can. 😁

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[-] TrumpLyftAlles | 1 points | Nov 02 2020 02:31:49

https://www.sciencedirect.com/science/article/pii/S0188440920308638

Taking all these data together, it is now apparent that inhibitors of the nsp13 activity offer potential therapeutic option for coronavirus including SAR-CoV-2. Among the various approaches of nsp13 activity inhibition are targeting ATP binding or direct NTPase activity, nucleic acids binding to the helicase, blocking helicase translocation, etc. The class of compounds identified with a promise through such mechanisms include benzotriazole, imidazole, imidazodiazepine, phenothiazine, quinoline, anthracycline, triphenylmethane, tropolone, pyrrole, acridone, small peptide, and bananin derivatives (8). For example, bananins have been shown to inhibit SARS-CoV ATPase activity leading to inhibition of viral replication in vitro with IC50 values far less than 10 mM (9). On these bases, studies on the potential of viral helicase inhibitors in SARS-CoV-2 infection or COVID-19 is well justified.

https://content.sciendo.com/configurable/contentpage/journals$002facph$002f70$002f2$002farticle-p145.xml

Helicases are proteins that catalyze the separation of duplex oligonucleotides into single strands exploiting the derived energy from ATP hydrolysis (11).

The MERS-CoV helicase non-structural protein 13 (M-nsp13) is a critical component for viral replication and is presently viewed as a possible drug target for potential coronavirus chemical inhibitors (12). Its substrates are double-stranded RNAs (dsRNA). The main mode of action is the unwinding of a substrate in a process depending mainly on ATP gradient in a 5’-to-3’ direction. Length of the 5’ loading strand of the partially duplex RNA substrate is another factor playing a crucial role affecting the efficiency of the unwinding reaction (13). Because of all these helicase functions, MERS helicase is considered a powerful antiviral target.

Triazoles are versatile heterocyclic moieties with a broad spectrum of pharmacological activities (14). He and coworkers (15) reported that triazole derivatives had shown potency as antiviral agents against H1N1influenza virus. The 1, 2, 4-triazole derivative was found to show the best activity against influenza B among all of compounds evaluated in a study by Zhao and Aisa (16). A limited number of possible inhibitors of nsp13 have been explored (17). SSYA10-001 is a 1, 2, 4-triazole derivative which was reported as an nsp13 non-competitive inhibitor through the blockage of SARS and MERS-CoV replication. It was postulated that SSYA10-001 binding pocket of SARS-CoV nsp13 is preserved among different coronavirus helicases, indicating the discovery of broad-spectrum coronavirus inhibitors. SSYA10-001was reported as potential effective inhibitor of viral replication in MERS-CoV replicon (Fig. 1) (18). All the above mentioned prompted us to design and synthesize new 1, 2, 4-triazole derivatives in order to be screened as helicase inhibitors that simply prevent the replication of MERS-CoV.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271831/

Bismuth Salts Inhibit the NTPase and RNA Helix-Unwinding Activities of SARS-CoV-2 Nsp13 As aforementioned, we have observed that certain divalent cations, like Ca2+ and Zn2+, did not support RNA helix unwinding by SARS-CoV-2 nsp13, while high concentrations of Mg2+ showed inhibitory effect (Fig. 3C, ​C,3D).3D). Moreover, previous studies reported that some bismuth salts could inhibit the NTPase and RNA helicase activities of SARS-CoV nsp13 as well as the replication of SARS-CoV in cells (Yang et al.2007a, b). Therefore, we sought to examine whether NTPase and RNA helix-unwinding activities of SARS-CoV-2 nsp13 can also be inhibited by the bismuth salts. Here, we used three different bismuth salts, including bismuth potassium citrate (BPC), ranitidine bismuth citrate (RBC), and bismuth citrate (BC). BPC and RBC are originally used to treat the gastrointestinal diseases, and BC is the intermediate of BPC. Our data showed that all these bismuth salts inhibited the ATPase activity of SARS-CoV-2 nsp13 at 10 μmol/L, as BPC and RBC showed stronger inhibitory effects than BC (Fig. 5A). Moreover, we found that 10 μmol/L BPC or RBC almost abolished the RNA helix unwinding activity of nsp13 (Fig. 5B, lanes 4 and 5); on the other hand, although BC treatment also effectively inhibited the RNA helicase activity of nsp13, its inhibitory efficiency was in much less than BPC or RBC (Fig. 5B, lane 6). To further characterize the inhibitory effect of BPC or RBC on the NTPase and RNA helicase activities of SARS-CoV-2, we treated recombinant nsp13 with increasing concentrations of either bismuth salts. Our data show that either BPC or RBC could inhibit the ATPase and helicase activities of MBP-nsp13 in a dose-dependent manner (Fig. 6).

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[-] No-Sandwich-777 | 2 points | Nov 02 2020 03:31:45

As far as ranitidine bismuth sulfate, it has been something of a recent rage.

https://www.thestandard.com.hk/section-news/section/11/223763/Ulcer-drug-found-to-be-potent-weapon-against-virus

https://www.nature.com/articles/s41564-020-00802-x

And do not confuse this with just ranitidine itself!

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[-] TrumpLyftAlles | 1 points | Nov 02 2020 03:36:06

Wow, you really are a font of information, not sarcasm. Welcome back!

The first link:

The drug RBC - ranitidine bismuth citrate - has been tested on hamsters and researchers found it can be as effective as the antiviral drug remdesivir, if not more, in suppressing the viral load.

Clinical trials could start in Hong Kong if it sees a fourth wave of infections but details on the dosage and whether it would be used on patients with serious or mild symptoms have yet to be confirmed.

The second:

Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters

So, really preliminary at this point, kind of where ivermectin was when Monash 48 hours came out on April 3. Seems like it's too late to be considering new wonder drugs. Maybe not.

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[-] tateTheMate2020 | 1 points | Oct 30 2020 02:27:39

If it prevents viral replication, could it be used to prevent infection?

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[-] Haitchpeasauce | 1 points | Oct 30 2020 02:31:18

If you mean prevent disease and replication, yes this modelling points to this and recent studies have demonstrated this. We need bigger population studies and more data.

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[-] TrumpLyftAlles | 1 points | Nov 01 2020 19:33:44

There are 2.5 studies (one was very small) showing that ivermectin provides prophylaxis -- prevents infection.

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