Home / Columns / Quirky RNA to combat SARS-CoV-2
2,15
π Health and biotech

Quirky RNA to combat SARS-CoV‑2

Jean-Louis Mergny
Jean-Louis Mergny
Biophysicist and Inserm Research Director at the Optics and Biosciences Laboratory (LOB*)

When the Covid-19 pan­dem­ic first arrived, we imme­di­ate­ly found our­selves faced with an infec­tion against which we had no effec­tive med­ica­tion. Admit­ted­ly, there were already basic treat­ments such as parac­eta­mol or aspirin that could be used to relieve cer­tain symp­toms (cough, fever, headaches, etc.) in mild cas­es but their effec­tive­ness for the more seri­ous forms of infec­tion is extreme­ly lim­it­ed. Nev­er­the­less, over time numer­ous avenues for bet­ter treat­ment emerged with more or less promis­ing effects. For severe forms, doc­tors have also made enor­mous progress in terms of inten­sive care pro­to­cols and in recog­nis­ing the patients ear­ly on who are like­ly to have the most seri­ous problems.

Medicines against Covid-19

Drugs that have been devel­oped so far to treat Covid-19 often tar­get the inap­pro­pri­ate inflam­ma­tion or immune response trig­gered by infec­tion with the SARS-CoV­‑2 virus. This over­ac­ti­va­tion in the patient is the cause of the more severe forms of Covid-19. Exam­ples include inter­fer­on-beta with ongo­ing clin­i­cal tri­als such as the Euro­pean project, DISCOVERY. Anoth­er effec­tive approach involves mon­o­clon­al anti­bod­ies such as the ones devel­oped by Amer­i­can biotech Regen­eron Phar­ma­ceu­ti­cals (REGEN-COV).

Nev­er­the­less, until now there have been very few anti-viral solu­tions in the ‘anti-Covid’ tool­box that could offer ear­li­er treat­ment of the dis­ease. Such options could increase our chances of avoid­ing seri­ous forms of Covid-19 or oth­er long-term effects, which we still know lit­tle about.

But tar­get­ing a virus is often very dif­fi­cult, as we have seen in the slow devel­op­ment of effec­tive treat­ments for HIV or hepati­tis. Even the best anti-viral treat­ment for com­mon flu, Tam­i­flu, is far from excep­tion­al. While bac­te­ria often respond to at least one of the antibi­otics on the mar­ket (aside from the grow­ing prob­lem of resis­tance), the way virus­es work makes them par­tic­u­lar­ly dif­fi­cult to reach. They work by ‘hack­ing’ into the cells of an infect­ed per­son, forc­ing them to pro­duce more virus which sub­se­quent­ly infects oth­er cells in their body. Bac­te­ria have their own cells with their own com­po­nents such as ribo­somes or cer­tain enzymes we can use as ther­a­peu­tic tar­gets. In con­trast, since virus­es do not have their own ‘fac­to­ries’, there are few­er tools or enzymes that can be specif­i­cal­ly targeted.

A new lead against SARS-CoV‑2

I have spent my career study­ing what we call ‘unusu­al con­for­ma­tions’ of DNA. When we think of DNA, we often think of its dou­ble helix. This is true for the most part, but some­times the dou­ble helix can bend out­wards into a ‘hair­pin’ shape, or some seg­ments even incor­po­rate more than two strands. These quirks are rare on DNA but more com­mon on RNA. Like all coro­n­avirus­es, SARS-CoV­‑2 has a sin­gle-strand­ed RNA genome. So, in Jan­u­ary 2020 when the SARS-CoV­‑2 genome was released, I looked to see if my exper­tise could be use­ful. How­ev­er, ini­tial analy­sis of the virus genome using an algo­rithm I designed sug­gest­ed that unusu­al con­for­ma­tions on the virus RNA was unlike­ly – so it was dif­fi­cult for my lab to intervene.

A few months lat­er though, thanks to a high­ly fruit­ful col­lab­o­ra­tion with Marc Lav­i­gne at Insti­tut Pas­teur, we realised there was anoth­er angle of attack. A pro­tein, called NSP3, pro­duced by a very close and high­ly infec­tious coro­n­avirus (SARS-CoV) can bind an unusu­al con­for­ma­tion called a ‘G‑quadruplex’.  From pre­vi­ous obser­va­tions we knew that the SARS-Cov­‑2 genome can­not form a G‑quadruplex, so we knew that the NSP3 pro­tein could not be tar­get­ing itself. Instead, we hypoth­e­sised that NSP3 inter­acts with a G‑quadruplex in infect­ed cells – there­fore, in the patients!

Blocking the virus, slowing down the infection

Remem­ber that virus­es are unable to mul­ti­ply on their own. To repro­duce, they must hack into the cel­lu­lar machin­ery of anoth­er organ­ism: this is called infec­tion. Thanks to the finan­cial sup­port of Insti­tut Pas­teur and ANR-flash Covid, we were able to show that the virus NSP3 pro­tein can bind to the G‑quadruplex of human RNA. We think that this inter­ac­tion helps the virus ‘hack’ the cel­lu­lar machin­ery of the host, pre­vent­ing the human cell from pro­duc­ing defences.

We then asked our­selves whether it was pos­si­ble to pre­vent the repro­duc­tion of the virus by block­ing this inter­ac­tion. Nat­u­ral­ly, the first approach was to test mol­e­cules capa­ble of block­ing the G‑quadruplex lig­ands. After two decades of research, we already had a large col­lec­tion of such mol­e­cules avail­able and so we designed screen­ing assays to test their effi­cien­cy to inhib­it viral repli­ca­tion. Among the pos­i­tive can­di­dates, we iden­ti­fied a group of small mol­e­cules which can block this inter­ac­tion between the NSP3 pro­tein and a G‑quadruplex. The com­pounds syn­the­sised in Bor­deaux by Prof. Jean Guil­lon were even more potent. As such, a clin­i­cal lead opened up for us in the form of a mol­e­cule that has promis­ing effects on cul­tured human cells.

This is the first time that such a quadru­plex-medi­at­ed effect has been demon­strat­ed to pre­vent the repli­ca­tion of SARS-CoV­‑2. The prepa­ra­tion of these com­pounds and their use for antivi­ral pur­pos­es have there­fore been patent­ed. How­ev­er, the devel­op­ment of a drug can­di­date is a long process and we have just start­ed the pre­clin­i­cal phase in rodents to first eval­u­ate their dis­tri­b­u­tion and pos­si­ble tox­i­c­i­ty in vivo and then to analyse their effects. This fam­i­ly of mol­e­cules has nev­er received FDA-approval, so they must pass a large num­ber of reg­u­la­to­ry stages before they can be test­ed in humans.

Fur­ther steps will prob­a­bly be del­i­cate since G4-lig­ands can inter­act with mul­ti­ple DNA and RNA frag­ments. It is there­fore essen­tial to check that they do not induce geno­tox­i­c­i­ty at both cel­lu­lar and whole organ­ism lev­els. Even if all goes well, this process will take years. But there is a great need for new antivi­rals. For Covid, most of the drugs test­ed ini­tial­ly were already approved or under eval­u­a­tion for oth­er dis­eases. This repo­si­tion­ing of the drugs has saved us a lot of time in the search for a treat­ment… unfor­tu­nate­ly, clin­i­cal tri­als have often dis­ap­point­ed. So, the chal­lenge is worth­while, and we def­i­nite­ly need to explore mul­ti­ple ways to tack­le the cur­rent (and next!) pandemic.

Pour en savoir plus

M. Lav­i­gne et al. Nucle­ic Acids Research, Vol­ume 49, Issue 13, 21 July 2021, Pages 7695–7712,

Contributors

Jean-Louis Mergny

Jean-Louis Mergny

Biophysicist and Inserm Research Director at the Optics and Biosciences Laboratory (LOB*)

A graduate of Ecole Normale Supérieure (Paris), Jean-Louis Mergny completed his PhD on the roles of nucleic acids followed by post-doctoral position in Basel, Switzerland. In 2009, he moved to the Institut Européen de Chimie Biologie (IECB) in Bordeaux where he was later appointed director. At the end of his 10-year term at IECB in 2020, he moved on to continue his research projects at the LOB (*a joint research unit CNRS, École Polytechnique - Institut Polytechnique de Paris, Inserm) in the Paris. The Covid crisis incited him to reorient my research projects towards pathogens with the aim of developing new therapeutic approaches against viral infections. He was appointed Head of the Biology department of Institut Polytechnique de Paris in September 2021. Co-author of over 200 original articles, he has gathered over 17,000 citations according to the Web of Science.