Brendan Frey (Deep Genomics)

Deep Ge­nomics, now flush with cash, plans to take dozens of RNA ther­a­pies to the clin­ic

It was 2002 when Bren­dan Frey no­ticed a huge gap in biotech. The hu­man genome had just been se­quenced, al­low­ing sci­en­tists to map ge­net­ic mu­ta­tions. But there weren’t enough da­ta to un­der­stand the con­se­quences of those mu­ta­tions, or re­al­ly do much about them.

Pre­dict­ing there would be an ex­plo­sion of new da­ta, Frey spent the next 13 years work­ing on a way to sift through it all. Now, thanks to ad­vances in RNA ther­a­peu­tics, med­i­cine is be­com­ing pro­gram­ma­ble, Frey said. And on Wednes­day, a slate of in­vestors bet $180 mil­lion that his com­pa­ny’s AI plat­form can make sense of it.

“What’s re­al­ly cool about RNA ther­a­peu­tics is that they’re ba­si­cal­ly a se­quence of let­ters,” Frey said. “Change the se­quence of let­ters one way, you tar­get a dif­fer­ent gene. Change it one way, you can in­crease the amount of pro­tein pro­duced by that gene. Change the se­quence of let­ters a dif­fer­ent way, you can de­crease the pro­tein.”

It’s all dig­i­tal in­for­ma­tion, Frey said. And thanks to AI and deep learn­ing tools, Deep Ge­nomics says it can do things like fig­ure out which mech­a­nisms of ac­tion will (or won’t) work against a spe­cif­ic gene, with­out per­form­ing a sin­gle ex­per­i­ment.

“We can take a gene where an­oth­er com­pa­ny would have spent two years on it and then failed and dropped it, and we can ac­tu­al­ly drug that gene, or we know to put it at the bot­tom of the list, just don’t do it now, it’s go­ing to be too hard,” he said.

In 2019, the com­pa­ny put for­ward its first pre­clin­i­cal can­di­date, a ther­a­py for Wil­son dis­ease that’s ex­pect­ed to hit the clin­ic along with three oth­er can­di­dates by 2023. Us­ing the AI sys­tem, the team says it was able to go from tar­get iden­ti­fi­ca­tion to de­clar­ing a win­ner in 18 months. Deep Ge­nomics has a to­tal of 10 can­di­dates hurtling to­ward the clin­ic, and Frey says he ex­pects to add 20 more in the near fu­ture.

The oth­er three can­di­dates ex­pect­ed to hit the clin­ic by 2023 are for fron­totem­po­ral de­men­tia, gout and Nie­mann-Pick type C dis­ease.

The AI space is teem­ing with play­ers, like Enve­da, which nabbed a $51 mil­lion Se­ries A round last month to pur­sue new ther­a­pies for Wil­son dis­ease, NASH and Parkin­son’s dis­ease. Up­on pulling in a $225 mil­lion Se­ries C round last month, In­sil­i­co CEO Alex Zha­voronkov laid out big plans to emerge as the Ama­zon or Google of the field. Around the same time, UK-based Ex­sci­en­tia splurged on the three-year-old mol­e­cule screen­ing biotech All­cyte in an at­tempt to edge out ri­vals.

What sep­a­rates Deep Ge­nomics from some of its peers — like Re­cur­sion, Ex­sci­en­tia or in­sitro — is its sole fo­cus on RNA bi­ol­o­gy, Frey said.

“We like RNA bi­ol­o­gy be­cause of that rock sol­id frame­work,” he said. “We have 100 petabytes of da­ta, so every­thing’s in place.”

Frey says the AI tech is less like a grand, all-know­ing com­put­er, and more like a work­bench, with dozens of tools that have de­fined func­tions and scopes. For ex­am­ple, one tool was built to go through data­bas­es of pa­tient mu­ta­tions and find drug tar­gets based on RNA bi­ol­o­gy — but re­searchers at the com­pa­ny re­al­ized it could al­so be used to an­a­lyze dif­fer­ent types of an­i­mal mod­els and fig­ure out which ones would re­ca­pit­u­late hu­man bi­ol­o­gy.

“That’s kind of the ad­van­tage of the work­bench metaphor is it sort of frees peo­ple up to be more cre­ative,” Frey said.

Soft­bank Vi­sion Fund 2 led the Se­ries C round, with a hand from Fi­deli­ty Man­age­ment & Re­search Com­pa­ny, Cana­di­an Pen­sion Plan In­vest­ment Board, True Ven­tures, Am­pli­tude Ven­tures, Khosla Ven­tures and Mag­net­ic Ven­tures. When asked if an IPO is in the near fu­ture, Frey said he doesn’t plan to take the com­pa­ny pub­lic at least un­til they reach the clin­ic.

“A lot of com­pa­nies have gone pub­lic pre­clin­i­cal­ly in the last year, and the prob­lem is that if they stum­ble in get­ting in­to the clin­ic, then the ex­is­tence of the com­pa­ny will be put in­to ques­tion,” he said. “We don’t want to be in that sit­u­a­tion.”

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His­toric drug pric­ing re­forms pass; Pfiz­er ac­quires GBT; The long search for non-opi­oid pain drugs; and more

Welcome back to Endpoints Weekly, your review of the week’s top biopharma headlines. Want this in your inbox every Saturday morning? Current Endpoints readers can visit their reader profile to add Endpoints Weekly. New to Endpoints? Sign up here.

The Endpoints Weekly has officially crossed the 60,000 mark on subscribers — thanks to all of your support. As the editorial team grows, we’ve been able to do a lot more, with many of those on display this week. Be sure to check out Lei Lei Wu’s deep dive on pain R&D. If you missed it, you may also rewatch her companion panel here.

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Gold for adults, sil­ver for in­fants: Pfiz­er's Pre­vnar 2.0 head­ed to FDA months af­ter Mer­ck­'s green light

Pfizer was first to the finish line for the next-gen pneumococcal vaccine in adults, but Merck beat its rival with a jab for children in June.

Now, two months after Merck’s 15-valent Vaxneuvance won the FDA stamp of approval for kids, Pfizer is out with some late-stage data on its 20-valent shot for infants.

Known as Prevnar 20 for adults, Pfizer’s 20vPnC will head to the FDA by the end of this year for an approval request in infants, the Big Pharma said Friday morning. Discussions with the FDA will occur first and more late-stage pediatric trials are expected to read out soon, informing the regulatory pathway in other countries and regions.

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Seagen interim CEO Roger Dansey and Daiichi Sankyo CEO Sunao Manabe

Paving the way for Mer­ck­'s buy­out, Seagen los­es ar­bi­tra­tion dis­pute with Dai­ichi over ADC tech

As Seagen awaits a final buyout offer from Merck that could be in the territory of $40 billion, Seagen revealed Friday afternoon that it lost an arbitration dispute with Daiichi Sankyo relating to the companies’ 2008 collaboration around the use of antibody-drug conjugate (ADC) technology.

But that loss likely won’t matter much when it comes to Merck’s deal.

After breaking off its pact with Daiichi in mid-2015, the two companies battled over “linker” tech — a chemical bridge between an ADC’s antibody component and the cytotoxic payload — that Seagen claims Daiichi would improve upon and implement in its current generation of ADCs.

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Tony Coles, Cerevel CEO

Cerev­el takes the pub­lic of­fer­ing route, with a twist — rais­ing big mon­ey thanks to ri­val da­ta

As public biotechs seek to climb out of the bear market, a popular strategy to raise cash has been through public offerings on the heels of positive data. But one proposed raise Wednesday appeared to take advantage not of a company’s own data, but those from a competitor.

Cerevel Therapeutics plans to raise $250 million in a public offering and another $250 million in debt, the biotech announced Wednesday afternoon, even though it did not report any news on its pipeline. However, the move comes days after rival Karuna Therapeutics touted positive Phase III data in schizophrenia, a field where Cerevel is pursuing a similar program.

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House pass­es his­toric drug pric­ing re­forms, lin­ing up decades-in-the-mak­ing win for Biden and De­moc­rats

The US House of Representatives today voted along party lines (all Dems voted for it), 220-207 to pass new, wide-ranging legislation that will allow Medicare drug price negotiations for the first time ever, and cap seniors’ drug expenses to $2,000 per year and seniors’ insulin costs at $35 per month.

Setting up a major victory for President Joe Biden, representatives returned from their summer recess to pass the Inflation Reduction Act, even as many noted the bill would only modestly reduce inflation.

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Senate Finance Committee Chair Ron Wyden (D-OR) (Francis Chung/E&E News/POLITICO via AP Images)

Sen­ate Fi­nance chair con­tin­ues his in­ves­ti­ga­tion in­to phar­ma tax­es with re­quests for Am­gen

Amgen is the latest pharma company to appear on the radar of Senate Finance Committee Chair Ron Wyden (D-OR), who is investigating the way pharma companies are using subsidiaries in low- or zero-tax countries to lower their tax bills.

Like its peers Merck, AbbVie and Bristol Myers Squibb, Wyden notes how Amgen uses its Puerto Rico operations to consistently pay tax rates that are substantially lower than the U.S. corporate tax rate of 21%, with an effective tax rate of 10.7% in 2020 and 12.1% in 2021.

FDA ap­proves sec­ond in­di­ca­tion for As­traZeneca and Dai­ichi's En­her­tu in less than a week

AstraZeneca and Daiichi Sankyo’s antibody-drug conjugate Enhertu scored its second approval in less than a week, this time for a subset of lung cancer patients.

Enhertu received accelerated approval on Thursday to treat adults with unresectable or metastatic non-small cell lung cancer (NSCLC) whose tumors have activating HER2 (ERBB2) mutations, and who have already received a prior systemic therapy.

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J&J to re­move talc prod­ucts from shelves world­wide, re­plac­ing with corn­starch-based port­fo­lio

After controversially spinning out its talc liabilities and filing for bankruptcy in an attempt to settle 38,000 lawsuits, Johnson & Johnson is now changing up the formula for its baby powder products.

J&J is beginning the transition to an all cornstarch-based baby powder portfolio, the pharma giant announced on Thursday — just months after a federal judge ruled in favor of its “Texas two-step” bankruptcy to settle allegations that its talc products contained asbestos and caused cancer. An appeals court has since agreed to revisit that case.