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.”

2023 Spot­light on the Fu­ture of Drug De­vel­op­ment for Small and Mid-Sized Biotechs

In the context of today’s global economic environment, there is an increasing need to work smarter, faster and leaner across all facets of the life sciences industry.  This is particularly true for small and mid-sized biotech companies, many of which are facing declining valuations and competing for increasingly limited funding to propel their science forward.  It is important to recognize that within this framework, many of these smaller companies already find themselves resource-challenged to design and manage clinical studies themselves because they don’t have large teams or in-house experts in navigating the various aspects of the drug development journey. This can be particularly challenging for the most complex and difficult to treat diseases where no previous pathway exists and patients are urgently awaiting breakthroughs.

Rick Modi, Affinia Therapeutics CEO

Ver­tex-part­nered gene ther­a­py biotech Affinia scraps IPO plans

Affinia Therapeutics has ditched its plans to go public in a relatively closed-door market that has not favored Nasdaq debuts for the drug development industry most of this year. A pandemic surge in 2020 and 2021 opened the doors for many preclinical startups, which caught Affinia’s attention and gave the gene therapy biotech confidence in the beginning days of 2022 to send in its S-1.

But on Friday, Affinia threw in the S-1 towel and concluded now is not the time to step onto Wall Street. The biotech has put out few public announcements since the spring of this year. Endpoints News picked the startup as one of its 11 biotechs to watch last year.

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Up­dat­ed: FDA re­mains silent on or­phan drug ex­clu­siv­i­ty af­ter last year's court loss

Since losing a controversial court case over orphan drug exclusivity last year, the FDA’s Office of Orphan Products Development has remained entirely silent on orphan exclusivity for any product approved since last November, leaving many sponsors in limbo on what to expect.

That silence means that for more than 70 orphan-designated indications for more than 60 products, OOPD has issued no public determination on the seven-year orphan exclusivity in the Orange Book, and no new listings of orphan exclusivity appear in OOPD’s searchable database, as highlighted recently by George O’Brien, a partner in Mayer Brown’s Washington, DC office.

Albert Bourla, Pfizer CEO (Efren Landaos/Sipa USA/Sipa via AP Images)

Pfiz­er makes an­oth­er bil­lion-dol­lar in­vest­ment in Eu­rope and ex­pands again in Michi­gan

Pfizer is continuing its run of manufacturing site expansions with two new large investments in the US and Europe.

The New York-based pharma giant’s site in Kalamazoo, MI, has seen a lot of attention over the past year. As a major piece of the manufacturing network for Covid-19 vaccines and antivirals, Pfizer is gearing up to place more money into the site. Pfizer announced it will place $750 million into the facility, mainly to establish “modular aseptic processing” (MAP) production and create around 300 jobs at the site.

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Vas Narasimhan, Novartis CEO (Thibault Camus/AP Images, Pool)

No­var­tis bol­sters Plu­vic­to's case in prostate can­cer with PhI­II re­sults

The prognosis is poor for metastatic castration-resistant prostate cancer (mCRPC) patients. Novartis wants to change that by making its recently approved Pluvicto available to patients earlier in their course of treatment.

The Swiss pharma giant unveiled Phase III results Monday suggesting that Pluvicto was able to halt disease progression in certain prostate cancer patients when administered after androgen-receptor pathway inhibitor (ARPI) therapy, but without prior taxane-based chemotherapy. The drug is currently approved for patients after they’ve received both ARPI and chemo.

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Pfiz­er-backed Me­di­ar Ther­a­peu­tics ropes in an­oth­er Big Phar­ma in­vestor

A biotech centered on treating fibrosis — born out of Mass General and Brigham and Women’s Hospital — has received a financial boost.

According to an SEC filing, the company has raised $31,761,186 in its latest funding round, which includes 17 investors. The filing lists six names attached to the company, including Meredith Fisher, a partner at Mass General Brigham Ventures and Mediar’s acting CEO.

Ken Greenberg, SonoThera CEO

Gene ther­a­py goes acoustic as ARCH-backed biotech launch­es with ul­tra­sound gene de­liv­ery plat­form

After co-founding two biotechs off virus-based therapies, one for pain and one for cancer, Ken Greenberg decided to go in a different direction for his newest biotech, SonoThera.

Based out of San Francisco, SonoThera announced Monday morning that it raised $60.75 million to develop new gene therapies — but delivered by ultrasound, which Greenberg says can address the major challenges facing more conventional viral gene therapies.

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Af­ter M&A fell through, Ther­a­peu­tic­sMD sells hor­mone ther­a­py, con­tra­cep­tive ring for $140M cash plus roy­al­ties

TherapeuticsMD, a women’s health company whose one-time billion-dollar valuation seems a distant memory as its blockbuster aspirations petered out, is finally cashing out.

Australia’s Mayne Pharma is paying $140 million upfront to license essentially TherapeuticsMD’s whole portfolio, including two prescription drugs that treat conditions relating to menopause, a contraceptive vaginal ring as well as its prescription prenatal vitamin brands.

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Big week for Alzheimer’s da­ta; As­traZeneca buys cell ther­a­py start­up; Dig­i­tal ther­a­peu­tics hits a pay­er wall; 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.

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