Omid Farokhzad (file photo)

Seer rais­es $55M as pro­teomics ap­proach­es prime time in dis­ease de­tec­tion, drug de­vel­op­ment

Omid Farokhzad was work­ing in his Har­vard nan­otech lab in 2017 when he found some­thing he knew would be­come his next com­pa­ny. Two years and, as of to­day, over $100 mil­lion in fund­ing for lat­er, he still hasn’t re­vealed what it is.

“We’ve seen them re­port­ed, but we don’t re­al­ly know what their tech­nol­o­gy is or what it does.” Stephen Williams, the CMO of So­ma­Log­ic, the most high-pro­file po­ten­tial com­peti­tor to Farokhzad’s com­pa­ny, Seer, told End­points News.

The tech­nol­o­gy was big, though, or at least Farokhzad thought so. Big enough for him to leave much of his work in Boston, where he launched two com­pa­nies, opened his own lab and spent 20 years across Har­vard and MIT, to spend most of his time build­ing Seer in Red­wood City, out­side San Fran­cis­co. What he said was this: They were try­ing to best-of-both-worlds a sci­en­tif­ic idea. They want­ed to take a study of hu­man pro­teins they said was of­ten con­duct­ed with ei­ther slip­shod speed or painstak­ing pre­ci­sion and make it both fast and metic­u­lous.

Now, ex­act­ly a year af­ter its pub­lic launch and just as So­ma­Log­ic eyes its biggest com­mer­cial ex­pan­sion, Seer is an­nounc­ing $55 mil­lion in Se­ries D fund­ing and its own piv­ot from a re­search-fo­cused com­pa­ny to one try­ing to bring the pro­teome in­to the med­ical main­stream.

“There was the mo­ment, where I said I need to do this my­self,” Farokhzad told End­points, “and if I don’t I’m go­ing to re­gret it for the rest of my life.” 

Seer, So­ma­Log­ic, and a hand­ful of oth­er com­pa­nies work on what’s be­come known as the pro­teome. For decades, it had been tossed around as a bi­o­log­i­cal what-if, as se­duc­tive as it was un­at­tain­able. Per­haps in­stead of look­ing at DNA and RNA to un­der­stand the hu­man body and its dis­or­ders, we could look at the pro­teins that ge­net­ic code makes, the ones that in most cas­es ul­ti­mate­ly do the dam­age.

The hy­po­thet­i­cals were huge. In­stead of pre­dict­ing, based on ge­net­ics, if a 50-year-old had a pre­dis­po­si­tion to heart at­tacks or di­a­betes, a doc­tor could check if there had been ac­tu­al changes in the blood that built to those ail­ments. Phar­ma com­pa­nies could bet­ter un­der­stand how their drugs worked, and re­fine ac­cord­ing­ly.

One ob­sta­cle was math­e­mat­i­cal. With pro­teins, there are sim­ply far more pos­si­bil­i­ties. DNA has four let­ters and bonds in very spe­cif­ic ways and struc­tures: A-T, G-C, the dou­ble he­lix. Pro­teins are formed from up to 20 amino acids and can bond in myr­i­ad ways, and then change af­ter their cre­ation in­to a va­ri­ety of states de­pend­ing on what bonds to them.

“You ac­tu­al­ly need a lot of com­put­ing pow­er to cal­cu­late the the­o­ret­i­cal com­plex­i­ty you can cre­ate with pro­teins,” Farokhzad said. “You’ll nev­er get there.”

The oth­er prob­lem was chem­i­cal. DNA and RNA can be repli­cat­ed and am­pli­fied in a lab. Pro­teins can­not. In­stead, re­searchers have re­lied on bi­o­log­i­cal fish­ing ex­pe­di­tions. First, they used an­ti­bod­ies, which bind to pro­teins and make them eas­i­er to spot. But each an­ti­body on­ly binds to one pro­tein. Us­ing them to iden­ti­fy every hu­man pro­tein would be, as the New York Times’ Michael Be­har put it last year, “like try­ing to cat­a­log every fish in the ocean with a net that cap­tured on­ly a sin­gle species at a time.”

So­ma­Log­ic built it­self on the dis­cov­ery that nu­cle­ic acids called ap­tamers could be used to iden­ti­fy far more pro­teins at once. They built a data­base of 5,000 hu­man pro­teins, and then use ma­chine learn­ing to see how changes in those pro­teins’ struc­tures and quan­ti­ty cor­re­late with cer­tain health fac­tors. Af­ter decades of de­vel­op­ment and years of clin­i­cal tests, they launched their So­maSig­nal for med­ical prac­tices in Sep­tem­ber and bur­nished it with a De­cem­ber study in Na­ture that scanned 17,000 par­tic­i­pants for those 5,000 pro­teins and pre­dict­ed for di­a­betes and heart at­tack, among oth­er health is­sues.

Those who test­ed as high-risk could then be re­ferred to pre­ven­ta­tive mea­sures they may not oth­er­wise have re­ceived.

Stephen Williams came to So­ma­Log­ic in 2009 af­ter near­ly 20 years in ex­per­i­men­tal and clin­i­cal de­vel­op­ment at Pfiz­er

Click on the im­age to see the full-sized ver­sion

“We tried to de­vel­op 13 mod­els for 13 health is­sues, and we suc­ceed­ed with 11,” Williams said, adding they failed on­ly on weight pre­dic­tions and cur­rent di­et. “We re­al­ly an­swered the ques­tion: Can pro­teins be­come a sole in­for­ma­tion source?”

Farokhzad’s cri­tique is that this is a ‘bi­ased’ ap­proach: So­ma­Log­ic can on­ly look for the pro­teins it has ap­tamers for and it al­so can’t look deeply in­to spe­cif­ic changes. He said his Seer will be ‘un­bi­ased,’ rapid­ly iden­ti­fy­ing every pro­tein – at least 20,000 – and all the changes that can oc­cur with­in them and then use their own ma­chine learn­ing to find pat­terns. “Fast and broad,” he likes to call it.

“To re­al­ly un­der­stand pro­teomics, you have to do it in an un­bi­ased ap­proach,” he said.  “New bi­ol­o­gy is al­ways dri­ven by what we don’t know yet.”

Out in Red­wood City, Farokhzad has set up a Seer head­quar­ters with 40 em­ploy­ees and plans to ex­pand to 80 with the new fund­ing. He said they’ve spent the last year with their heads down try­ing to per­fect the sci­ence. Afraid biobanks might con­t­a­m­i­nate sam­ples with poor pro­ce­dures, they’ve set up 70 clin­i­cal sites na­tion­wide to build their data­base.

Oth­er folks have used an un­bi­ased ap­proach – help­ing build data­bas­es like the Hu­man Pro­teome Pro­ject, which now counts 19,823 pro­teins – but comb­ing through all those amino acids takes for­ev­er. Farokhzad has promised to make it fast enough to work with drug com­pa­nies (they al­ready have part­ners) and un­veil scans like those of­fered by So­ma­Log­ic.

If the tech holds up, it would have big im­pli­ca­tions for ear­ly de­tec­tion, un­veil­ing pre­vi­ous­ly hid­den changes in the body that presage dis­ease. Farokhzard claims it could help clin­i­cal tri­als, nam­ing Alzheimer’s and the hy­poth­e­sis that some of the drugs that failed might work if they treat a pa­tient ear­ly – at a stage we can’t yet de­tect. Like many in pro­teomics, he talks about it like a new fron­tier.

“We’re ba­si­cal­ly open­ing the flood­gate of ac­cess to pro­teom­ic in­for­ma­tion,” he said.

In So­ma­Log­ic’s view, though, that grand vi­sion isn’t nec­es­sary. All ap­proach­es are bi­ased, Williams said. The ques­tion is whether you can make pre­dic­tions that can be put to med­ical use.

“The ques­tion is whether you can mea­sure some­thing that is use­ful or ac­tion­able, not whether there’s some in­her­ent truth,” he said. “For our busi­ness, we don’t need to un­der­stand what the bi­ol­o­gy is. We let the ma­chine learn­ing pick out the best com­bi­na­tion of mea­sure­ments.”

Still, Williams said that when their long­time part­ner No­var­tis – which us­es So­ma­Log­ic’s tech to un­der­stand the mech­a­nisms of their drugs, among oth­er things – needs a high­er res­o­lu­tion look at what So­ma­Log­ic tech­nol­o­gy turns up, they di­rect them to a dif­fer­ent plat­form. Seer is de­vel­op­ing a com­mer­cial scan like So­ma­Log­ic’s and, like So­ma­Log­ic, even­tu­al­ly hopes to put out a (some­what con­tro­ver­sial) chip any­one can use, but their eas­i­est niche may be in drug de­vel­op­ment.

The in­dus­try will know soon enough. So­maSig­nal is on­ly avail­able in Col­orado for now, but a big­ger roll­out is pend­ing and they just hired a new com­mer­cial of­fi­cer. Af­ter two years in rel­a­tive ob­scu­ri­ty, Farokhzad said Seer will soon be open­ing up, and a prod­uct launch is sched­uled for 2021.

“Our tech­nol­o­gy risk is now large­ly put to rest and what lays ahead of us is ba­si­cal­ly prod­uct de­vel­op­ment and com­mer­cial­iza­tion,” he said.  “Now we’ve got to ex­e­cute.”

Once fu­ri­ous over No­var­tis’ da­ta ma­nip­u­la­tion scan­dal, the FDA now says it’s noth­ing they need to take ac­tion on

Back in the BP era — Before Pandemic — the FDA ripped Novartis for its decision to keep the agency in the dark about manipulated data used in its application for Zolgensma while its marketing application for the gene therapy was under review.

Civil and criminal sanctions were being discussed, the agency noted in a rare broadside at one of the world’s largest pharma companies. Notable lawmakers cheered the angry regulators on, urging the FDA to make an example of Novartis, which fielded Zolgensma at $2.1 million — the current record for a one-off therapy.

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Covid-19 roundup: GSK, Am­gen tai­lor R&D work to fit the coro­n­avirus age; Doud­na's ge­nomics crew launch­es di­ag­nos­tic lab

You can add Amgen and GSK to the list of deep-pocket drug R&D players who are tailoring their pipeline work to fit a new age of coronavirus.

Following in the footsteps of a lineup of big players like Eli Lilly — which has suspended patient recruitment for drug studies — Amgen and GSK have opted to take a more tailored approach. Amgen is intent on circling the wagons around key studies that are already fully enrolled, and GSK has the red light on new studies while the pandemic plays out.

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In a stun­ning set­back, Amarin los­es big patent fight over Vas­cepa IP. And its high-fly­ing stock crash­es to earth

Amarin’s shares $AMRN were blitzed Monday evening, losing billions in value as reports spread that the company had lost its high-profile effort to keep its Vascepa patents protected from generic drugmakers.

Amarin had been fighting to keep key patents under lock and key — and away from generic rivals — for another 10 years, but District Court Judge Miranda Du in Las Vegas ruled against the biotech. She ruled that:
(A)ll the Asserted Claims are invalid as obvious under 35 U.S.C.§ 103. Thus, the Court finds in favor of Defendants on Plaintiff’s remaining infringementclaim, and in their favor on their counterclaims asserting the invalidity of the AssertedClaims under 35 U.S.C. § 103.

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Covid-19 roundup: J&J, BAR­DA set ear­ly 2021 fin­ish line for $1B vac­cine race; FDA al­lows emer­gency drug use, ahead of piv­otal da­ta

J&J has zeroed in on a Covid-19 vaccine candidate that it hopes to begin testing in humans by September this year — with the extraordinary goal of getting it ready for emergency use in early 2021. And together with BARDA, it’s committing $1 billion to make it happen.

That kind of accelerated timeline would fall on the fast side of NIAID director Anthony Fauci’s well-publicized prediction that it would be another 12 to 18 months before a vaccine can be available for public use. A Phase I trial of Moderna’s mRNA vaccine began two weeks ago, and both the biotech and fellow mRNA player CureVac have discussed similar, if not even faster, timelines for emergency use among healthcare workers.

Mene Pangalos via YouTube

As­traZeneca says its block­buster Farx­i­ga proved to be a game-chang­er in CKD — wrap­ping PhI­II ear­ly

If the FDA can still hold up its end of the bargain, AstraZeneca is already on a short path to scooping up a cutting-edge win with a likely approval for their SGLT2 drug Farxiga in cutting the risk of heart failure. Now the pharma giant says it can point to solid evidence that the drug — initially restricted to diabetes — also works for chronic kidney disease, potentially adding a blockbuster indication for the franchise.

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It is 'kind of a proven tech­nol­o­gy': Hep B vac­cine mak­er joins glob­al hunt for coro­n­avirus vac­cine

Using lab-grown proteins that are engineered to mimic the architecture of viruses to induce an immune response, VBI Vaccines is joining the hunt for a coronavirus vaccine — harnessing technology that has initially been proved safe in early trials as a prophylactic for cytomegalovirus (CMV) infection.

Unlike the raft of the companies in the Covid-19 vaccine race — including Moderna, CureVac and J&J — VBI is taking a pan-coronavirus approach, by developing a vaccine that will encompass Covid-19, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS).

Can a pair of top AveX­is alum­ni steer a new gene ther­a­py up­start to R&D glo­ry? 3 VCs bet $60M on it

VCs love few things more than a proven executive team when it comes to launching a new company. And now a group of A-listers has turned to a pair of top execs out of AveXis to steer the latest gene therapy player into the clinic.

The biotech is Waltham, MA-based Affinia and the two execs are Sean Nolan and Rick Modi — the former CEO and CBO respectively of AveXis, the gene therapy pioneer that fetched $8.7 billion in a sale to Novartis. Nolan has now taken the chairman’s role at Affinia while Modi moves up to the CEO post at the company.

Un­de­terred by a pan­dem­ic, Gilde Health­care rais­es their largest fund yet

When Pieter van der Meer started raising the capital for Gilde Healthcare’s fifth fund in the waning months of 2019, he had his eyes on a different chain of events that could change the healthcare system and perhaps even play to his firm’s advantage: The US presidential election.

Since raising their third fund in 2011, the 34-year-old Dutch firm had focused on value-based care. They chose late-stage biotechs that came up with new devices and delivery systems for de-risked established compounds, and when they chose preclinical biotechs, they spoke with potential pharma partners, payers and regulators to ask where and at what prices the drug made sense. As the Democratic primary became a contest over how to lower healthcare costs, it looked like a strategy that could pay off.

Daniel O'Day (AP Images)

Gilead CEO Dan O'­Day of­fers a de­tailed ex­pla­na­tion on remde­sivir ac­cess — re­as­sur­ing an­a­lysts that Covid-19 da­ta are com­ing fast

After coming under heavy fire from consumer groups ready to pummel them for grabbing the FDA’s orphan status for remdesivir — reserved to encourage the development of rare disease therapies — Gilead CEO Daniel O’Day had some explaining to do about the company’s approach to providing access to this drug to patients suffering from Covid-19. And he set aside time over the weekend to patiently explain how they are making their potential pandemic drug available in a new program — one he feels can better be used to address a growing pack of infected patients desperately seeking remdesivir under compassionate use provisions.

In addition to trying to reassure patients that they will once again have an avenue to pursue access, O’Day also reassured some analysts who had been fretting that China’s quick comeback from the coronavirus outbreak could derail its ultra-fast schedule for testing the drug in patients. The data are still expected in a few weeks, he says in the letter, putting the readout in April.

O’Day emphasizes that Gilead intends to pursue a pricing approach that will make this drug widely available — if it proves effective and safe. But no one is quite sure just what the longterm value would be, given the work being done on a variety of vaccines that may be rolled out as early as this fall — at least to the most heavily threatened groups.

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