Betting Early on an AI Niche, RA Capital Seeds a Young Founder’s Quest to Unlock ‘Holy Grail’ Targets

On June 16, 2021 New Equilibrium Biosciences reported Endpoints News that intelligence, with its grandiose claims and sweeping promises to revolutionize drug discovery, may seem omnipresent in biopharma now (Press release, New Equilibrium Biosciences, JUN 16, 2021, View Source [SID1234584057]). But Virginia Burger and RA Capital believe there are niches it has yet to touch.

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After taking up residency at the star-studded Boston accelerator Petri, Burger’s startup — named New Equilibrium Biosciences — has scored $10 million in seed cash from the VC firm to prove that by reaching into those corners, they could uncover drugs against "Holy Grail" targets in everything from cancer to neurodegenerative diseases.

Specifically, the biotech is interested in a class of proteins called intrinsically disordered proteins that doesn’t have a single folded structure. MYC, for instance, is a cancer-causing IDP.

"They break this paradigm of sequence to structure to function because it’s really sequence to multiple of different conformations which have many different functions," she told Endpoints News.

They can also range from fully unstructured to partially structured ones containing a disordered region, something condensate players like Dewpoint are focused on.

Cracking this special class, RA Capital principal Nathaniel Brooks Horwitz said, required a new breed of company that integrates AI in physics modeeling for drug discovery, beyond what the pioneers — he counts Schrödinger, Relay, Silicon Atomwise, Recursion and Exscientia among others — are doing.

"What we’re really excited about is when a company like New Equilibrium can enable a target about which we can say the following — ‘If only we could develop a drug for this target’ — we’re confident it will be successful," he said.

As a PhD in Pittsburgh and later postdoc at MIT, Burger would read papers highlighting their importance as drug targets. But they were so hard to target that until midway through her postdoc, scientists weren’t even sure if ligands could bind to them — they wiggle around too quickly to be even seen in experiments. Even when they did find molecules that bound weakly to the proteins, there was no real way to optimize them into drug candidates.

Immersed in the entrepreneurial environment at MIT, it seemed natural to build a startup around the computational methods she had been developing to identify the set of conformations the proteins would switch between. First, though, she took a job at XtalPi, the US-China AI biotech startup backed by Tencent and later SoftBank and Morningside.

It was during that two-year stint that she met Peter Tompa, a professor at Flanders Institute for Biotechnology who’s devoted his career to studying IDP structure and function. He was interested in starting a company together.

Two weeks later, she was out.

The first thing she did after receiving funding from Petri — an accelerator set up to tailor to the needs of young founders — was to buy quantum chemical software and start generating their own training data for a new kind of physics model.

Existing computational models, Burger said, were built on what’s already known about folded structures, which renders them the wrong fit for intrinsically disordered proteins. By using AI to learn quantum chemistry — the energies and forces on each atom that give rise to a shape at any given moment — New Equilibrium’s algorithms can "see," in silico, thousands or even millions of possible structures over time.

"We’re redoing how simulations have been done in the past by rebuilding the underlying simulation architecture to use AI for each step instead of introducing a single — the standard calculation for each step," she said.

The next step is to zero in on the structures that are more stable or appear more frequently, screen ligands against them in a wet lab, and then fuse the fragments binding to different structures in the same molecule. Burger can’t yet reveal how many fragments they’d need for each drug made this way, but noted that the seed funding will get them closer to preclinical candidates.

For RA Capital, the deal marks another move in their shift toward earlier stages of venture financing.

Quantum computing, Horwitz noted, is looming on the horizon with hardware starting to take shape. And the technology will ultimately make it possible to "fully model the true biophysical state of even the most complex molecular interactions."

"Which will be the companies that are the first to use quantum computing and all the power that brings to rationally design medicines for meaningful targets?" he said. "I think New Equilibrium can be that company."

New Equilibrium Biosciences Awarded Competitive Grant from the National Science Foundation

On June 16, 2021 New Equilibrium Biosciences reported it has been awarded a National Science Foundation (NSF) Small Business Innovation Research (SBIR) for [$$$ AMOUNT] to conduct research and development (R&D) work on drug candidates that regulate intrinsically disordered proteins implicated in cancers and neurodegenerative disorders (Press release, New Equilibrium Biosciences, JUN 16, 2021, View Source [SID1234584055]).

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New Equilibrium Biosciences is dedicated to developing new medicines through cutting edge sciences and cross-disciplinary collaborates. New Equilibrium combines big data, artificial intelligence, and biophysical experiments to accurately visualize the many different conformations that IDP’s, a class of shapeshifting proteins, may adopt. The overarching motivations for this work is to benefit the greater good by specifically targeting and drugging malfunction IDPs to restore normal cell function in those with cancer and neurodegenerative disorders.

"NSF is proud to support the technology of the future by thinking beyond incremental developments and funding the most creative, impactful ideas across all markets and areas of science and engineering," said Andrea Belz, Division Director of the Division of Industrial Innovation and Partnerships at NSF. "With the support of our research funds, any deep technology startup or small business can guide basic science into meaningful solutions that address tremendous needs."

Once a small business is awarded a Phase I SBIR/STTR grant (up to $256,000), it becomes
eligible to apply for a Phase II grant (up to $1,000,000). Small businesses with Phase II grants
are eligible to receive up to $500,000 in additional matching funds with qualifying third-party
investment or sales.

Startups or entrepreneurs who submit a three-page Project Pitch will know within three weeks if
they meet the program’s objectives to support innovative technologies that show promise of
commercial and/or societal impact and involve a level of technical risk. Small businesses with
innovative science and technology solutions, and commercial potential are encouraged to apply.
All proposals submitted to the NSF SBIR/STTR program, also known as America’s Seed Fund powered by NSF, undergo a rigorous merit-based review process. To learn more about
America’s Seed Fund powered by NSF, visit: View Source

About the National Science Foundation’s Small Business Programs: America’s Seed Fund
powered by NSF awards $200 million annually to startups and small businesses, transforming
scientific discovery into products and services with commercial and societal impact. Startups
working across almost all areas of science and technology can receive up to $1.75 million to
support research and development (R&D), helping de-risk technology for commercial success.
America’s Seed Fund is congressionally mandated through the Small Business Innovation
Research (SBIR) program. The NSF is an independent federal agency with a budget of about
$8.1 billion that supports fundamental research and education across all fields of science and
engineering.

Mustang Bio to Present at the Raymond James Human Health Innovation Conference

On June 16, 2021 Mustang Bio, Inc. ("Mustang") (NASDAQ: MBIO), a clinical-stage biopharmaceutical company focused on translating today’s medical breakthroughs in cell and gene therapies into potential cures for hematologic cancers, solid tumors and rare genetic diseases, reported that Manuel Litchman, M.D., President and Chief Executive Officer, will present at the Raymond James Human Health Innovation Conference, taking place virtually from June 21 – 23, 2021(Press release, Mustang Bio, JUN 16, 2021, View Source [SID1234584089]). The company will present on Wednesday, June 23, 2021, at 8:00 a.m. ET and will also participate in one-on-one meetings during the conference. A webcast of the company’s presentation will be available on the Events page of the Investor Relations section of Mustang’s website, www.mustangbio.com, for approximately 30 days after the meeting.

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Acorda Therapeutics Announces Repayment of Convertible Senior Notes

On June 15, 2021 Acorda Therapeutics, Inc. (Nasdaq: ACOR) reported that on June 15, 2021, it repaid in full its 1.75% Convertible Senior Notes due 2021(Press release, Acorda Therapeutics, JUN 16, 2021, View Source [SID1234584039]). Prior to their maturity and repayment, there were $69.0 million aggregate principal amount of 2021 notes outstanding. The 2021 notes were repaid using cash on hand.

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"The repayment of the 2021 notes removes an overhang on the company and is another important milestone in our strategy, following the sale of our manufacturing operations earlier this year. We are focused on accelerating the growth of INBRIJA, continuing to maintain the strength of AMPYRA, and optimizing the company’s financial structure," said Ron Cohen, M.D., Acorda’s President and Chief Executive Officer. "We have maintained cost discipline since our restructuring announcement in February and are continuing to drive toward cash flow breakeven.

FDA Approves Blueprint Medicines’ AYVAKIT™ (avapritinib) for the Treatment of Adults with Advanced Systemic Mastocytosis

On June 16, 2021 Blueprint Medicines Corporation (NASDAQ: BPMC) reported that the U.S. Food and Drug Administration (FDA) has approved AYVAKIT (avapritinib) for the treatment of adult patients with advanced systemic mastocytosis (Advanced SM), including aggressive SM (ASM), SM with an associated hematological neoplasm (SM-AHN) and mast cell leukemia (MCL)(Press release, Blueprint Medicines, JUN 16, 2021, View Source [SID1234584058]). For the first time, advanced SM patients can now receive a targeted therapy designed to potently and selectively inhibit D816V mutant KIT, the central driver of the disease.

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"Today’s approval of AYVAKIT for advanced systemic mastocytosis – the fourth FDA approval across our portfolio in 18 months – culminates nearly a decade of hard work, from our scientists in the laboratory and clinical team conducting trials, to our commercial organization who will now bring AYVAKIT to patients," said Jeff Albers, Chief Executive Officer of Blueprint Medicines. "As shown in two clinical trials, AYVAKIT provides remarkable clinical efficacy to patients with advanced systemic mastocytosis, and this approval solidifies the therapy’s strong value proposition in this population. With a deep commitment to driving continued research innovation in collaboration with the mast cell disease community, we are now building on this progress with the goal of bringing the benefits of precision therapy to a broader range of patients through our ongoing and planned clinical trials for non-advanced systemic mastocytosis."

SM is a rare hematologic disorder caused by the KIT D816V mutation in nearly all cases. Across advanced SM subtypes, the median overall survival is approximately 3.5 years in ASM, approximately two years in SM-AHN and less than six months in MCL.1

"Advanced systemic mastocytosis is a debilitating disease characterized by extensive damage in multiple organ systems due to mast cell infiltration, and new treatment options are urgently needed to address these life-threatening complications," said Daniel DeAngelo, M.D., Ph.D., Chief of the Division of Leukemia at Dana-Farber Cancer Institute. "Avapritinib will clearly establish a new standard of care for patients with advanced systemic mastocytosis. The FDA approval was based on data showing robust and durable responses, including complete remissions, and a favorable safety profile. For advanced SM patients, the approval of avapritinib shifts the treatment paradigm toward precision therapy that targets the primary driver of mastocytosis.

The FDA granted full approval to AYVAKIT for adults with advanced SM based on data from the Phase 1 EXPLORER trial and Phase 2 PATHFINDER trial.2 Treatment response was evaluated using modified IWG-MRT-ECNM criteria, with assessments based on at least 12 weeks of response duration, resolution of at least one finding of non-hematologic and hematologic organ damage, and 50 percent or greater reductions in biomarker response, mast cell burden and serum tryptase. The overall response rate (ORR) in the U.S. prescribing information is defined as complete remission with full or partial hematologic recovery (CR/CRh), or partial remission (PR).

AYVAKIT showed durable clinical efficacy in advanced SM patients across disease subtypes and regardless of prior therapy. In 53 evaluable patients who had a median follow-up of 11.6 months, the ORR was 57 percent (95% CI: 42%, 70%), and the proportion of patients with CR/CRh (28 percent), PR (28 percent) and clinical improvement (15 percent) is in line with previously reported results. The median duration of response was 38.3 months (95% CI: 19 months, not estimable). Warnings and precautions include intracranial hemorrhage, cognitive effects and embryo-fetal toxicity. AYVAKIT is not recommended for the treatment of patients with advanced SM with low platelet counts (less than 50,000/µL), which is consistent with current patient eligibility criteria in the EXPLORER and PATHFINDER trials. The most common adverse reactions were edema, diarrhea, nausea and fatigue/asthenia.

"People with advanced systemic mastocytosis face a scary, uncertain future due to life-threatening complications of the disease, as well as debilitating symptoms that often profoundly alter their ability to perform daily activities, and the FDA approval of a new therapy, AYVAKIT, brings much needed hope to these patients," said Valerie Slee, Board Chair of The Mast Cell Disease Society.

"This milestone is also the culmination of many years of work across the systemic mastocytosis community, and we’re proud of the contributions The Mast Cell Disease Society has made to improve the understanding of this disease, pioneer new approaches to measuring the impact of therapeutic interventions, and support the development of important medicines like AYVAKIT," said Lauren Denton, Executive Director of The Mast Cell Disease Society. "We look forward to continuing our collaboration with Blueprint Medicines, scientific and clinical experts, and other stakeholders across our community to improve diagnosis, treatment and care for all patients living with systemic mastocytosis."

Blueprint Medicines is committed to advancing precision therapies for the benefit of SM patients. The company is developing AYVAKIT for the treatment of non-advanced SM patients, and BLU-263, a next-generation KIT D816V inhibitor, to further address the range of medical needs in this patient population.

For advanced SM patients receiving AYVAKIT, Blueprint Medicines provides access and affordability programs through YourBlueprint. For more information, visit YourBlueprint.com or call 1-888-BLUPRNT (1-888-258-7768), Monday to Friday, 8:00 a.m. to 8:00 p.m. ET. Healthcare providers who prescribe AYVAKIT can fill out an enrollment form at YourBlueprint.com/HCP to help patients access Blueprint Medicines’ support programs.

The recommended dose of AYVAKIT in advanced SM is 200 mg once daily. AYVAKIT is available in 200 mg, 100 mg, 50 mg and 25 mg dose strengths for advanced SM patients.

Conference Call Information

Blueprint Medicines will host a live webcast beginning at 4:30 p.m. ET today to discuss the FDA approval of AYVAKIT in advanced SM. To access the live call, please dial (833) 921-1639 (domestic) or (236) 389-2650 (international) and refer to conference ID 4328214. A webcast of the conference call will be available under "Events and Presentations" in the Investors & Media section of Blueprint Medicines’ website at View Source The archived webcast will be available on Blueprint Medicines’ website approximately two hours after the conference call and will be available for 90 days following the call.

About AYVAKIT (avapritinib)

AYVAKIT (avapritinib) is a kinase inhibitor approved by the FDA for the treatment of two indications: adults with Advanced SM, including ASM, SM-AHN and MCL, and adults with unresectable or metastatic gastrointestinal stromal tumors (GIST) harboring a PDGFRA exon 18 mutation, including PDGFRA D842V mutations. For more information, visit AYVAKIT.com. This medicine is approved in Europe (AYVAKYT) for the treatment of adults with unresectable or metastatic GIST harboring the PDGFRA D842V mutation, and in Mainland China (AYVAKIT) for the treatment of adults with unresectable or metastatic PDGFRA exon 18 mutant GIST.

AYVAKIT/AYVAKYT is not approved for the treatment of any other indication in the U.S., Europe or Greater China, or for any indication in any other jurisdiction by any other health authority.

Blueprint Medicines is developing AYVAKIT globally for the treatment of advanced and non-advanced SM. The FDA granted breakthrough therapy designation to AYVAKIT for the treatment of advanced SM, including the subtypes of ASM, SM-AHN and MCL, and for the treatment of moderate to severe indolent SM.

To learn about ongoing or planned clinical trials, contact Blueprint Medicines at [email protected] or 1-888-BLU-PRNT (1-888-258-7768). Additional information is available at pioneertrial.com or clinicaltrials.gov.

Blueprint Medicines has an exclusive collaboration and license agreement with CStone Pharmaceuticals for the development and commercialization of AYVAKIT in Mainland China, Hong Kong, Macau and Taiwan. Blueprint Medicines retains development and commercial rights for AYVAKIT in the rest of the world.

About SM

SM is a rare disease driven by the KIT D816V mutation. Uncontrolled proliferation and activation of mast cells result in chronic, severe and often unpredictable symptoms for patients across the spectrum of SM. The vast majority of those affected have non-advanced (indolent or smoldering) SM, with debilitating symptoms that lead to a profound, negative impact on quality of life. A minority of patients have advanced SM, which encompasses a group of high-risk SM subtypes including ASM, SM-AHN and MCL. In addition to mast cell activation symptoms, advanced SM is associated with organ damage due to mast cell infiltration and poor survival.

Debilitating symptoms, including anaphylaxis, maculopapular rash, pruritis, diarrhea, brain fog, fatigue and bone pain, often persist across all forms of SM despite treatment with a number of symptomatic therapies. Patients often live in fear of severe, unexpected symptoms, have limited ability to work or perform daily activities, and isolate themselves to protect against unpredictable triggers. Historically, there had been no approved therapies for the treatment of SM that selectively inhibit D816V mutant KIT.

Important Safety Information

Serious intracranial hemorrhage (ICH) may occur with AYVAKIT treatment; fatal events occurred in <1% of patients. Overall, ICH (eg, subdural hematoma, ICH, and cerebral hemorrhage) occurred in 2.9% of 749 patients who received AYVAKIT. In Advanced SM patients who received AYVAKIT at 200 mg daily, ICH occurred in 2 of 75 patients (2.7%) who had platelet counts ≥50 x 109/L prior to initiation of therapy and in 3 of 80 patients (3.8%) regardless of platelet counts. Monitor patients closely for risk of ICH including those with thrombocytopenia, vascular aneurysm or a history of ICH or cerebrovascular accident within the prior year. Permanently discontinue AYVAKIT if ICH of any grade occurs. A platelet count must be performed prior to initiating therapy. AYVAKIT is not recommended in Advanced SM patients with platelet counts <50 x 109/L. Following treatment initiation, platelet counts must be performed every 2 weeks for the first 8 weeks. After 8 weeks of treatment, monitor platelet counts every 2 weeks or as clinically indicated based on platelet counts. Manage platelet counts of <50 x 109/L by treatment interruption or dose reduction.

Cognitive adverse reactions can occur in patients receiving AYVAKIT. Cognitive adverse reactions occurred in 39% of 749 patients and in 28% of 148 SM patients (3% were Grade >3). Memory impairment occurred in 16% of patients; all events were Grade 1 or 2. Cognitive disorder occurred in 10% of patients; <1% of these events were Grade 3. Confusional state occurred in 6% of patients; <1% of these events were Grade 3. Other events occurred in <2% of patients. Depending on the severity, withhold AYVAKIT and then resume at same dose or at a reduced dose upon improvement, or permanently discontinue.

AYVAKIT can cause fetal harm when administered to a pregnant woman. Advise pregnant women of the potential risk to a fetus. Advise females and males of reproductive potential to use an effective method of contraception during treatment with AYVAKIT and for 6 weeks after the final dose of AYVAKIT. Advise women not to breastfeed during treatment with AYVAKIT and for 2 weeks after the final dose.

The most common adverse reactions (≥20%) at all doses were edema, diarrhea, nausea, and fatigue/asthenia.

Avoid coadministration of AYVAKIT with strong and moderate CYP3A inhibitors. If coadministration with a moderate CYP3A inhibitor cannot be avoided, reduce dose of AYVAKIT. Avoid coadministration of AYVAKIT with strong and moderate CYP3A inducers.

To report suspected adverse reactions, contact Blueprint Medicines Corporation at 1-888-258-7768 or FDA at 1-800-FDA-1088 or www.fda.gov/medwatch.

Please click here to see the full Prescribing Information for AYVAKIT.