Team Deep Origin at Lake Sevan (photo courtesy Ashot Papoyan)

Ashot Papoyan Advances Biotech in US and Armenia

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By Raffi V. Arkun

Special to the Mirror-Spectator

ARLINGTON, Mass. — Deep Origin is a company working on simulating molecular interactions to accelerate drug discovery, with a team of about 80 people, in locations spanning from California and Arlington, MA, to Europe and Armenia. Its specialty is making simulation tools, to predict, for example, how a novel medicine interacts with a disease-causing protein, or determine how proteins interact with each other, at either molecular or cellular scales. In the foreseeable future, the company plans to develop technology for simulating processes on organ, tissue, and organism levels. The long-term goal is to replace costly physical experiments in the lab with computer simulations, accelerating drug discovery and treatments. As the current Chief Scientific Operations Officer (CSOO), Dr. Ashot Papoyan oversees tech development and wet lab operations across 11 time zones. “The moonshot goal” of Deep Origin, Papoyan said, “is simulating life.”

Dr. Ashot Papoyan (photo Aram Arkun)

Even as a child, Papoyan knew that biology was his calling, and today he loves his job so much that he said, “I don’t know what a 9 to 5 feels like.” Born in Yerevan to engineer parents, Papoyan was surrounded by the sciences throughout his whole youth. He graduated from Artashes Shahinyan Physics-Mathematics School (known colloquially as Phys-Math School), continuing his education at Yerevan State University. By 1999, Papoyan had completed a degree in biophysics and met his college sweetheart, Yelena Bisharyan, who was pursuing studies in genetics. During the summer prior to his senior year of university, Papoyan visited Cornell University in Ithaca, New York, to take summer classes. He also learned about the admission process, what differences exist between American and Armenian schools, the process of obtaining a doctorate, and much more.

Ashot Papoyan, looking at the camera, during his graduation from Cornell (photo courtesy Ashot Papoyan)

Upon returning to Armenia after graduation, Papoyan’s life journey began with his marriage to Yelena. Soon after, he completed the standardized exams and gained admission to Cornell’s doctoral program in plant molecular biology. The couple relocated to Ithaca, NY, where Yelena also pursued her doctorate in immunology and cell and molecular biology.

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At the conclusion of his studies at Cornell, Papoyan became the first employee and a founding team member of a newly formed biotech company focused on producing transmembrane proteins, difficult to generate in bacteria or yeast, using Tetrahymena thermophila, a single-celled organism. In 2011, Tetragenetics secured a grant from the state of Massachusetts to relocate to Cambridge and later to Arlington. The company was ultimately acquired by AbCellera Biologics, a Vancouver-based biotech firm.

In 2019 Papoyan founded a new company, Elm Tree Research, together with Dr. Zorayr Manukyan, to focus on research and clinical trial design, execution and data utilization to provide effective treatment for addictions. The biggest challenge in creating this company, he said, was finding funding, relying on friends and family first before expanding to outside investors. Another connected company, Elm Tree Clinic, of which Papoyan was a managing partner, is associated with the research arm, and treats mental health disorders such as addictions to alcohol or opioids, plus behavioral health services.

After running this company for around four years, Papoyan joined the BiosimAI team, transitioning to a less involved role in Elm Tree. Biosim was a biotech company based in Armenia founded in 2020 by Papoyan’s older brother Garegin (“Garyk”) Papoian, a professor of chemistry and biophysics at the University of Maryland (who also obtained his Ph.D. at Cornell). The main reason for this switch is what Papoyan termed a once-in-a-lifetime opportunity: the chance to work with his brother on something as cutting edge as accelerating drug discovery, while also being involved with Armenian science in a business sense rather than philanthropically, was too much to pass up.

In January, 2024, BiosimAI was acquired by and merged with the biotechnology firm Deep Origin, which itself was founded in 2022 by Michael Antonov and was based in South San Francisco, California. Garegin became the chief science officer of Deep Origin. The headquarters remained in South San Francisco, but around half of the company’s employees, around forty people, remain in Armenia, Papoyan said, where a lot of deep-tech R&D and software development takes place. Papoyan, who still lives and works in Massachusetts, said he goes to both places quite often. There are also employees working remotely from other parts of the US and Europe.

Two big advantages related to Armenia are its bright scientists, plus the fact that they are also less expensive to hire than their American counterparts. Historically, Armenians have always been strong in mathematical sciences and computer sciences, which is exactly what the company taps into. One difficulty that comes with having employees in different countries is dealing with the different time zones in setting up meetings.

Dr. Ashot Papoyan, at left end, and Dr. Garegin Papoian at the right end, with the winners of Deep Origin Hackathon in Armenia (photo courtesy Ashot Papoyan)

To avoid problems concerning intellectual property rights, Papoyan said that most patents are completed through the US system, due to its intellectual property laws being well designed and more comprehensive.

Papoyan organizes the experiments of the lab in San Francisco, which tests whether the computational predictions are correct in real life. This proves to the world the reliability of the simulation process or tools that the company has developed. He said that the proof of concept, making a prediction, synthesizing molecules, then doing the experiments in the lab, will take roughly six months. Many such tests must be done so Papoyan said it will take two to three years of such testing of predictions to create a good foundation from which to move forward.

Giving Back

Dr. Papoyan has not only been a successful entrepreneur, but he also gives back to the Armenian community, both in the homeland and the United States. Since his first year at Cornell, he has been involved in giving grants to Armenian scientists through the Armenia National Science and Education Fund (ANSEF), founded by Cornell astrophysicist Professor Yervant Terzian. Proposals are sent from Armenia to peers in America for review, and the highest scored innovations receive grants. ANSEF is part of the Fund for Armenian Relief (FAR), which is the umbrella organization of the Eastern Diocese of the Armenian Church of American for philanthropy to Armenia. Currently, he is the co-chair of ANSEF alongside Prof. Vatche Sahakian, a physicist at Harvey Mudd College in Claremont, California. Throughout the past 25 years, over 3 million dollars have been given to Armenian scientists through these programs. Armenian science did not have a lot of funding, especially in the early years of ANSEF, which is why it is so important to give young Armenians the chance to really compete with the rest of the world through ANSEF.

Papoyan is a member of the Armenian Society of Fellows (ASOF), where he is involved in several educational initiatives, as well as biology related organizations. He works on coordinating classes in the mathematical and biological fields.

Dr. Papoyan also has some ideas for how Armenia can continue to be at the cutting edge of science. Computational biology is the “lowest hanging fruit” in his field, in the sense that it is both important and viable. Since the main requirement is software, there will not have to be the costs of new infrastructure or massive industrial needs. This is a prerequisite to moving on to experimental biology, which is more costly and does need the infrastructure of laboratories, freezers, animal housing, etc.

Appropriate available education is important to create the basis for Armenian advancements in science. Private companies have recently realized that Armenians need to have better education, so they are investing in internships and classes in order to improve the pipeline of a qualified workforce. However, Papoyan said that as a small country, Armenia cannot produce large numbers of specialists in all fields, so it needs to carefully choose particular fields on which to focus.

In addition to his support of Armenia, Dr. Papoyan is also active in the Armenian-American community. He is a member of the Knights of Vartan’s Ararat Lodge of Boston, but he also has made a great impact as one of the founding members of the Armenian Biotech Group of Boston. He established it together with his wife, Yelena Bisharyan and several colleagues in 2012 as an initiative to connect Armenians in this field. He said that “it started as lunch with a few friends” but it expanded into an organization of over 250 members. There are regular in-person meetings, every quarter, where a member makes a presentation about his work, talking about his company, various initiatives, and what can specifically be done for Armenia. The organization is intended to be especially impactful for young professionals in biotechnology field, allowing the rare opportunity for an intern to meet a CEO. Bisharyan at present is in charge of the organization.

Advice

“Love what you do and you will become outstanding” are the words Dr. Papoyan lives by. Rather than being a mediocre worker at an unsatisfying job, everybody has the potential to become excellent at something they love, he stressed. One of the biggest worries is finding support for taking a leap of faith, yet Papoyan said he felt that people’s nature is to be receptive and forthcoming, something Dr. Papoyan sees every day through the Armenian biotech group. Someone starting out should look for and use all possible resources, Papoyan said, which of course includes Armenian networking.

American citizens have the advantage of various resources through the Small Business Innovation Research (SBIR) and Small Business Technology Transfer (STTR) programs of the US government, Papoyan said. The government takes the risk of investing in small startups, and as a result of this the best innovations continually are created in America.

The easiest way to get started is to find a mentor, someone or something you would consider smarter than you, as early as possible, Papoyan advised. This doesn’t have to be a person – it could even be a philosophy or book. This holds true for both personal life and profession, he noted. After this step, with a continual desire to learn, everything will fall into place. As long as you love what you are doing, Papoyan concluded, “work” does not feel like a job, and you will never count the hours.

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