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✅ The hidden power of “proximity” in biology. ✅ How chemoproteomics maps drug interactions inside living cells. ✅ A founder chasing his “white whale”. ✅ Why small molecules were left behind - and why they’re back.

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Longevity Builders tells the stories of those aiming to tackle aging - focusing on the science they’re building, the hurdles they face, and the people willing to do whatever it takes.

In this installment, we feature General Proximity, a San Francisco biotech reimagining what small molecules can do - by turning them into tools to control biology’s most elusive processes.

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Control proximity and you control biology

Armand Cognetta tells me there’s one target he’s obsessed with. ”Above all the others,” he says. While the rest of the world considers it undruggable - and pharma companies have failed, time and again - his startup, San Francisco–based General Proximity, has it in its crosshairs. This target is his white whale - so critical, he says, that it would be worth ”spending your entire life on.”

He won’t tell me what it is. Not yet. But I get the sense he’s counting the days until he can.

”Our first clinical trial won't be an aging trial,” Armand says, “but it'll be for a target that we then can, with the same drug, expand into an aging indication. It’s in an area where we think it will have massive impact. It’s for every human on the planet. There’s not many drugs like that.”

So how do you go after a target the world has already given up on?

That’s where a reimagining of small molecules comes into the picture.

To understand how General Proximity plans to drug the undruggable, we first need to talk about what small molecules are - and why they’ve been both the foundation of modern medicine and one of its biggest limitations.

Small molecules are the classic workhorses of medicine - simple, chemically synthesized compounds that are usually taken as pills and can easily enter cells to affect their targets. They dominate the pharmaceutical landscape because they’re cheap to manufacture, easy to deliver, and well understood, with decades of infrastructure built around them.

But they also come with major drawbacks: most small molecules fail during drug development, and those that succeed often come with off-target effects, limited specificity, or difficulty addressing complex intracellular processes.

And so, in the recent past, attention shifted elsewhere. Biologics, gene therapies, RNA-based drugs - these newer modalities offered fresh hope for reaching targets that small molecules couldn’t. They promised greater precision and the ability to hit previously untouchable biology.

They too came with steep trade-offs: they're often expensive to produce, complex to manufacture, and difficult to deliver - especially into cells or across the blood-brain barrier. Most can’t be taken orally. Still, the excitement around these modalities was so great that it reshaped the industry's imagination. Small molecules - once the foundation of modern medicine - were increasingly seen as blunt instruments. Not obsolete, but outclassed. They were pushed to the sidelines, overshadowed by therapies that felt like they belonged to the future, not the past.

This shift has become especially visible in the longevity space.

Case in point: In 2024, the Longevity Biotech Fellowship released their comprehensive roadmap, A Technical Plan to Solve Aging. Notably, small molecules weren’t even included. One of the roadmap’s key contributors, Mark Hamalainen, explained why in an episode of the LEVITY podcast:

”People talk about how [drug] trials have become so expensive, but a large portion of the reason for that is that we are in the diminishing returns, right? We found the low hanging fruit and going further down that pathway, everything that you try to find is going to be harder. You're going to have to screen more compounds. The ratio of failure to success just keeps getting worse, right?”

But not everyone agrees that the small molecule story is over. Companies like ThirdLaw Molecular (which I told you about a few weeks ago) are building synthetic molecules that mimic the best of both biologics and small molecules.

And General Proximity? It is going a step further: by giving small molecules superpowers.

Armand began his career working on traditional drug discovery at Alnylam Pharmaceuticals, one of the early pioneers of RNAi-based therapies*. But it wasn’t until his time at Scripps Research in La Jolla, California, during a PhD in Ben Cravatt’s lab, that the limitations of conventional approaches became personal - and painfully clear.

* RNAi is a natural biological process that regulates gene expression by ”interfering” with messenger RNA (mRNA), which carries DNA’s instructions for making new proteins. Alnylam’s RNAi therapeutics mimic that process.

While Armand was surrounded by some of the most advanced tools in chemical biology, his mother was diagnosed with breast cancer. Despite all the science at his fingertips, he realized he couldn’t do anything to help her. That moment stuck with him.

His work at Scripps focused on chemoproteomics - a field that, despite being less famous than genomics, may be just as revolutionary. Pioneered in large part by Cravatt, chemoproteomics gave scientists a new lens for drug discovery.

Instead of playing the genomics-era guessing game - where researchers picked a protein based on genetic data and hoped it was both relevant and druggable - chemoproteomics* let scientists do something radically different: start with a drug that works, then ask what it’s actually doing inside a real biological system.

* For more on how chemoproteomics works - see below.

As Armand puts it, ”Phenotypic drug discovery is sort of like the original form of drug discovery […] Back then we didn’t know what a protein was. We didn’t know what a gene was. We just threw dyes at bacteria to see if they died. It was very outcome-focused, very functional.”

That spirit is still alive in phenotypic screening today, where thousands of molecules are tested in living systems - cancer cells, organoids, whole organisms - to find those that produce a beneficial effect. The catch of course being that just because a molecule works doesn’t mean you know how it works. Without knowing its molecular targets, you can’t refine it, predict side effects, or extend its use to other conditions.

That’s where chemoproteomics became essential. Now, for the first time, researchers could map drug–protein interactions at scale, in living cells. You could trace not only on-target activity, but also off-target effects and mechanisms no one had predicted.

”We'll put it in a cell and ask, what does it bind to across 20,000 proteins, the entire proteome, right? Which is just far, far more comprehensive and useful data”, Armand says.

One case that drove this home was the 2016 Bial FAAH inhibitor trial, where a participant died and several others became seriously ill. In a study published in Science, Armand helped uncover why: the drug was binding to unintended lipases in the brain - off-target effects that had gone completely undetected in preclinical testing. Chemoproteomics made the invisible visible.

”That study made the dangers of blind spots in drug development incredibly real,” Armand tells me.

But it also pointed to something more hopeful: that starting from function, not theory, could lead to discoveries that traditional approaches would have missed. In this way, chemoproteomics wasn’t just a tool for explaining biology - it became a way to explore it. A kind of cartography for the molecular wilderness inside every cell.

🔬 How Chemoproteomics Actually Works

Chemoproteomics is a way to figure out which proteins a drug interacts with - inside living cells, not just in theory. The process involves chemical probes, mass spectrometry, and some clever competition experiments. Here's how it works, step by step:

🧪 Step 1: Design a Chemical Probe

Scientists create a small molecule that’s known to bind a specific class of proteins. For example, serine hydrolases - a large and important family of enzymes - all share a unique chemical feature in their active site.

“You can make a small molecule that binds to that active site across all of the different serine hydrolases,” Armand explains. “So it non-specifically binds to all the serine hydrolases.”

To make this molecule useful as a probe, they attach a chemical handle - something that lets them ”grab” the proteins the molecule binds to later on.

🧲 Step 2: Drop It Into a Living System

The probe is then introduced into a live cell or tissue extract, where it binds to its protein targets. Because it’s been designed to bind broadly (like to all serine hydrolases), it captures many potential interactions at once.

“You can put a handle on it so whatever it’s bound to, you can pull down.”

This allows researchers to isolate and identify the bound proteins later using mass spectrometry.

⚖️ Step 3: Run a Competition Experiment

Here’s the trick: researchers now run two parallel experiments:

1. One with the probe only.

2. One with the probe plus the drug of interest.

The idea is to see which proteins get displaced by the drug. If the drug binds tightly to a specific protein, the probe can’t attach — so that protein won’t get ”pulled down” in the second experiment.

“So you put in the drug or not the drug and then the probe in both. And then you look at what gets pulled down. And so if the drug is interacting with this active site […] then the probe can’t bind […] and those don’t get pulled down.”

🧬 Step 4: Analyze With Mass Spectrometry

The proteins that were pulled down are analyzed using mass spectrometry, a technique that identifies and quantifies proteins with high precision. By comparing the two conditions - with and without the drug - researchers get a high-resolution map of what proteins the drug is interacting with in a real biological context.

💡 Why This Matters

This technique is now used across nearly all types of proteins, not just hydrolases. It gives scientists insight into:

• A drug’s on-target effects,

• Any off-target bindings that might cause side effects,

• And entirely new mechanisms that weren’t predicted.

“It lets you just read out a sort of level of detail that it’s just not really possible otherwise,” Armand says. “And so that’s one of the major areas where proteomics is really powerful.”

After Scripps, Armand’s work began converging with another revolutionary idea: PROTACs (proteolysis-targeting chimeras). These were heterobifunctional small molecules - part glue, part guided missile - that didn’t just block proteins, but instead flagged them for destruction by hijacking the cell’s own degradation machinery.

It was a clean, elegant concept: one end of the molecule binds to your protein of interest, the other binds to an E3 ubiquitin ligase, an enzyme responsible for tagging proteins with ubiquitin so they get degraded. Bring the two together, in proximity, and your disease-driving protein gets shredded by the cell’s proteasome*. No need for a traditional functional binding pocket. No enzymatic activity required. You could now go after the ”undruggable.”

* Proteasomes are essential protein complexes responsible for the degradation of proteins by proteolysis, a chemical reaction that breaks peptide bonds.

”PROTACs are extremely cool,” Armand says. ”They’re the only clinical modality that lets you systemically control the abundance of a protein in a human. Nothing else can do that, right? Because PROTACs, you can take them orally, they permeate well, they can even get into the [central nervous system].”

But Armand also saw the limitations. PROTACs were powerful, but narrow - they were only designed to do one thing: degrade. And they were still fundamentally rational designs: known protein, known mechanism, build the bridge.

”They’re like this amazing technology and simultaneously the least interesting thing you could do with proximity,” he tells me. ”To really go beyond that […] you can't really guess from first principles which effector protein to use in the same way you can for PROTACs.”

That’s where the idea for General Proximity came from. By fusing the exploratory power of chemoproteomics with the precision of induced proximity, Armand envisioned a new kind of platform - one that could not only destroy proteins, like PROTACs, but reprogram them.

📦 What Are PROTACs?

PROTACs (Proteolysis Targeting Chimeras) are a type of smart drug that doesn’t just inhibit bad proteins - they get rid of them entirely.

🔧 How it works:

• PROTACs are chimeric molecules with two ends:

  • One end binds to a disease-causing protein.

  • The other binds to an E3 ubiquitin ligase, a cell’s natural "degradation tagging" enzyme.

• The PROTAC brings these two together. Once connected, the E3 ligase tags the target protein with ubiquitin, signaling it for destruction.

• The cell’s proteasome then degrades the tagged protein - effectively erasing it from the system.

🧠 Why it matters: This is a paradigm shift in drug discovery. Instead of only being able to effectively modulate just the small molecule binding site on a target protein, PROTACs enable you to effectively “turn off” the whole protein, which is superior for many drug targets.  That means even proteins once thought undruggable can now be removed from cells.

PROTACs were first described in 2001 in a seminal paper by Crews, Deshaies, et al., where a synthetic molecule called Protac-1 successfully targeted a protein (MetAP-2) for degradation by the cell’s internal machinery.

🌐 How it connects to chemoproteomics: Chemoproteomics helps find the right proteins to target - even if you didn’t know they were druggable. PROTACs help remove those proteins.

The result is OmniTAC — a system that turns proximity into a kind of molecular language. A way to degrade, stabilize, activate, or even transport proteins inside the cell.

PROTACs can destroy a protein. OmniTACs can rewrite its role entirely.

It’s a deceptively simple idea: Control proximity and you control biology.

”Proximity is a master regulator of biology,” Armand says. ”Why don’t our medicines work in the same way?”

Turns out that in biology, proximity governs almost everything - not just degradation, but also transcription, translation, protein folding and localization. Virtually all cellular processes are driven by bringing the right molecules together, at the right time, in the right place.

One can view OmniTAC as a sort of molecular matchmaking. OmniTAC brings two proteins together - one being the target (say, a disease-driving protein), and the other being a functional partner. It could be an enzyme or chaperone* from what General Proximity calls the effectome - the ~10% of your genome that includes proteins that modify other proteins. Chemoproteomics helps identify which of these functional partners to bring together - mapping the interactions that can be harnessed to control biology.

* A chaperone is a type of protein whose job is to help other proteins fold into their correct three-dimensional shapes. Protein folding is essential because a protein's function depends entirely on its shape - misfolded proteins can lead to dysfunction or disease.

In other words, the same chemoproteomic lens that once revealed how drugs behave inside cells is now being repurposed to design drugs that behave in entirely new ways. And remember: OmniTACs are still small molecules - orally bioavailable, easy to deliver, and cost-effective to manufacture.

”If we could do everything with a small molecule, simpler is better. The fewer atoms you have in your drug, the better and the cheaper it is to make.”

One class of ”undruggable” proteins stands out in particular: transcription factors (TF).

”If DNA is the code of the human body,” Armand wrote on X, ”TFs are the programs”. They control which genes get expressed and when - orchestrating how cells respond to stress, DNA damage, nutrient levels, inflammation, immunity, and more.

But they’ve long been considered out of reach. Transcription factors are often intrinsically disordered, lack small-molecule binding pockets, and don’t operate in isolation. They form complex, dynamic interactions with hundreds of proteins and modifications.

General Proximity, however, sees them as a perfect fit.

”TF activity is tuned by symphonies of hundreds of post-translational modifications and thousands of proximity events,” Armand explained. ”So the best way to control them may be through proximity.”

And when transcription factors bind to partner proteins, they often gain structure - creating new binding interfaces that can be targeted with small molecules. That’s where OmniTAC shines: scanning the ”effectome” to discover not just ways to block transcription factors, but to reprogram them.

General Proximity isn’t just a platform company in the traditional sense - one that builds a technology and then waits for pharma to license it. Armand is adamant about this.

”There are platform companies that are just developing a technology and then are licensing it to pharma. And then there's platform companies that are developing a new technology and then applying it themselves. We're very firmly in the latter camp.”

It’s an ideological stance, but also a strategic one. If your platform unlocks new biological space - if it makes the previously impossible doable - then you’re the one best positioned to go after those breakthroughs.

”If you don’t work on the targets that are really kind of the high-impact, low-hanging fruits - what are you doing? It feels like you just don't believe that your technology is valuable.”

But building a technology like this - and a company around it - hasn’t exactly been easy. In fact, for the first few years, it was brutal. General Proximity was incorporated in late 2019, just as the COVID-19 breakout had begun, but few outside China knew about it.

Armand had the idea for General Proximity barely a year after finishing grad school. ”I was planning to spend another five or ten years in industry before starting a company,” he told me. ”But I just... knew. From day one, I was like, I know this will happen. This is the future. Either I'm going to do it or someone's going to do it later on, but I might as well just do it.”

And yet, starting out with no IP, no data, no team - and trying to pitch undruggable targets with a platform that didn’t exist yet during the beginning of a global pandemic - was, in his words, ”a terrible place to be fundraising from.”

”I was really bad at pitching in the beginning,” Armand said. ”I would fundraise like a scientist. I’d be like, here’s what we’ve done - which was nothing. Here’s all the caveats. Can we have some money?”

Even worse, General Proximity didn’t fit cleanly into any of the investor boxes. He wasn’t spinning out from a famous academic lab or running a traditional pharma playbook. But he wasn’t a Stanford dropout building an AI-powered screening tool either.

”I had a bunch of people constantly be like, ’you know, this is too early’ or ’the targets you're going are not possible. People have tried to drug them and they failed’. Or, like, ’who are you? We've never heard of you’.”

So he bootstrapped. Scraped by. Kept the runway alive for years - sometimes just three months at a time.

”I think startups are so fucking hard. You’re going to get punched in the face over and over,” he said. ”You might as well do it for something that matters.”

Over time, the platform started working. They began generating data that no one else in the field had seen. And Armand got better at telling the story.

”I used to have this imposter syndrome: why would I be the one who's able to do this thing? But then another part of me would think, ’the data, the approach we're taking makes perfect sense and it's working and it's for the most impactful targets that exist. This is incredible. They should be lucky to invest in my company’.”

In the meantime, General Proximity gradually evolved into what Armand describes as one of the most accomplished biotech teams for a company of their size. Collectively, the team - with experience from Alnylam, Genentech, Merck, Novartis, and GSK - has contributed to 36+ FDA-approved medicines, 146 Investigational New Drug (IND) filings, 245 patents, and 958 scientific publications.

All the while, he held on to the vision, and to the target he says is still the company’s crown jewel.

After years in stealth, the company emerged in early 2025 with $16 million in funding. The investor list reads like a who’s who of tech and biotech: Felicis, Y Combinator, age1, ARPA-H, and angels like Jeff Dean (Google AI) and Trevor Martin (Mammoth Biosciences).

Now, General Proximity is going after undruggable targets across cancer, cardiometabolic disease, neurodegeneration, and longevity.

Somewhere among those diseases, you’ll find Armand’s white whale - the one the rest of the world walked away from, but he’s still chasing.

Hey, you’ve made it all the way here! Thank you so much for reading! 🫶🏼