Seven companies using metabolomics to decode biology

Metabolomics is the comprehensive study of small molecules – metabolites – within cells, biofluids, tissues, or organisms. These metabolites are the end products of cellular processes, and their analysis provides a snapshot of the physiological state of a biological system. And biotech companies using metabolomics are advancing promising candidates.

By profiling metabolites, researchers can identify novel biomarkers for diseases, understand disease mechanisms, and monitor therapeutic responses. This approach accelerates the identification of potential drug targets and aids in evaluating drug efficacy and toxicity during the development process.

While metabolomics has been instrumental in diagnostic applications, its impact extends into therapeutic development. By elucidating metabolic alterations associated with diseases, metabolomics enables the design of targeted interventions, enhancing the precision and effectiveness of new treatments. 

While service companies provide the backbone of metabolomics research, an increasing number of biotech firms are now integrating metabolomics into their drug development processes. In this article, we take a look at seven companies leveraging the insights drawn from metabolomics.

Akero Therapeutics

• Disease area: MASH
• Candidate: EFX
• Recent news: Presented positive phase 2 data

Founded in 2017, Akero Therapeutics is a clinical-stage biotechnology company headquartered in South San Francisco, California. The company is developing treatments for serious metabolic diseases, with a primary focus on metabolic dysfunction-associated steatohepatitis (MASH).

Akero’s lead product candidate, Efruxifermin (EFX), is an Fc-FGF21 fusion protein engineered to mimic the balanced biological activity of native fibroblast growth factor 21 (FGF21). FGF21 is an endogenous hormone that alleviates cellular stress and plays a crucial role in regulating lipid and glucose metabolism, energy expenditure, and insulin sensitivity. Akero utilizes metabolomics to understand the role of FGF21 in metabolic regulation and to guide the development of EFX.

EFX is currently being evaluated in multiple phase 3 clinical trials for the treatment of MASH. Recent data from a phase 2b study demonstrated that 39% of patients treated with EFX experienced a reversal in cirrhosis without worsening of MASH, compared to 15% in the placebo group.

Holoclara

• Disease area: Allergic and autoimmune disorders
• Candidate: HC002
• Recent news: Initiated phase 1 for HC002

Holoclara is based in Pasadena, California, pioneering the development of worm-derived therapies aimed at treating allergic and autoimmune diseases. The company’s approach is rooted in the discovery of immunomodulatory molecules secreted by gut roundworms, which have co-evolved with humans and possess natural properties that can modulate the immune system.

The company employs metabolomics to analyze the secretions of therapeutic worm species, mapping their individual effects on a comprehensive panel of immune cells known to drive allergic and autoimmune diseases. This approach enables the identification and characterization of bioactive small molecules with potential therapeutic applications.

Holoclara’s lead investigational drug, HC002, is an orally bioavailable small molecule derived from worm secretions. In December 2024, the company initiated a phase 1 clinical trial to evaluate the safety, tolerability, and pharmacokinetics of HC002 in healthy adults. The trial is being conducted in Australia, with results expected in 2025.

The company has selected eosinophilic esophagitis (EoE) as the lead indication for HC002. EoE is a chronic inflammatory disorder characterized by elevated levels of eosinophils in the esophagus, leading to symptoms such as difficulty swallowing, chest and abdominal pain, vomiting, and loss of appetite.

MAX BioPharma

• Disease area: IPF, NASH, chronic inflammation
• Candidate: Oxy210
• Recent news: Partnership with Metaba 

Founded in December 2010, MAX BioPharma is a preclinical-stage biopharmaceutical company based in California. The company specializes in developing novel small-molecule lipids, specifically oxysterols.

MAX BioPharma develops oxysterol drugs for several indications such as NASH, idiopathic pulmonary fibrosis (IPF), and chronic inflammation. The company’s lead candidate, Oxy210 inhibits two pro-fibrotic signaling pathways: Hedgehog (Hh) and transforming growth factor-beta (TGF-β). Additionally, it possesses anti-inflammatory activity through inhibition of toll-like receptor 2 (TLR2) and TLR4. 

Preclinical studies have demonstrated that Oxy210 effectively ameliorates hepatic fibrosis, inflammation, and hypercholesterolemia in mouse models, suggesting its potential as a therapeutic candidate for conditions such as NASH, atherosclerosis, and other chronic inflammatory diseases associated with metabolic dysfunction.

In February 2024, MAX BioPharma announced a collaboration with Metaba, to study the effects of their oxysterol drug candidates on metabolic processes. Utilizing Metaba’s metabolomics platform technology, the partnership aims to identify changes in metabolites induced by oxysterols. 

This collaboration should deepen the understanding of the mechanisms of action of their therapeutics but also identify potential biomarkers for assessing drug efficacy.

Seres Therapeutics

• Disease area: Microbiome therapeutics
• Candidate: SER-109
• Recent news: FDA approval of SER-109

Founded in 2010 and headquartered in Cambridge, Massachusetts, Seres Therapeutics is a microbiome therapeutics company developing a novel class of multifunctional bacterial consortia designed to interact with host cells and tissues to treat disease. The company’s therapeutics are composed of selected bacteria in oral capsules, optimized for specific pharmacological properties, including infection prevention, restoration of epithelial barrier integrity, and immune modulation.

The company employs metabolomics to understand the functional impact of their microbiome therapeutics on host metabolism. By analyzing metabolic changes induced by their bacterial consortia, the company aims to elucidate mechanisms of action, identify biomarkers for therapeutic efficacy, and optimize their drug candidates. 

The company’s lead candidate, SER-109, is an oral microbiome therapeutic composed of a consortium of highly purified firmicutes spores, designed to prevent recurrent clostridiodes difficile infection (rCDI) by modulating the disrupted microbiome to resist clostridiodes difficile colonization and growth. Clostriodes difficile is a bacterium that causes severe diarrhea and colitis, often following antibiotic use, by disrupting the gut microbiome and producing toxins that inflame the intestinal lining. SER-109 has been approved by the U.S. Food and Drug Administration (FDA) in 2023.

Another notable candidate is SER-155, an investigational oral live biotherapeutic designed to decolonize gastrointestinal pathogens, improve epithelial barrier integrity, and modulate immune responses to prevent bacterial bloodstream infections and other complications in patients undergoing allogeneic hematopoietic stem cell transplantation. Seres is also advancing two preclinical programs for chronic liver disease and ulcerative colitis.

Siolta Therapeutics

• Disease area: Atopic diseases
• Candidate: STMC-103H
• Recent news: $12 million series C

Founded in 2016 and headquartered in San Carlos, California, Siolta Therapeutics develops live biotherapeutic products (LBPs) and molecular diagnostic tools. The company’s research focuses on the “maternal-infant axis,” addressing conditions such as atopic diseases, women’s health issues, and rare pediatric indications.

The company employs metabolomics to understand the relationships between microbial activity in the gut and human health. By analyzing the metabolites produced by the microbiome, the company gains insights into the functional contributions of microbial communities to human physiology. This approach aids in characterizing both general phenomena through untargeted metabolomics and specific mechanisms of action via targeted metabolite analysis, thereby informing the drug development process.

Siolta’s lead investigational product, STMC-103H, is a multi-strain live biotherapeutic currently in phase 2 for the prevention of atopic diseases, including atopic dermatitis, food allergies, and asthma.

In March 2024, Siolta Therapeutics raised $12 million in a series C financing round to advance the clinical development of its lead program.

Sinopia Biosciences

• Disease area: Parkinson’s disease
• Candidate: SB-0110
• Recent news: Received 2 SBIR grants in 2024

Sinopia Biosciences leverages its proprietary artificial intelligence and machine learning (AI/ML) drug discovery platform to identify novel therapeutics in neurology, oncology, and genetic diseases. The company’s platform integrates high-throughput multi-omics data, including metabolomics, to uncover unique therapeutic opportunities.

By analyzing large-scale metabolomic datasets, the company identifies novel drug targets and therapeutic candidates. SB-0110 is the company’s lead candidate, a first-in-class small molecule targeting Parkinson’s disease and levodopa-induced dyskinesia (LID). SB-0110 has demonstrated significant efficacy in preclinical models and is currently advancing through investigational new drug (IND)-enabling studies, with plans to initiate phase 1a/b clinical trials in early 2025.

In May 2024, Sinopia received a Small Business Innovation Research (SBIR) grant from the National Institute of General Medical Sciences to advance its LEarn And DiScover (LEADS) platform and explore applications in oncology and immunology. This funding supports the company in the development of novel algorithms to analyze proprietary metabolomics datasets and the exploration of new therapeutic areas.

Sinopia received another SBIR grant later in 2024 from the National Institute of Dental and Craniofacial Research to support its program for oral mucositis.

STALICLA

• Disease area: Autism spectrum disorder
• Candidate: STP1
• Recent news: $17.4 million series B round

Headquartered in Geneva, Switzerland, STALICLA specializes in the development of precision medicine therapies for patients with neurodevelopmental disorders (NDDs), with an initial focus on autism spectrum disorder (ASD). The company’s mission is to identify clinically actionable patient subgroups and develop tailored treatments to address the specific needs of these populations.

The company has developed the Databased Endophenotyping Patient Identification (DEPI) platform, an AI-driven and clinically validated technology that integrates comprehensive metabolomics, whole-genome sequencing, RNA sequencing, and advanced computational analysis. This platform enables the identification of patient subgroups with similar disease signatures, facilitating the pairing of these subgroups with targeted drug candidates.

STALICLA’s lead investigational product, STP1, is designed for a specific subgroup of patients with ASD identified through the DEPI platform. The company has completed a phase 1b clinical trial for STP1, demonstrating its safety and tolerability.

In 2022, STALICLA in-licensed mavoglurant from Novartis, a metabotropic glutamate receptor 5 (mGluR5) negative allosteric modulator. Originally developed for fragile X syndrome, mavoglurant is now being advanced as STP-7 for the treatment of cocaine use disorder, with a phase 3 trial in collaboration with the U.S. National Institute on Drug Abuse (NIDA) initiated in 2024.

The Swiss company secured $17.4 million in a series B round in early 2024.

Metabolomics, the next big thing for precision medicine?

Metabolomics is increasingly recognized as an important component in the advancement of precision medicine. This field is predominantly represented by specialized service companies that offer expertise and technological platforms to support research and development.

Several key companies have established themselves as leaders in providing metabolomics services: Metabolon, Agilent Technologies, Thermo Fisher, Biocrates Life Science, and Sapient are notable examples of important players in this area.The metabolomics market is experiencing notable growth, reflecting its expanding role in research and clinical applications. According to a report by Verified Market Research, the global metabolomics market was valued at $2.69 billion in 2024 and is projected to reach $7.22 billion by 2031, growing at a compound annual growth rate (CAGR) of 13.13%.