Hypothesis: Matrix metalloproteinase inhibition with low-dose doxycycline in Long COVID and ME/CFS

by Erin C. Sanders, MSN, WHNP-BC [1,2]

1 Nurse Practitioner
2 Clinical Scientist at MIT

Cite as: Sanders, E.C. (2023). Hypothesis: Matrix metalloproteinase inhibition with low-dose doxycycline in Long COVID and ME/CFS. Patient-Generated Hypotheses Journal for Long COVID & Associated Conditions, Vol. 1, 21-29


Nonselective matrix metalloproteinase (MMP) inhibition with FDA approved subantimicrobial dose doxycycline formulations could improve systemic symptoms in at least a subset of patients with Long COVID and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) as compared to those who receive placebo.


The chronic inflammatory state induced by Long COVID and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) likely increases systemic collagenase activity, causing pathologic collagen breakdown and loss of tissue structural support. A cascade of symptomatology across organ systems could follow, including those stemming from increased tissue laxity and distention, as well as increased permeability of important tight junctions in mucosal barriers1, 2, vasculature3 and the blood-brain barrier4, 5. Existing subantimicrobial or low-dose doxycycline (LDD) formulations with established efficacy to inhibit matrix metalloproteinase (MMP) activity are worth exploring to stabilize symptoms in parallel to the development and trial of other therapeutics.

MMPs have been found to be elevated in patients with various infections and chronic illnesses6, 7. A recent study also showed that MMP-9 produced from cancer cells was able to induce remodeling of capillary endothelial cells and support early brain metastasis8. Similarly, studying the biomechanics of neuroinvasive pathogens that cause infectious diseases like COVID-19 and Lyme may help us better understand transport across the blood-brain barrier, seeding of infection, and persistence into the central nervous system (CNS)9, 10. Due to its ability to cross the blood-brain barrier, doxycycline has long been used as standard of care to treat Lyme disease, including facial palsy, meningitis, or radiculoneuritis from neuroborreliosis in both adults and children11. Doxycycline has shown the ability to reduce neuroinflammation12, 13, which is a leading hypothesis for the widespread neuropsychological symptoms observed in patients with Long COVID14-16 and to a lesser extent in  ME/CFS17. More generally, in addition to their antibiotic mechanism of action, the tetracycline class of antibiotics can induce immunomodulatory and anti-inflammatory activity in patients with autoimmune diseases18. Enzymes like MMPs that are secreted to degrade connective tissue are triggered by immune cell signaling, but are also a part of a feedback loop where subsequent tissue damage or breakdown provokes additional immune responses19. Immunomodulating therapies like LDD that inhibit MMPs have the potential to disrupt this inflammatory cycle, which may allow the tissues to heal. Despite the first tetracycline being discovered in 1948, the use of doxycycline for non-antibiotic indications has not been widely adopted in clinical practice20.Currently, only two LDD formulations have FDA approval with indications of periodontal disease (Periostat®21) and rosacea/acne (Oracea®22), granted in 200123 and 200624, respectively. For decades, many synthetic MMP inhibitors have shown remarkable potential in vivo and in vitro, but their translation into advanced clinical trials has largely failed due to musculoskeletal toxicity or lack of efficacy25-27. Fascinatingly, what has helped make doxycycline a clinically useful MMP inhibition therapy is its incomplete blockade, causing side effects to be less profound and overall more tolerable28.

If chronic immune activation is contributing to endothelial dysfunction29, 30,hypercoagulability, and fibrinaloid microclot formation31, 32 already observed in patients with both Long COVID and ME/CFS, could it also compromise connective tissue integrity and the structural stability of critical joints that protect the nervous system? This process may partially explain why many patients receive comorbid diagnoses like mast cell activation syndrome (MCAS)33, 34 and hypermobile Ehlers Danlos Syndrome (hEDS)35, 36. In fact, when researchers took the skin cells of patients with hEDS and treated them with doxycycline in vitro, the antibiotic restored extracellular matrix organization and significantly attenuated myofibroblast-like features37. This work shows that the cellular structural changes in hEDS have the potential to be reversible, and that doxycycline can modulate at least a part of that process. Growing literature is revealing the complex interplay of the extracellular matrix and the immune system19, which may help to explain the overlap of connective tissue disorders like hEDS with Long COVID and ME/CFS. Importantly, treatment with LDD does not preclude the use of other medications utilized in tandem to help control chronic inflammatory responses like dual antihistamine blockade with or without mast cell stabilization to help prevent further tissue breakdown and aid in tissue repair38. Furthermore, clinical trials have shown LDD can be safely taken for up to two years in a population of postmenopausal women39.

Sex differences in fluctuation of MMPs due to the cyclical tissue breakdown required for menstruation40-42 should be given close consideration, as many chronic illnesses, including Long COVID and ME/CFS, disproportionately impact females. Progesterone downregulates MMPs and can either trigger or prohibit the sloughing of the endometrium to support a pregnancy40. Anecdotally, Long COVID and/or ME/CFS patients who menstruate have reported significant symptom fluctuation throughout their menstrual cycles, in addition to bleeding pattern changes after a COVID-19 infection43 and even COVID-19 vaccination44-46. Dysregulation of MMPs has also been implicated in uterine pathologies like endometriosis40-42. The impact of menstruation or illness on systemic collagenase activity and chronic symptoms is largely unexplored. Sex differences in MMPs raise the important question of whether the biologically conserved process of menstruation that is necessary for perpetuating the human species also comes at a cost associated with a higher risk for systemic barrier permeability or pathogen translocation. Namely, do the sex differences in MMPs required for the cyclical tissue breakdown of the endometrium put menstruating people at a higher risk for infection, disease, or cyclical symptom exacerbation?

How to test the hypothesis

Testing the main hypothesis in patients with Long COVID and/or ME/CFS would require a Phase 3 double-blind, placebo-controlled, randomized trial of participants in 4 potential treatment arms, including the two FDA approved low-dose options that could be considered for expanded use.

1)     Doxycycline (Oracea®) 40 mg capsule per oral route once daily

2)     Doxycycline hyclate (Periostat®) 20 mg tablet per oral route twice a day

3/4)     Matching placebo of each

Investigators should assess for symptoms before and after treatment with validated questionnaires, physical assessment, and lab measurements of MMP-9 (Labcorp has a commercially available assay)42, plus other objective metrics of common symptoms, such as the NASA lean test for autonomic dysfunction43, the Beighton Score for hypermobility44, CNS Vital Signs45 or BrainCheck46 for cognitive impairment, and abbreviated Depaul Symptom Questionnaires (DSQ-SF47 or DSQ-PEM48) for post-exertional malaise. For a chronic illness with no existing cure, another important question is how long a patient can take these therapies safely. Therefore, treatment duration should be at least 6 months with potential for crossover design extending to 1 year. Additionally, by using data and frozen blood samples collected from existing funded and IRB approved research like the MIT MAESTRO Study, baseline levels of MMPs in a chronic illness population could be assessed in acute Lyme disease, Long Lyme, and Long COVID, compared to healthy controls. Participants could be followed to pair additional blood samples timed prior to or during menstruation. Menstruation is a complex and modifiable variable that can influence both chronic disease state and treatment response. However, this variable also suggests that hormone modulation or suppression of menstruation could potentially help some patients.

No FDA approved treatments for Long COVID or ME/CFS currently exist. Access to off-label therapies continues to be a significant barrier for patients who are suffering. Urgent funding must be prioritized to study multi-pronged treatment regimens, including repurposed drugs with established safety profiles. LDD holds unique promise to aid in tissue repair by interfering with a pathologic immune response, while not causing immune suppression, which is a primary concern in patient populations with established latent infections and diseases caused by pathogens capable of persistence.


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