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Efficacy and safety of a synthetic biotic for treatment of phenylketonuria: a phase 2 clinical trial


Despite available treatment options, many patients with phenylketonuria (PKU) cannot achieve target plasma phenylalanine (Phe) levels1. We previously modified Escherichia coli Nissle 1917 to metabolize Phe in the gut after oral administration (SYNB1618) and designed a second strain (SYNB1934) with enhanced activity of phenylalanine ammonia lyase2,3. In a 14-day open-label dose-escalation study (Synpheny-1, NCT04534842), we test a primary endpoint of change from baseline in labeled Phe (D5-Phe AUC0−24; D5-Phe area under the curve (AUC) over 24 hours after D5-Phe administration) in plasma after D5-Phe challenge in adult participants with screening Phe of greater than 600 µM. Secondary endpoints were the change from baseline in fasting plasma Phe and the incidence of treatment-emergent adverse events. A total of 20 participants (ten male and ten female) were enrolled and 15 completed the study treatment. Here, we show that both strains lower Phe levels in participants with PKU: D5-Phe AUC0−24 was reduced by 43% from baseline with SYNB1934 and by 34% from baseline with SYNB1618. SYNB1934 led to a decrease in fasting plasma Phe of 40% (95% CI, −52, −24). There were no serious adverse events or infections. Four participants discontinued because of adverse events, and one withdrew during the baseline period. We show that synthetic biotics can metabolize Phe in the gut, lower post-prandial plasma Phe levels and lower fasting plasma Phe in patients with PKU.

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Fig. 1
Fig. 2: Plasma D5-Phe.
Fig. 3: Percent change from baseline in fasting Phe.

Data availability

Data in this article (and the Supplementary Information) have been presented where possible as group-level summaries. Any data presented to illustrate individual participant performance have been de-identified. The data sets generated during and/or analyzed during the current study are available from the corresponding author (N.S.) upon reasonable request including a methodologically sound proposal, although restrictions may apply owing to participant privacy and HIPAA regulations. Source data are provided with this paper.


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We thank the study participants and their families as well as the research nurses and study staff. We also acknowledge the support of the National PKU Association.

Author information

Authors and Affiliations



J.V., M.P., W.S.D., K.H., C.K. and A.M.B. conceived and designed the work. J.V., M.P., G.A.D., I.G., D.K.G., C.H., H.N., J.P., S.S., J.A.T., R.Z., S.L.E., K.H. and N.M. acquired the data. J.V., N.S., W.S.D., S.L.E., N.M., C.K. and A.M.B. analyzed and interpreted the data. J.V., N.S., C.K. and A.M.B. wrote the original draft of the manuscript. All co-authors reviewed and approved the manuscript.

Corresponding author

Correspondence to Neal Sondheimer.

Ethics declarations

Competing interests

N.S., M.P., W.S.D., S.L.E., K.H., N.M., C.K. and A.M.B. are current or former employees of Synlogic and hold equity in Synlogic. J.V. and G.A.D. have consulted for Synlogic. J.V., G.A.D., I.G., D.K.G., C.H., H.N., J.P., S.S., J.A.T. and R.Z. received research funding from Synlogic. Funding for this study was provided by Synlogic. The funder participated in the study design, data analysis, preparation of the manuscript and decision to publish.

Peer review

Peer review information

Nature Metabolism thanks the anonymous reviewers for their contribution to the peer review of this work. Primary Handling Editor: Ashley Castellanos-Jankiewicz, in collaboration with the Nature Metabolism team.

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Extended data

Extended Data Fig. 1 SYNB strain design and key engineering features.

SYNB1618 (A) and SYNB1934 (B) are shown. Abbreviations; LAAD = L-amino acid deaminase from Proteus mirabilis; laad = gene for LAAD. PAL = phenylalanine ammonia lyase from Photorhabdus luminescens; pal = gene for PAL; mPAL = modified phenylalanine ammonia lyase with higher potency. mpal = gene encoding mPAL. PheP = high-affinity phenylalanine transporter; pheP = gene encoding high-affinity phenylalanine transporter; PFNR = promoter regulated by fumarate and nitrate reductase regulator; Ptac = synthetic promoter controlling PAL expression and regulated by the LacI transcriptional repressor; PBAD = promoter for laad, regulated by arabinose; ΔdapA = deletion of dapA gene leading to diaminopimelate auxotrophy; Phe = phenylalanine, PP = phenylpyruvate; TCA = trans-cinnamic acid.

Extended Data Fig. 2 D5-Phe metabolite study.

The LS mean change from baseline Day −1 in D5 Phe metabolites was determined at day 14 for SYNB1618, (navy; n = 10) and SYNB1934 (orange; n = 5). A. Plasma D5 TCA AUC change from baseline in LS mean AUC 0–24 µM*h. B. Urinary D5 HA change from baseline in amount excreted (AeT) in mmol over 6 hours.

Source data

Extended Data Table 1 AUC0-24 values for D5-Phe
Extended Data Table 2 Individual Phe levels during Arm 1 and Arm 2
Extended Data Table 3 Summary of Change from Baseline in Plasma and Urine Phe metabolites from Biomarker study
Extended Data Table 4 Selected data from CANTAB analysis
Extended Data Table 5 Adverse Events
Extended Data Table 6 Incidence of Treatment-Emergent Adverse Events by System Organ Class, Preferred Term, and Maximum Severity. Safety Population – SYNB1618
Extended Data Table 7 Incidence of Treatment-Emergent Adverse Events by System Organ Class, Preferred Term and Maximum Severity. Safety Population – SYNB1934
Extended Data Table 8 Dose ramping regimen of IMP in SYNB1618-CP-003

Supplementary information

Supplementary Information

The final protocol of SYNB1618-CP-003.

Reporting Summary

Supplementary Data 1

Protocol SYNB1618-CP-003.

Source data

Source Data Fig. 2

Statistical Source Data.

Source Data Fig. 3

Statistical Source Data.

Source Data Extended Data Fig. 2

Statistical Source Data.

Source Data Extended Data Table 3

Statistical Source Data.

Source Data Extended Data Table 4

Statistical Source Data.

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Vockley, J., Sondheimer, N., Puurunen, M. et al. Efficacy and safety of a synthetic biotic for treatment of phenylketonuria: a phase 2 clinical trial. Nat Metab 5, 1685–1690 (2023).

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