feat(qc): detect N-terminal pyroglutamate cyclization risk (Q1 only)

src/openamp_foundry/qc/presynth_check.py

@@ -118,6 +118,9 @@ class SynthQC:
     deamidation_sites: list[str] = field(default_factory=list)  # e.g. ["N3G", "Q5S"]
     isomerization_sites: list[str] = field(default_factory=list)  # e.g. ["D2G", "D9S"]
 
+    # N-terminal pyroglutamate cyclization
+    pyroglutamate_risk: bool = False   # N-terminal Q or E → pGlu (activity loss)
+
     # Tryptophan photolability
     tryptophan_count: int = 0
     trp_photolability_risk: bool = False   # ≥ 3 Trp → photooxidation risk under assay lighting
@@ -169,6 +172,7 @@ def to_dict(self) -> dict:
             "chymotrypsin_sites": self.chymotrypsin_sites,
             "deamidation_sites": self.deamidation_sites,
             "isomerization_sites": self.isomerization_sites,
+            "pyroglutamate_risk": self.pyroglutamate_risk,
             "tryptophan_count": self.tryptophan_count,
             "trp_photolability_risk": self.trp_photolability_risk,
             "has_uv_chromophore": self.has_uv_chromophore,
@@ -237,6 +241,15 @@ def check_sequence(candidate_id: str, seq: str, mu_h: float = 0.0) -> SynthQC:
         for m in _ISOMERIZATION_RE.finditer(seq)
     ]
 
+    # N-terminal pyroglutamate cyclization: Q at position 1 cyclises spontaneously to
+    # pyroglutamic acid (pGlu) at physiological pH (t½ hours–days at 37°C, 5–50× MIC loss).
+    # The same ring-closure occurs for E1 but requires acid catalysis (pH 2–4); at pH 7.4 the
+    # E1 rate is negligible (t½ months–years) and is not flagged here to avoid overcalling
+    # synthesis_difficulty. Nα-acetylation (zero synthesis cost) locks the free amine and
+    # completely blocks Q1 cyclisation. Literature: Chelius et al. (2006) Anal Chem 78:2370;
+    # Goolcharran & Borchardt (1998) J Pharm Sci 87:425.
+    qc.pyroglutamate_risk = len(seq) > 0 and seq[0] == "Q"
+
     # Tryptophan photolability: ≥3 Trp residues → UV-sensitive under assay lighting.
     # Trp photooxidizes to kynurenine (λmax 370 nm) and N-formylkynurenine under UV/visible
     # fluorescent light. Peptides with ≥3 Trp lose >20% activity within 4h under standard
@@ -359,6 +372,13 @@ def check_sequence(candidate_id: str, seq: str, mu_h: float = 0.0) -> SynthQC:
         qc.flags.append(f"DEAMIDATION_RISK: {', '.join(qc.deamidation_sites)} — avoid >pH 7.5 storage; use pH 5–6 lyophilization buffer")
     if qc.isomerization_sites:
         qc.flags.append(f"ISOMERIZATION_RISK: {', '.join(qc.isomerization_sites)} — Asp→β-Asp rearrangement at neutral pH; store lyophilized at −20°C")
+    if qc.pyroglutamate_risk:
+        qc.flags.append(
+            "PYROGLUTAMATE_RISK: N-terminal Q cyclises to pGlu (t½ hours–days at 37°C, pH 7.4); "
+            "blocks N-terminus, typically 5–50× MIC loss — specify N-terminal Ac (Nα-acetylation) "
+            "in synthesis order (zero extra cost) to prevent cyclisation; or substitute Q1 → K1/R1 "
+            "(note: K1/R1 adds a trypsin site; only use if serum stability is not gated)"
+        )
     if qc.charge_ph74 < 2.0:
         qc.flags.append(f"LOW_CHARGE (pH7.4={qc.charge_ph74:.1f}): reduced membrane affinity")
     if qc.c_amidation_recommended:

tests/test_presynth_qc.py

@@ -107,6 +107,59 @@ def test_met_flag_in_flags_list(self):
         assert "Nle" in met_flags[0], "Met flag must recommend Nle substitution (regression guard for PR #102)"
 
 
+# ---------------------------------------------------------------------------
+# Pyroglutamate risk
+# ---------------------------------------------------------------------------
+
+class TestPyroglutamate:
+    def test_q_terminal_sets_risk(self):
+        qc = check_sequence("q", "QRLMKKIGSAIKFL")
+        assert qc.pyroglutamate_risk
+
+    def test_no_risk_for_all_non_q_starts(self):
+        # All canonical AAs except Q — includes E (negligible at pH 7.4, not flagged)
+        non_q = "ACDEFGHIKLMNPRSTUVWY"
+        for aa in non_q:
+            if aa == "U":
+                continue  # selenocysteine not canonical here
+            qc = check_sequence("x", aa + "RLMKKIGSAIKFL")
+            assert not qc.pyroglutamate_risk, f"False positive for N-terminal {aa}"
+
+    def test_e_terminal_does_not_set_risk(self):
+        # E→pGlu requires acid catalysis (pH 2–4); negligible at physiological pH
+        qc = check_sequence("e", "ERLMKKIGSAIKFL")
+        assert not qc.pyroglutamate_risk
+
+    def test_pyroglutamate_flag_emitted_for_q(self):
+        qc = check_sequence("q", "QRLMKKIGSAIKFL")
+        pglu_flags = [f for f in qc.flags if "PYROGLUTAMATE" in f]
+        assert len(pglu_flags) == 1
+        assert "pGlu" in pglu_flags[0]
+        assert "Nα-acetylation" in pglu_flags[0]
+        assert "hours–days" in pglu_flags[0]
+
+    def test_pyroglutamate_not_flagged_for_internal_q(self):
+        # Internal Q triggers deamidation (if followed by G/S), not pyroglutamate
+        qc = check_sequence("x", "KQRLMKKIGSAIKFL")
+        assert not qc.pyroglutamate_risk
+
+    def test_q_with_qg_motif_gets_both_pyroglutamate_and_deamidation_flags(self):
+        # QGKLRK: Q1 → pyroglutamate risk AND Q1G deamidation (two independent mechanisms)
+        qc = check_sequence("qq", "QGKLRK")
+        assert qc.pyroglutamate_risk
+        assert any("Q1G" in s for s in qc.deamidation_sites)
+        pglu_flags = [f for f in qc.flags if "PYROGLUTAMATE" in f]
+        deam_flags = [f for f in qc.flags if "DEAMIDATION" in f]
+        assert len(pglu_flags) == 1
+        assert len(deam_flags) == 1
+
+    def test_pyroglutamate_in_to_dict(self):
+        qc = check_sequence("q", "QRLMKKIGSAIKFL")
+        d = qc.to_dict()
+        assert "pyroglutamate_risk" in d
+        assert d["pyroglutamate_risk"] is True
+
+
 # ---------------------------------------------------------------------------
 # Trypsin/chymotrypsin sites
 # ---------------------------------------------------------------------------