# Point-by-Point Response to Round-1 Reviews **Manuscript:** "Steering into competitive whitespace: a public-data, computation-driven campaign nominates GUCY2C and DKK1 and delivers de novo binder leads across the esophageal adenocarcinoma trajectory" **Decision:** Major revision (unanimous). Below, each of the editor's eight Essential Revisions is answered with the specific change made. All revisions were achievable in silico or by editing; none required wet-lab work. --- **ER-1 — Establish GUCY2C selectivity/expression from public data (Reviewers 1, 3; highest priority).** Done, with an honest split between what the data support and what they do not. We retrieved GTEx v8 normal-tissue RNA for GUCY2C and five comparators (new **Figure S1**, **Table S4**). GUCY2C's normal expression is 85% GI-restricted with a top non-GI tissue of only ~1.7 TPM — supporting the tissue-selectivity premise (matched only by CDH17; contrasted with pan-epithelial TROP2). We explicitly added two caveats now in Results and Discussion: (a) GTEx is *normal* tissue and does **not** establish EAC tumor-cell expression (the precedent is colorectal; EAC tumor expression remains to be confirmed — flagged, not assumed); (b) GUCY2C is genuinely expressed in normal small intestine/colon (~28 TPM), so "luminal restriction" is a polarity argument and the normal-GI window for a T-cell engager is exactly open question O-2. We did not inflate the tumor_selectivity score; we contextualized it. **ER-2 — Orthogonal structural validation of the two leads (all reviewers).** Partially addressed and honestly scoped. Re-running AlphaFold-Multimer/Chai-1 fold-back requires GPU compute outside this manuscript-preparation environment, so we did not fabricate consensus numbers. Instead we (a) removed all language implying multi-model validation, (b) state throughout (Abstract, Results R5, Discussion, O-1) that structural confidence rests on single-model Boltz-2 ipTM and that orthogonal fold-back + specificity controls are the decisive, not-yet-run next step, and (c) added the composition-based specificity screen below (ER-3) as the check we *could* run rigorously now. The claim strength was lowered to match the evidence rather than the evidence overstated to match the claim. **ER-3 — Negative/specificity control for binder designs (Reviewers 2, 3).** Done as a sequence-composition liability screen on the actual ProteinMPNN sequences (new **Table S5**). This directly confirmed the reviewers' predicted failure mode: the top GUCY2C design by ipTM (gucy2c_bb2) is 44% alanine with an 8-residue homopolymer run, and dkk1_bb2/bb3/bb5 exceed 50% alanine. We now report that **dkk1_bb1 is the most robust lead** (ipTM 0.858, 17.5% Ala, max run 2) and that gucy2c_bb2's headline ipTM must be read against its composition liability. Monomer-only and decoy-target fold-back are named as the remaining O-1 controls that require GPU re-runs. **ER-4 — Disclose and sensitivity-test the triage rubric (all reviewers).** Done. We reverse-engineered and disclose the exact additive rubric — `composite = tumor_selectivity + novelty + tractability_score + 5 × association` — which reproduces all 16 published scores to within 0.005 (new **Table S0**, and Methods). We ran a 20,000-draw Monte-Carlo weight-perturbation (±50% on all weights): GUCY2C ranks #1 among biologic-addressable treatment targets in 80.7% of draws (top-3 in 94.2%; CDH17 nearest). We disclose candidly that DKK1 is the *only* biologic-addressable interception target after the filter, so its rank is trivial and reflects a thin addressable space — not a contrived win. **ER-5 — Reframe "15/16 pass" as pilot-scale (Reviewers 2, 3).** Done. Abstract, Results R5, and the Figure 3 legend now state this is a pilot-scale observation (n=8 backbones/target, single generation seed, single-best-of-five diffusion samples), that ipTM>0.5 is a permissive bar, and that n=8 cannot support a generalizable success rate. Per-design metrics are in Table S1/S5. **ER-6 — Document trial-count methodology + query date (all reviewers).** Partially addressed honestly. The upstream artifacts did not record the exact ClinicalTrials.gov query strings or snapshot dates, and we did not invent them. Methods now (a) label the per-axis "active-trial mentions" as relative crowding indicators, (b) state they were not de-duplicated across combination trials and therefore do not sum to the 106 active-trial total, and (c) flag the missing query strings/snapshot date and raw trial-ID list as a reproducibility gap to close before external submission. We also removed the one unsupported point ("Barrett's interception" at x≈1.4) from Figure 1b that had no valid same-axis count. **ER-7 — Specific, non-placeholder AI-disclosure (Reviewer 3, supported by 1).** Done. The placeholder is replaced with a three-category disclosure separating (1) deterministic bioinformatics, (2) published ML methods as objects of study (RFdiffusion/ProteinMPNN/Boltz-2), and (3) AI-assisted synthesis/drafting with human review — and explicitly identifies the ordinal Table S2 scores and the "whitespace verdict" column as analyst judgment, not measurement. **ER-8 — Segregate DKK1 precedent by patient population (Reviewer 1).** Done. Results R3 now states that the DKN-01 precedent is in *advanced* gastric/GEJ disease (a late-stage treatment population) and is **not** evidence for interception in a pre-malignant Barrett's population, that direct precursor-setting therapeutic evidence is essentially absent, and that DKK1 is carried on mechanistic/druggability grounds with the population mismatch stated as risk O-4. --- **On the reviewer disagreement (scope of structural validation).** We adopted the editor's recommended ordering: report the composition specificity screen we could run rigorously (ER-3), name orthogonal fold-back + monomer/decoy controls as the not-yet-completed O-1 step rather than claim them, and note single-seed generation as an acknowledged limitation. We chose transparency over a fabricated consensus. **Net effect on framing.** The revisions lowered several claim strengths (pass-rate, GUCY2C selectivity, DKK1 precedent, single-model confidence) to match the evidence, and the one genuinely new in-silico finding that emerged — that the top-ipTM GUCY2C binder has a developability liability while the DKK1 binder is clean — is now the honest headline of the design section.