LNPredict — In Silico LNP Formulation Workbench

Formulation parameters

TP53 variant

p.Arg175His · Structural · Core domain misfolding; dominant-negative + GOF. Paper strategy: mutant-p53 siRNA (GOF silencing).

Cancer type

Cargo

p53 mRNA (wild-type restoration) · 1750 nt · full-length wild-type TP53 CDS + UTRs — for TP53-null / loss-of-function alleles

Platform

Helper lipid

Release trigger

N/P ratio6.0

Ionizable %50.0%

Helper % · DSPC10.0%

Cholesterol %38.5%

PEG-lipid %1.5%

Σ molar = 100.0% · balanced

Flow ratio (aq:org)3.0:1

Flow rate8.0 mL/min

▸ ENDOSOMAL ESCAPEpKa 6.44 sits in the 6.0–7.0 window for low-pH protonation & membrane disruption.

Recommended formulation

DLin-MC3-DMA · R175H p53-mRNA

Alnylam / Onpattro · Approved · tertiary amine

Ionizable

50.0%

pKa 6.44

Helper · DSPC

10.0%

saturated C18 · lamellar stabiliser

Cholesterol

38.5%

membrane rigidity

PEG-lipid

1.5%

DMG-PEG2000

Encapsulation95.0%

Endosomal escape96.0%

Particle size93.3 nm

PDI0.078

delivery score 92.2model confidence 96.0%N/P 6.0 · 3.0:1 @ 8.0 mL/min

Targeting ligand

Platform · preclinical

Folic acid · FR-α

Folate/HA targeting for ovarian contexts; TP53 restoration strategies reviewed by Zhang et al. 2025. · modelled tumour dose 1.90% ID vs 0.7% passive

Top-3 alternate lipids

1
TT3 (FTT5)
pKa 6.35 · escape 91%
95%
2
L319
pKa 6.25 · escape 93%
95%
3
306Oi10
pKa 6.55 · escape 87%
95%

Microfluidic alignment

Droplets snap into monodisperse alignment · flow 3.0:1, 8.0 mL/min · D₅₀ 93.3 nm

3D particle cross-section

molecular viewer →

PEG-lipid corona
Ionizable / helper lipid shell
Cholesterol layer
Nucleic-acid cargo
Targeting ligand 1.0 mol%

mRNA core · 95% encapsulatedD₅₀ 93 nm · PDI 0.078 · drag to orbit

Ionizable lipid library

pKa5.50–7.50

Lipid	pKa	logP	Tail	Encap.	Size	PDI	Escape	Score	Status
DLin-MC3-DMAAlnylam / Onpattro	6.44	4.8	C18:2 x2	95%	93 nm	0.078	96%	92	selected
TT3 (FTT5)Dong lab	6.35	4.3	C15 branched	95%	91 nm	0.080	91%	91	preclinical
L319Alnylam	6.25	4.5	C18:2 ester	95%	93 nm	0.083	93%	91	preclinical
306Oi10Anderson lab	6.55	4.4	C10 branched	95%	86 nm	0.080	87%	91	preclinical
Lipid 5Moderna	6.56	4.9	C9/C8 ester	95%	92 nm	0.080	87%	89	preclinical
C12-200Anderson lab	6.20	3.9	C12 x5	95%	88 nm	0.085	84%	89	preclinical
A18-Iso5-2DC18Xu lab	6.60	5.0	C18 x2	95%	93 nm	0.081	84%	88	preclinical
cKK-E12Anderson lab	6.14	3.7	C12 x4	95%	88 nm	0.089	79%	87	preclinical
DLin-KC2-DMATekmira	6.10	4.6	C18:2 x2	95%	93 nm	0.091	81%	87	phase i
SM-102Moderna / Spikevax	6.68	4.2	C10/C7 ester	95%	92 nm	0.084	77%	86	approved
ALC-0315Acuitas / Comirnaty	6.09	5.1	C14 branched	95%	90 nm	0.092	74%	85	approved
BAMEA-O16BDong lab	6.75	4.7	C16 disulfide	95%	92 nm	0.088	71%	84	preclinical
9A1P9Siegwart lab	6.90	4.1	C9 ester	95%	85 nm	0.098	56%	79	preclinical
OF-Deg-LinWhitehead lab	5.80	4.0	C18:2 oxidized	91%	93 nm	0.113	54%	75	preclinical
SS-33/4PE-15Harashima lab	7.15	5.3	C15 disulfide	89%	91 nm	0.116	39%	70	preclinical

15 of 15 lipids · sorted by delivery score ↓ · click a row to pinPredictions are in silico — validate in vitro before use.

Paper framework modules

Reference paper · https://doi.org/10.1186/s12645-026-00431-9 ↗

p53 strategy · cargo class

R175H → p.Arg175His is a gain-of-function missense mutant — mutant-p53 siRNA is indicated; use the dual siRNA + mRNA LNP if wild-type, null and mutant clones coexist.

⚠ Therapeutic window is limited by the duration of p53 expression; transient transfection may be insufficient.

Paper · p53 as a master therapeutic target

Nanocarrier architecture

pH-responsive ionizable lipid layer around a nucleic-acid core with PEG corona; pKa 6.0–7.0 optimum.

Size: 50–150 nm
Drug loading: 10–20 %
Encapsulation: 85–95 %
Cargo compatibility: mRNA, siRNA, sa-mRNA
Clinical status: Approved
Key limitation: Liver-dominant biodistribution; anti-PEG immunogenicity

Predicted size 93nm vs Table 1 50–150nmin range
Predicted encapsulation 95% vs Table 1 85–95%in range

Paper · Table 1 · Fig. 1

Active targeting vs passive EPR

Ligand

Ligand surface density1.0 mol%

Folic acid · FR-α

Folate/HA targeting for ovarian contexts; TP53 restoration strategies reviewed by Zhang et al. 2025.

Limitation: Off-target accumulation in kidneys; requires high FR-α expression.

Passive EPR (median)
0.7% ID
Modelled with ligand
1.9% ID

Passive 0.7% is the Wilhelm et al. 2016 median cited in the paper; the ligand gain (2.71×) is an illustrative saturating model — the paper reports no fold-gain. No p53-directed ligand-targeted LNP has entered clinical trials.

Paper · Table 2 · passive targeting

Stimuli-responsive release

ionizable-lipid protonation; TME pH 6.5–6.8, endosome pH 4.5–6.0

pH-responsive release (Fig. 3A)

pH 5.5 · endosome
pH 6.5 · tumour microenvironment
pH 7.4 · blood

Ionizable-lipid protonation in the endosome destabilises the membrane; the TME (pH 6.5–6.8) gives partial release, blood (pH 7.4) almost none (Fig. 3A). Selectivity at 24 h: 92 pts triggered vs off.

Paper · Fig. 3 · stimuli-responsive and triggered release

SORT charged lipid · biodistribution

SORT charged-lipid fraction0 mol%

Predicted organ share of dose

Liver
66%
Spleen
10%
Lung
4.0%
Tumour
1.9%

Standard ionizable formulations are liver-dominant, limiting extrahepatic efficacy.
SORT charged lipids alter protein-corona composition and shift uptake to spleen / lung.
Trade-offs: endosomal escape can drop, non-specific uptake rises, scale-up is harder; re-optimise ionizable pKa and PEG-lipid.

Organ percentages are an illustrative, qualitative model of the paper's statements.

Paper · AI-driven LNP design · SORT trade-offs

Anti-PEG immunogenicity

Standard hydrophilic corona; reduces opsonisation, prolongs circulation.

Chronic / multi-cycle regimen (repeat dosing)

Accelerated blood clearance risklow · 29/100

Complement activation-related pseudoallergy needs monitoring in p53 LNP development.

Paper · Immunogenicity and safety

Immunotherapy combination & clinical benchmarks

Combine with anti-PD-1 checkpoint blockade

p53-LNP monotherapy

p53 mRNA restoration induces immunogenic cell death and enhances antigen presentation; with checkpoint blockade it increased CD8+ T-cell infiltration and gave durable suppression in HCC models (Xiao et al. 2022).
Enable anti-PD-1 to see the combination rationale: p53 restoration can sensitise resistant tumours to checkpoint blockade.
Platform proof-of-concept: KEYNOTE-942 Phase IIb — mRNA-4157 + pembrolizumab cut recurrence risk by 44% vs pembrolizumab alone (neoantigen vaccine; does not encode p53).

Product (Ionizable LNP)	Cargo	Phase
mRNA-4157	mRNA neoantigens	Phase III
BNT122	mRNA neoantigens	Phase II
BNT111	mRNA (fixed)	Phase II
mRNA-2752	OX40L/IL-23/36	Phase I
p53 mRNA-LNP	p53 mRNA	Preclinical / Exploratory Phase I (no published results)

mRNA-4157 and BNT122 are personalized neoantigen vaccines and do not encode p53; they are included to illustrate clinical validation of the ionizable LNP-mRNA platform in oncology, not as p53-directed therapies.

Paper · p53 LNPs in cancer immunotherapy · Table 3

LNPredict — in silico lipid nanoparticle formulation platform