ADJACENT DOMAIN — ROADMAP

Microbial pharmacology — cascade roadmap.

A parallel domain engine for antibacterial, antiviral, antifungal, and antiparasitic pharmacology. Same cascade architecture as the human Flux Pharmacology engine; pathogen-specific content at every step. This page is a roadmap document — nothing here is shipping today.

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Status: mixed-tier roadmap view. The binding-affinity layer reaches most pathogen targets today via the same target-engagement engine that scored CASF-2016 (r = 0.772) on diverse target classes — so most Phase 3 (Target engagement) chips below are in pilot. Pathogen-specific infrastructure (envelope crossing, efflux modeling, MIC determination, biofilm / persister states, lifecycle-stage selectivity) is on the roadmap.

Full domain delivery is gated on the human-pharmacology cascade reaching primary-endpoint validation across its full scope. Microbial pharmacology is treated as a parallel domain engine that inherits the cascade architecture and the target-engagement engine but has its own envelopes, resistance enzymes, mechanism outputs (MIC, MBC, time-kill kinetics), and validation datasets (CLSI / EUCAST MIC databases, ChEMBL antimicrobial subsets, CO-ADD, Stanford HIVdb, MARS, MMV, NCATS).

Validated — published benchmark accuracy
In pilot — same physics as validated targets
In development — newer physics, wider uncertainty
Future — on the roadmap, not available today

How to read these tiers. Validated items have published benchmark numbers — use as primary screening criterion. Pilot items run the same physics that validated other targets in the same family — usable as primary screening criterion with the per-endpoint validation caveat. In-development items are operational prototypes with newer or scope-capped physics — treat output as directional input and cross-check experimentally. Future items aren't available today.

Pick a pathogen domain

Each tab shows the planned cascade content for that domain. The cascade structure (envelope crossing → accumulation → target engagement → mechanism → selectivity) is shared across domains; the specific modules differ at every step.

Compound + pathogen species
1 Envelope crossing Pathogen entry
4
Gram-positive peptidoglycan + cytoplasmic membrane
Gram-negative outer membrane · LPS · porins · periplasm · inner membrane
Mycobacterial mycolic acid waxy layer · arabinogalactan
Atypicals Mycoplasma · Chlamydia · Rickettsia · Spirochetes
2 Accumulation & resistance enzymes Efflux · degradation · persistence
7
Pathogen efflux pumps
RND efflux AcrAB-TolC · MexAB-OprM · MtrCDE
MATE / MFS efflux NorA · EmrAB · MdfA
Mycobacterial efflux EfpA · Tap · Mmr
Drug-degrading enzymes
β-lactamases TEM · SHV · CTX-M · KPC · NDM · OXA
Aminoglycoside-modifying enzymes
Persistence niches
Biofilm matrix 4-1000× MIC shift
Persister-cell state metabolically dormant
3 Target engagement Bacterial drug targets
7 4
Cell wall & membrane
PBPs penicillin-binding proteins · transpeptidases · transglycosylases
MurA-F peptidoglycan precursor biosynthesis
LPS biosynthesis multimeric membrane complex · polymyxins · lipid II
Protein synthesis (ribosome)
Ribosome 50S very large RNP complex · macrolides · oxazolidinones
Ribosome 30S large RNP complex · aminoglycosides · tetracyclines
Nucleic-acid replication & transcription
DNA gyrase GyrA / GyrB · fluoroquinolones
Topoisomerase IV ParC / ParE
RNA polymerase RpoB · rifamycins
Metabolism & energy
Folate biosynthesis DHFR · DHPS · sulfonamides + trimethoprim
FAS-II lipid biosynthesis FabI · FabF
Energy metabolism ATP synthase AtpE · cytochrome bc1 · membrane complexes
4 Mechanism & outcome Bacteriostatic · bactericidal · kinetics
5
Bacteriostatic vs bactericidal MBC/MIC ratio
Resistance-breaker classification β-lactamase-stable · efflux-evading
Time-kill kinetics concentration- vs time-dependent
Post-antibiotic effect (PAE)
Biofilm MIC
5 Selectivity & decision Host vs pathogen · resistance · PK/PD bridge
1 4
Host-vs-pathogen selectivity index composition of human cascade (validated) × pathogen binding (pilot)
Resistance frequency mutational escape rate
Combination synergy FIC index
MIC50 / MIC90 vs CLSI / EUCAST reference panels
PK/PD bridging f%T>MIC · fCmax/MIC · fAUC/MIC
Compound + viral target
1 Envelope & replication-site access Pathogen entry
3
Enveloped virus host bilayer + viral envelope
Non-enveloped virus capsid pore / disassembly route
Replication compartment access membranous web · viroplasm
2 Viral persistence & resistance Polymerase proofreading · intracellular accumulation
3
Polymerase proofreading 3′-5′ exonuclease · coronavirus nsp14
Intracellular pharmacology activation of nucleotide prodrugs
Latent reservoir access HIV proviral integration sites
3 Target engagement Viral drug targets
8 2
Polymerases
RNA polymerases (RdRp) coronavirus · influenza · HCV NS5B
DNA polymerases HSV pol · HBV pol · HCMV pol
Reverse transcriptase HIV RT · NRTIs / NNRTIs
Proteases & enzymes
Viral proteases HIV PR · HCV NS3/4A · SARS-CoV-2 Mpro · PLpro
Integrase HIV IN · INSTIs
Helicase NS3 helicase
Neuraminidase influenza NA
Entry, capsid, assembly
Entry proteins multimeric · HIV gp120/gp41 · influenza HA · coronavirus spike
Capsid assembly / disassembly multimeric · maturation inhibitors
NS5A HCV polymerase cofactor
4 Mechanism & outcome Lifecycle-stage selectivity
1 3
Lifecycle-stage selectivity entry · replication · assembly · release
Nucleotide incorporation kinetics chain terminator · obligate / non-obligate
Viral load reduction kinetics
Resistance mutation profiles scored against mutant target structures
5 Selectivity & decision Host polymerase selectivity · resistance · combinations
3 2
Host polymerase selectivity direct composition with human pol-γ / pol-β via canonical cascade
EC50 vs CC50 selectivity index composition of viral pilot + host validated
Resistance database matching Stanford HIVdb · HCV resistance
Combination antiviral synergy
Mutation barrier prediction derived from binding scored against mutant structures
Compound + fungal species
1 Cell wall & membrane crossing Pathogen entry
3
Fungal cell wall β-glucan + chitin + mannoprotein outer layer
Plasma membrane ergosterol-rich bilayer
Fungal vacuole / mitochondrial access
2 Accumulation & resistance CDR/MDR efflux · CYP51 upregulation
3
CDR / MDR efflux CDR1 · CDR2 · MDR1 (Candida)
CYP51 upregulation azole-resistance mechanism
Candida biofilm formation
3 Target engagement Fungal drug targets
5 3
Ergosterol biosynthesis
CYP51 / Erg11 heme protein · azoles · same family as CYP-as-target
Squalene epoxidase (Erg1) allylamines · terbinafine
Erg6 / Erg2 morpholines · amorolfine
Cell wall biosynthesis
β-1,3-glucan synthase (FKS1) large membrane complex · echinocandins
Chitin synthase membrane enzyme · nikkomycins
Other targets
DNA / RNA synthesis flucytosine (5-FC) targets
Mitochondrial respiration fungal electron transport complexes
β-tubulin griseofulvin
4 Mechanism & outcome Fungistatic · fungicidal · MIC / MFC
3
Fungistatic vs fungicidal MFC/MIC ratio
MIC / MFC determination
Resistance frequency
5 Selectivity & decision Host-CYP vs fungal-CYP51 selectivity
1 3
Host-CYP vs fungal-CYP51 selectivity direct composition with canonical CYP-as-target panel · known field-wide problem
MIC vs Candida / Aspergillus / Cryptococcus reference panels
MARS resistance database matching
Combination antifungal synergy
Compound + parasite species & lifecycle stage
1 Multi-membrane access Host + parasitophorous vacuole + parasite membrane
4
Host cell entry for intracellular parasites
Parasitophorous vacuole crossing Plasmodium · Toxoplasma
Parasite plasma membrane
Helminth cuticle / tegument nematode collagen · trematode tegument
2 Accumulation & resistance Parasite-specific transport · metabolism
4
PfMDR1 · PfCRT chloroquine + artemisinin resistance
Plasmodium food vacuole accumulation heme detoxification site
Trypanosomatid kinetoplast access
Parasite drug metabolism PfCYP · PfFNR · aldo-keto reductases
3 Target engagement Parasite drug targets
8 2
Plasmodium (malaria)
PfDHFR-TS antifolates · pyrimethamine
Cytochrome bc1 (PfCytB) atovaquone
PfATP4 Na+ pump · cipargamin class
PfActin · PfPI4K
Trypanosomatid (Chagas, sleeping sickness, leishmaniasis)
T. cruzi CYP51 heme protein · same family as canonical CYP-as-target
Trypanothione reductase
Kinetoplast topoisomerase
Helminths (worms)
Helminth-specific β-tubulin benzimidazoles · albendazole / mebendazole
Glutamate-gated Cl channels parasite-specific channels · avermectins · ivermectin
GABA-gated Cl channels · calcium homeostasis parasite-specific · praziquantel
4 Mechanism & outcome Lifecycle-stage selectivity · parasitemia kinetics
1 2
Lifecycle-stage selectivity schizonticide · gametocytocide · hypnozoiticide
Parasitemia reduction kinetics
Resistance mutation profiles scored against mutant target structures
5 Selectivity & decision Host-vs-parasite selectivity · reference panels
2 2
Host-vs-parasite selectivity composition with canonical structural-proteins panel · CYP51 conservation
EC50 vs host cytotoxicity (CC50) composition of parasite pilot + host validated
WHO / MMV reference panels
Resistance database matching

Microbial pharmacology shares the canonical cascade architecture (entry → accumulation → target engagement → mechanism → decision) but has its own targets, envelopes, resistance enzymes, and validation datasets. Host-vs-pathogen selectivity is composed at the result-assembly layer by running the human cascade in parallel against host homologs. Planned phasing: bacterial flagship → antiviral flagship → antifungal + antiparasitic → resistance + combinations → productization.

Interested in this roadmap?

If your program would benefit from microbial pharmacology capabilities — antimicrobial discovery, resistance liability, host-vs-pathogen selectivity — we'd like to hear about the use case as we plan execution sequencing.

See what ships today

Our human-pharmacology cascade is validated and shipping — 5 of 8 ADMET endpoints at public-benchmark SOTA, all 8 modes of binding physics operational.

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