competitive-enzyme-inhibition.bngl

begin model
begin parameters
    # Competitive inhibition: Inhibitor (I) and Substrate (S) compete for the same
    # active site of Enzyme (E).
    
    # Reaction rates
    k_bind_s 1e-3      # Substrate binding
    k_unbind_s 0.1     # Substrate dissociation
    k_cat 1.0          # Catalysis (Product formation)
    
    k_bind_i 1e-4      # Inhibitor binding (Higher affinity proxy)
    k_unbind_i 0.01    # Inhibitor dissociation
    k_recovery 0.05    # Product clearance
    
    # Multi-substrate extension
    k_bind_s2 5e-4     # Competitor substrate
    
    # Initials
    Enzyme_tot 100
    Substrate_tot 1000
    Substrate2_tot 0
    Inhibitor_tot 500
    Product_init 0
end parameters

begin molecule types
    Enzyme(s,state~free~bound)
    Substrate1(b)
    Substrate2(b)
    Inhibitor(b)
    Product()
end molecule types

begin seed species
    Enzyme(s,state~free) Enzyme_tot
    Substrate1(b) Substrate_tot
    Substrate2(b) Substrate2_tot
    Inhibitor(b) Inhibitor_tot
    Product() Product_init
end seed species

begin observables
    # KEY BIOLOGICAL OUTPUTS
    Molecules Free_Enzyme    Enzyme(state~free)         # Working capacity
    Molecules ES_Complex     Enzyme(s!1).Substrate1(b!1) # Catalytic intermediate
    Molecules EI_Complex     Enzyme(s!1).Inhibitor(b!1)  # Sequestrated/Inhibited enzyme
    Molecules Total_Product  Product()                  # Reaction velocity proxy
    Molecules S_Remaining    Substrate1()               # Mass balance
end observables

begin reaction rules
    ## CLASSIC COMPETITION
    # Enzyme + Substrate <-> ES -> Enzyme + Product
    Enzyme(s,state~free) + Substrate1(b) <-> Enzyme(s!1,state~bound).Substrate1(b!1) k_bind_s,k_unbind_s
    Enzyme(s!1,state~bound).Substrate1(b!1) -> Enzyme(s,state~free) + Product() k_cat
    
    # Enzyme + Inhibitor <-> EI (Dead end complex)
    Enzyme(s,state~free) + Inhibitor(b) <-> Enzyme(s!1,state~bound).Inhibitor(b!1) k_bind_i,k_unbind_i
    
    ## MULTI-SUBSTRATE EXTENSION
    # Enzyme + Substrate2 <-> ES2
    Enzyme(s,state~free) + Substrate2(b) <-> Enzyme(s!1,state~bound).Substrate2(b!1) k_bind_s2,k_unbind_s
    
    ## CLEARANCE
    Product() -> 0 k_recovery
end reaction rules

begin actions
    generate_network({overwrite=>1})
    simulate({method=>"ode",t_end=>150,n_steps=>300})
end actions
end model