Drug permeability prediction using PMF method
Fancui Menga,*, Weiren Xub
aState Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
bTianjin Key Laboratory of Molecular Design and Drug Discovery , Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
Supporting Information:
Figure S1. Atom name of three drugs
Table S1. The atom name(see Figure S1) and corresponding charges derived through the PRODRG server.
Table S2.Comparison of the partial charges of ibuprofen with reference 13.
Figure S2. Potential energy for one of the runs indicating that equilibration happens well after 5ns, so the final 2ns (8ns~10ns) production was used to do PMF and other analyses.
Figure S3. Drug center of mass movement x-y plane
Figure S4. Mean square displacement of the drugs
Figure S5. RDF between the COM (center of mass) of drug (located at z ~1.0nm from the bilayer center) with water.
Figure S1. Atom name of three drugs
Table S1. The atom name(see Figure S1) and corresponding charges derived through the PRODRG server.
doxorubicin / atenolol / ibuprofenatom / charge / atom / charge / atom / charge / atom / charge
CAT / 0.000 / HBK / 0.029 / CAA / 0.000 / OAN / -0.257
CAU / 0.037 / CBL / 0.005 / CAL / 0.000 / CAL / 0.371
NAL / 0.134 / HBL / 0.039 / CAB / 0.000 / OAO / -0.257
HBP / 0.003 / CBJ / 0.005 / NAM / 0.221 / CAK / 0.143
HBQ / 0.003 / HBJ / 0.039 / HAT / -0.005 / CAM / 0.024
HAL / 0.003 / CBH / -0.003 / HAU / -0.005 / CAC / -0.024
CAV / 0.036 / CBF / 0.152 / CAN / 0.019 / CAD / -0.017
OAD / -0.315 / OAJ / -0.237 / CAO / 0.041 / HAD / 0.002
HAD / 0.012 / CBB / -0.005 / OAK / -0.206 / CAE / -0.018
CAW / 0.055 / CAZ / 0.085 / HAS / 0.014 / HAE / 0.002
CBC / 0.032 / OAF / -0.110 / CAP / 0.072 / CAB / -0.018
OAB / -0.145 / HAF / 0.035 / OAQ / -0.195 / HAB / 0.002
CAS / 0.112 / CAR / -0.005 / CAI / 0.044 / CAA / -0.018
OAA / -0.145 / CAP / 0.097 / CAJ / -0.008 / HAA / 0.003
CAM / 0.112 / CAN / 0.107 / HAL / 0.012 / CAF / -0.027
CAO / 0.066 / OAC / -0.103 / CAE / -0.008 / CAG / 0.029
CAQ / -0.005 / HAC / 0.037 / HAI / 0.012 / CAH / 0.060
CAX / 0.085 / CAY / 0.232 / CAH / -0.008 / CAJ / 0.000
OAE / -0.110 / OAG / -0.401 / HAK / 0.012 / CAI / 0.000
HAE / 0.035 / CBD / 0.097 / CAG / -0.008
CBA / -0.005 / OAH / -0.103 / HAJ / 0.012
CBE / 0.115 / HAH / 0.037 / CAF / -0.016
OAI / -0.313 / CAD / 0.077
CBG / -0.004 / CAC / 0.253
CBI / 0.115 / OAR / -0.359
OAK / -0.077 / NAS / 0.035
CBM / 0.131 / HAW / -0.003
CBK / 0.004 / HAV / -0.003
Table S2: Comparison of the partial charges of ibuprofen with reference 13.
ours / Ref13atom / charge / neutral / charge
OAN / -0.257 / OAD / -0.263 / -0.754
CAL / 0.371 / CAK / 0.374 / 0.361
OAO / -0.257 / OAE / -0.263 / -0.753
CAK / 0.143 / CAO / 0.128 / 0.123
CAM / 0.024 / CAC / 0.024 / 0.023
CAB / -0.018 / CAI / -0.023 / -0.038
CAA / -0.018 / CAG / -0.023 / -0.038
CAF / -0.027 / CAL / -0.012 / -0.020
CAG / 0.029 / CAJ / 0.042 / 0.069
CAI / 0.000 / CAB / 0.016 / 0.027
Figure S2. Potential energy for one of the runs indicating that equilibration happens well after 5ns, so the final 2ns (8ns~10ns) production was used to do PMF and other analyses.
Figure S3. Drug center of mass movement x-y plane
Figure S4. Mean square displacement of the drugs
Figure S5. RDF between the COM (center of mass) of drug (located at z ~1.0nm from the bilayer center) with water.