US 2019/0262453 Al  16  Aug. 29, 2019  TABLE 3-continued  Table 1: Model Parameters  Baseline Input  Symbol  Description  Value  Range of Input Value  R  Gas constant  8.314  Fixed  T  Absolute  0  Fixed  96485  Fixed  Units  J • K- 1  • mo1- 1  Kelvin  J/volt  temperature  Faraday’s constant  Avogadro’s number  Rate of proton and  chloride  sequestration by  CFZ  6.02 X 10 23  0  Fixed  molecules/mo!  1.16 x 10-$^{23 }$to 1.16 x 10- 20  Moles/day  Baseline input values are literature values (Heuser et al., 1993; Van Dyke, 1993; Gambale et al., 1994; Sonawane et al.,  2002; Alberts, 2008) representing physiological lysosomes and are in agreement with previously published model (Grabe  and Oster, 2001; Ishida et al., 2013).  *estimated intrinsic surface potentials for inner  CWin)  and outer  CW  out)  leaflets of the lysosomal membrane accounted for  when modeling membrane transporter mediated dynamic lysomal and cytoplasmic ion concentration at the membrane  surface (Grabe and Oster, 2001).  [0159]  Simulating lysosomal CFZ-HCl accumulation. To  simulate the dose-dependent lysosomal CFZ-HCl accumu› lation, the rates of proton and chloride sequestration by CFZ  were adjusted to either 0.01 or 0.1 picomoles/cell/day, which  equal to  1.2x10- 21  moles/lysosome/day and 1.2x10- 20  moles/lysosome/day, respectively, as calculated by assum› ing there are approximately 100 lysosomes in a cell. Inter› changeably from here onwards, these rates; 0.01 and 0.1  picomoles/cell/day, are referred to as I-fold (lx) and 10-fold  (lOx) CFZ-HCl accumulation, respectively.  Calculating the effect of CFZ-HCl accumulation on lyso› somal ion homeostasis. The set of differential equations  detailed earlier (equations 27-29) was solved by numerical  integration in Berkeley Madonna (BM) using Rosenbrock  stiff solver as numerical integrator. Upon performing para› metric simulations in the absence and presence ofCFZ-HCl  accumulating at either 1 x or 1 Ox, along with different ranges  of lysosomal parameters such as V-ATPase, CLC7, and  cytoplasmic chloride (as elaborated earlier), final lysosomal  pH, chloride and membrane potential were chosen as read› out values. The readout values in the absence of CFZ-HCl  were subtracted from the ones in the presence of CFZ-HCl  to determine the effect oflysosomal CFZ-HCl accumulation  on lysosomal ion homeostasis represented by the changes in  lysosomal pH, Cl, and membrane potential.  [0162]  Calculating the effects of V-ATPase, CLC7, and  cytoplasmic chloride on the physiological lysosomal accu› mulation of CFZ-HCI. Time-plot simulations were per› formed to obtain final lysosomal pH, chloride, and mem› brane potential values (specifically chosen because they are  direct indicators of lysosomal ion homeostasis and physiol› ogy) while adjusting all of the lysosomal parameters to their  respective baseline values in the absence of CFZ-HCl accu› mulation. This allowed us to obtain physiological lysosomal  pH of 4.53, chloride concentration of 224.6 mM, and  membrane potential of 0.79 m  V,  which from here onwards  thes values are referred to as "physiological baseline readout  values" as they are associated with no changes to physi› ological baseline lysosomal parameters and contents.  [0160]  Simulating the inhibition oflysosomal proteins and  cytoplasmic chloride. In order to study the role ofV-ATPase,  CLC7, and cytoplasmic chloride concentration on the lyso› somal accumulation of CFZ-HCl, the total number of active  V-ATPase and CLC7 molecules per lysosome, as well as the  cytoplasmic chloride concentration were varied, while fixing  the values of other lysosomal parameters at their baseline  physiological input values in the presence and absence of  lysosomal CFZ-HCl accumulation. More specifically, to  simulate the simultaneous inhibition of V-ATPase and  CLC7, the total number of CLC7 molecules per lysosome  was varied from O to 5000 in geometric interval of 2.09  while one simulation at a time the total number ofV-ATPase  molecules per lysosome was manually varied from O to 300  in arbitrary intervals. Moreover, to simulate the simultane› ous inhibition ofV-ATPase and cytoplasmic chloride, cyto› plasmic chloride concentration was varied from O to 10 mM  in arithmetic intervals of 6.67xl 0-4 while one simulation at  a time the total number of V-ATPase molecules per lyso› some was manually varied from O to 300 in arbitrary  intervals.  [0161]  Using the aforementioned ranges of the adjustable  lysosomal parameters, the corresponding inhibition range of  0 to 100% was calculated; where 0% represents no change  from respective physiological baseline input value whereas  100% represents maximum change from respective physi› ological baseline input value. The inhibition range was  calculated as follows by comparing its corresponding input  value from the aforementioned given range (Adjusted Input  Value) with its respective physiological input value (Base› line Input Value).  [0163]  Moreover, in the presence ofCFZ-HCl accumulat› ing at 1 x and 1 Ox, final lysosomal pH, Cl and membrane  potential values were chosen as readout values while per› forming parametric simulation runs in the presence of simul› taneous V-ATPase-CLC7 and V-ATPase-cytoplasmic chlo› ride inhibitions. These values were then subtracted from the  physiological baseline readout values to calculate the effects  of the simultaneous lysosomal parameter inhibitions on  dose-dependent lysosomal CFZ-HCl accumulation.  [0164]  Steady state and mass balance check. For all of the  aforementioned simulations, the final readout values were  confirmed that they were steady state values by performing  the simulation for >24 hrs. Moreover, mass balance was  maintained in all of the simulations in the presence as well  as absence ofCFZ-HCl accumulation as long as physiologi- Baseline Input Value-Adjusted Input Value  % Inhibition= --------------*100  Baseline Input Value  30 