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[0256] Baseline input values are literature values (Van Dyke R W. Am J Physiol. 1993;265(4 Pt 1):C901-17; Gambale et al, 1994, supra; Heuser et al, 1993, supra; Sonawane et al, 2003, supra; Alberts et al., 2008, supra) representing physiological lysosomes and are in agreement with previously published model (Ishida et al., 2013, supra; Grabe et al., 2001, supra). 

[0257] * estimated intrinsic surface potentials for inner (Win) and outer (Wout) leaflets of the lysosomal membrane accounted for when modeling membrane transporter medi› ated dynamic lysosomal and cytoplasmic ion concentrations at the surface (Grabe et al., 2001, supra). 

[0258] Simulating Drug Induced Changes in Lysosomal Morphology 

[0259] To study how drug-induced changes in lysosomal morphology affect ion homeostasis, simulations were per› formed in lysosomes of different surface areas and volumes. First, lysosomes were modeled as perfect spheres. Assuming there are approximately around 100 lysosomes in a cell, which occupy 1 % of cellular volume, the volume of a single lysosome was set to 1.65xl0-$^{16 }$L. For a spherical vesicle, this volume corresponds to a lysosomal radius of 0.34 um and a surface area of 1.45x10+cm 2 . 

[0260] For comparison, tubular lysosomes (represented in FIG. 22B) possessing different radii in the range 40 nm to 270 nm and heights in the range 585 nm to 5.73 um were modeled using a range of volumes 2.88xl0-$^{17 }$L to 1.34x 10-$^{16 }$L. The dimensional relationship between the tubular radius and height, at constant lysosomal surface area of 1.45xl o-s cm 2 ( equivalent to the surface area of a spherical lysosome of 0.34 um in radius), was calculated using cylindrical equation (V=itrh, where r is radius and h is height). These morphologies are consistent with measure› ments by other publications (Swanson J, et al., J Cell Biol. 1987;104(5):1217-22; Knapp PE, et al., J Cell Sci. 1990;95 (Pt 3):433-9). 

[0261] Next, to mimic disc-shaped lysosomes as have been reported in different cell types under other biologically relevant conditions (Agarwal R, et al., Proc Natl Acad Sci U SA. 2013;110( 43):17247-52; Doshi N, et al., Proc NatlAcad Sci US A. 2009;106(51):21495-9; Mitragotri S, et al., Nat Mater. 2009;8(1):15-23), lysosomal radius in the range 422 nm to 10 um and height in the range 0.5 nm to 294.9 nm were modeled using a rage of lysosomal surface area 1.90x 10- 3 cm 2 to 6.28xl0- 6 cm 2 . The dimensional relationship between the disc-shaped lysosomal radius and height, at constant lysosomal volume of 1.65xl0-$^{16}$L (equivalent to the volume of a spherical lysosome of 0.34 um in radius, as previously mentioned in the study of spherical lysosomes), 

was calculated using cylindrical equation (S=2itr2+2mh, where r is radius and h is height). 

[0262] Simulating Stress Tolerance Following Drug Induced Changes in Lysosomal Morphology 

[0263] To understand how lysosomes possessing different structural and functional characteristics may respond differ› ently to drugs, the number of V-ATPase and membrane proton permeability were individually varied. These two particular lysosomal parameters are referred to "stress tol› erance inducers". Thus, the number ofV-ATPase molecules per lysosome was increased from physiological baseline input value of 300 to 1.3xl 0 $^{5 }$in arbitrarily chosen intervals, while proton permeability was decreased from physiological baseline input value of 6x10- 5 emfs to 1.38xl0- 7 emfs in arbitrarily chosen intervals. These ranges of input values for both V-ATPase number and proton permeability allowed us to quantitatively compare and contrast the relationship of lysosomal surface area to the number of V-ATPase mol› ecules and membrane proton permeability per lysosome. For example, different fold increments in lysosomal surface area (say, 20- or 400-fold) were chosen and in one simulation at a time set the corresponding lysosomal surface area as an input. So, in the case of a lysosome with a 20-fold lysosomal surface area expansion, its surface area was set to 2.9x10- 7 cm 2 . Then, to study the effect of the number of V-ATPase molecules on this expanded lysosome, parametric simula› tion was performed for the V-ATPase number ranging O to 6000, which corresponds to O to 20-fold increment m V-ATPase number per lysosome. 

[0264] Simulating Drug Induced Lysosomal Stress 

[0265] Parametric simulations were run to study the effects of the following four drug-induced stresses on lyso› somal physiology: V-ATPase inhibition, CLC7 inhibition, lysosomal membrane permeabilization, and decreased mem› brane potential dissipation based on lower cytoplasmic chloride concentration (FIG. 22). 

[0266] More specifically, membrane proton permeability was varied from physiological baseline input value of 6xl0- 5 emfs to 6 emfs in geometric intervals of 1.78, the number ofV-ATPase molecules per lysosome was manually varied from O to physiological value of 300 in arbitrarily chosen intervals, the number of CLC7 molecules per lyso› some was varied using parametric feature of BM from O to physiological value of 5000 in geometric intervals of 2.09, and the cytoplasmic chloride concentration was manually varied from Oto physiological value of 10 mM in arbitrarily chosen intervals. For cytoplasmic chloride concentration, and V-ATPase and CLC7 numbers the individual ranges of input values were chosen to represent the corresponding 

