The gelatinases (MMP-2 and MMP-9) are members of the matrix metalloproteinase (MMP) family, a class of enzymes that are responsible for the restructuring of the extracellular matrix. Upregulation of expression of gelatinases has been implicated in the pathology of cancer metastasis, neurological diseases and in making diabetic wounds refractory to healing. SB-3CT, a potent and selective gelatinase inhibitor, is effective in mouse models of cancer metastasis, stroke and traumatic brain injury. However, it is limited by extensive metabolism and poor aqueous solubility. SB-3CT is rapidly metabolized due to hydroxylation at the para-position of the terminal phenyl to a more potent gelatinase inhibitor, and oxidation at the alpha-position to the sulfonyl moiety to generate the inactive sulfinic acid.  alpha-Methyl analogs of SB-3CT were conceptualized to block metabolism at the alpha-position to the sulfonyl group. Enzyme kinetics and metabolism of the alpha-methyl variants showed a 10-fold decrease in potency against the gelatinases, but with a significant improvement in metabolic stability. Pharmacokinetics and brain distribution of gelatinase inhibitors were explored to correlate with the in vivo efficacy of SB-3CT in animals models of neurological diseases. A sensitive bioanalytical method based on ultraperformance liquid chromatography with multiple-reaction monitoring detection was developed to measure levels of gelatinase inhibitors in plasma and brain. The compounds were rapidly absorbed and distributed at therapeutic concentrations in the brain.  Amino acid prodrugs were developed to increase >5,000-fold the water solubility of SB-3CT. In vivo, prodrug ND-478 is hydrolyzed to ND-322, which is further N-acetylated to ND-364. N-Hydroxylation of the aromatic amine was not observed and both ND-478 and ND-322 were non-mutagenic in the Ames II mutagenicity assay. ND-364 was shown to be highly brain-penetrant and distributed five times higher in brain than in plasma, following intravenous (iv) infusion of prodrug ND-478. The high water solubility, metabolic stability, lack of toxicity, and favorable PK properties make the thiirane class of selective gelatinase inhibitors suitable for iv administration in treatment of acute gelatinase-dependent neurological diseases. ND-322 was evaluated in a diabetic mouse model of wound healing. Using an MMP inhibitor-tethered resin, which binds all active MMPs, elevated levels of active MMP-9 in diabetic wounds were documented by quantitative MRM-MS. Treatment with the selective gelatinase inhibitor ND-322 accelerated wound healing by re-epithelialization in the first demonstration of a potential therapy for this disease.  Finally, second-generation lipophilic MMP-9 inhibitors, amenable for formulation as ointments, were synthesized and evaluated for stability in in vitro systems of wound fluids. Evaluation of MMP inhibition unexpectedly led to highly selective MMP-2 inhibitors, which may render useful in studies where MMP-2 selectivity is desired.