A charged mesoporous silica nanoparticle (MSN)-based drug delivery system for controlled release and enhanced bioavailability is disclosed. The system comprises a positively charged MSN, which has a silica matrix and an array of pores and/or nanochannels in the matrix. The entire substance of the matrix, all the surfaces and the pores and/or nanochannels comprise a plurality of silanol (Si—OH) and quaternary ammonium functional groups. The bioavailability of a negatively charged bioactive compound can be increased by loading it into the pores and/or nanochannels. The silanol (Si—OH) functional groups on the surfaces lining the walls of the pores and/or nanochannels are free to deprotonate in a fluid having pH above the pI of the positively charged MSN and lead to a sustained release of the negatively charged drug from the pores and/or nanochannels, and thereby enhance the bioavailability of the drug.