The review present the literature data and the authors findings on perspective technologies for design of active chemical and natural compounds based on small molecules for highly specific therapy and correction of a wide variety of pathophysiological conditions in humans, that show overlapping development processes and have common mediators. The following strategies are discussed: chemogenomics strategy using computer screening libraries for generating of small molecule compounds with advantageous properties; strategy of chemokine network that provide control of many processes, from immunosurveillance to inflammation and from viral infections to cancer; strategy of using cytochrome P450 enzymes that guarantee maximum bioavailability of drugs and prevent their interaction and toxic effect; strategy of using superoxide dismutase enzymes (SOD) correcting superoxide anions overproduction in tissue injury and inflammation, from ischemia, organ transplantation to AIDS and cancer; strategy of telomer maintenance directed to anticancer and antiviral therapy as well as to correction of the aging processes; and strategy of short interfering RNAs capable to induce intracellular immunity to antigens of various origin.