The development of novel drugs active against multi-drug resistant (MDR) HIV-1 strains is urgently required. HIV protease inhibitors and reverse transcriptase inhibitors constitute two categories of important drugs, which have greatly improved the clinical treatment of HIV-infected patients by their cocktail use designated as highly active anti-retroviral therapy (HAART). By combinatorial chemistry involving substructure units contained in known HIV protease inhibitors, we found effective protease inhibitors, TYA5 and TYB5, which showed potent anti-HIV activity even against MDR strains. Selection of drug-resistant viruses is also decreased when these new agents are tested in vitro. Subsequently, introduction of an (E)-alkene dipeptide isostere into TYB5 led to the development of a pure non-peptide protease inhibitor, TYB1. We have also studied the development of effective inhibitors for blocking HIV-entry into host cells based on recent discovery of an HIV entry mechanism involving the viral usage of chemokine receptors as coreceptors, CXCR4 and CCR5. We developed highly selective CXCR4 antagonists, T22 and T140 (18-mer and 14-mer peptides, respectively), which strongly suppress T-cell line-tropic HIV-1 (X4-HIV-1) entry through their specific binding to CXCR4. Recently, molecular-size reduction of T140 yielded low molecular weight CXCR4 antagonists, which might be more useful leads to drug-like structures. In this review, we discuss the development of two types of anti-HIV agents, protease inhibitors and CXCR4 antagonists, which would improve clinical AIDS chemotherapy.