Antiretroviral and pre-exposure prophylaxis therapy has reduced the number of new human immunodeficiency virus (HIV) infections per year, but new strategies are required to meet the goal of ending the epidemic by 2030. This work explores small molecule inhibitors and enhancers of HIV infection, both natural and synthetic, and how this information can be leveraged to disrupt transmission chains.The first theme of this thesis involves studying small molecule inhibitors of HIV infection. We focus on a new class of antiretrovirals that target the HIV capsid (CA) protein. These inhibitors, like certain CA mutations, can redirect the integration targeting system in cellular chromosomes. Here we compare the effects of two potent inhibitors: GSK878, a novel inhibitor, and the previously studied lenacapavir. We find that both inhibitors reduce integration in nuclear speckles and active transcription units and report epigenetic, genetic, and protein binding sites associated with viral integration. We newly report that capsid inhibitors increase integration in centromeric/satellite DNA sequences, mimicking the proviral signature found in the reservoir of elite controllers and associated with transcriptional repression, inducibility, and latency. Collectively, this data reinforces the role of capsid in determining target sites for HIV integration and highlights new consequences of perturbing this system. The second theme of this thesis explores small molecule enhancers of HIV infection in the vaginal microbiome. Colonization with highly diverse, Lactobacillus- deficient microbial communities (HDCs) increases HIV acquisition risk through an undetermined mechanism. Here we analyzed conserved changes in the metabolome of cervicovaginal fluid from women colonized by HDCs versus protective Lactobacillus- dominant communities to identify metabolites that enhance infection. We report changes in global amino acid homeostasis and identify a catabolite of the amino acid valine, 2- hydroxyisovalerate (2-HV), that is consistently enriched in dysbiotic communities and boosted HIV infection 3-6x in resting primary CD4+ T cells. We identify specific bacteria from HDCs and characterize putative microbial synthesis pathways capable of high-level 2-HV secretion. This work implicates 2-HV as a candidate mediator linking vaginal microbiome structures and HIV transmission in women.