Carbon-rich aromatic molecules have been historically utilized as major building blocks for assembly of complex molecular architectures due to the vast development of methods for fine-tuning their properties. Yet, the classical toolbox of 2D aromatic building blocks presents inherent topological limitations, which sometimes is referred to as “molecular flatland”. Boron clusters introduce potentially a powerful solution for addressing this limitation by offering an inherently rigid, three-dimensional scaffold available for dense functionalization. In biological systems, this dense functionalization can be exploited to enhance specific interactions with protein surfaces. In this thesis, the application of boron clusters as novel pharmacophores has been investigated in two cases: 1) development of rigid and atomically precise nanomolecules and 2) development of isoform-specific and blood-brain barrier permeable histone deacetylase inhibitors.