The development of methodology for the solid-phase synthesis of fused 2,5-diketopiperazines with an emphasis on structural and stereochemical control, has been accomplished through two different approaches. The first approach was based on a highly trans-stereoselective (82% d.e.) intramolecular N-acyliminium ion cyclization of N-terminal peptide glyoxylamides, assembling the complete molecular skeleton in a single step. The second approach aimed for the use of a cis-stereoselective intermolecular Pictet-Spengler cyclization to construct the first part of the ringsystem and a subsequent diketopiperazine formation to close the second ring. In the first approach, four different methods for accessing the glyoxylamide cyclization precursor were developed; oxidative cleavage of a serine, dihydroxylation/oxidative cleavage of an acrylamide, oxidation of a glycolamide and acidic release from a diethoxy acetamide. The scope of the methodology was found to be broad, allowing for numerous variations in the western amino acid part, including components such as proline, homoproline and Nmethylated amino acids, delivering products in moderate to excellent purities (52 to 93%). The methodology also allowed for modifications in the eastern nucleophilic part, including components such as neutral or electron rich phenyl-derivatives, 2-substituted furans and thiophenes, olefines, alcohols as well as sulfides, generating products in good to excellent purities (61 to >95%). Furthermore a proton exchange pathway, active under basic conditions and showing convergence towards the trans-product, was identified. The second approach included two distinct routes involving an ethyl glyoxylate or a glyoxylic acid Pictet-Spengler cyclization. The ethyl glyoxylate route was found to be nonstereoselective but well-suited for the synthesis of diastereoisomeric mixtures of 2,5-diketopiperazino[6,1-a]tetrahydroisoquinolines in high purities (74 to 90%), allowing for the separation of the cis-diastereoisomers. The route based on glyoxylic acid was found to be cis-stereoselective (1:2) generating the 2,5-diketopiperazino[6,1-a]tetrahydroisoquinoline product in a high purity (71%). Unfortunately an issue with incomplete conversion in the final step (20%) rendered separation of the diastereoisomers, by preparative RP-HPLC, problematic. Employing the developed methods, a diastereoisomeric matrix of aminomethylthiophene hydroxamic acid biased HDAC inhibitors based on the 2,5-diketopiperazino[6,1-a]tetrahydroisoquinoline scaffold was prepared and subsequently evaluated for biologically activity. The compounds showed inhibitory activity against a nuclear extract of HeLa cells, on average 200-fold lower than the activity of SAHA. When screened towards HDAC 1 the compounds showed a lower inhibitor activity, compared to the nuclear extract, except for one of the compounds which showed increased activity. The compound represents a clear case of stereodifferentiation. Finally, and most importantly, when screening the compounds towards HDAC 8 an activity which was on average 5-fold higher than the activity of SAHA was found. The profound difference in HDAC 1 and HDAC 8 inhibitor activity identifies the compounds as potential sub-type inhibitors.