Coating of gold nanoclusters with peptides is an important targeting method in biomedical applications. However, their synthetic method highly influences their targeting ability. Current methods often use harsh reagents and organic solvents to control morphology, which are not preferred for biomedical applications. Recently, several peptides with specific amino acid sequences have successfully been used to reduce Au ions and synthesize biocompatible peptide-covered gold particles in situ. However, the molecular mechanism of peptide-assisted nanocluster formation is yet unclear. Thus, reactive abilities of different amino acids should be studied to improve design of peptides with predetermined amino acid content and consequently, synthesize gold nanoclusters with improved performance. In this theoretical study, we have approximated the reactive abilities of 20 natural amino acids in their neutral state using density functional theory calculations, such as Fukui indices and HOMO/LUMO composition analysis. We have found that the top reducing agents are tryptophan, histidine, and tyrosine, and the strongest binding can be expected from methionine and cysteine. Further study of the exact reactive sites in these high reactive amino acids provided the deep insight for the peptide design route for the targeted gold nanocluster formation.