PRISM BioLab Blog – PPI Pursuit
Commentary on Protein-Protein and Protein-Peptide Interactions, peptidomimetics and related topics in drug discovery.

Intensive investigation has been conducted in order to rationally identify the “hotspot” of PPI for a decade or even more. In spite of the presence of a myriad of PPI in human, estimated to be 130,000¹⁾ to 650,000²⁾ This issue originates from the difficulty in controlling and modulating the PPI of interest by a small molecule. Generally speaking, the contact area of a small molecule inhibitor is thought to be 300 to 1,000 Ų⁾.³⁾

Conformational restriction has long been recognized in medicinal chemistry as a rational and effective way for structural design in both drug discovery and optimization stages. This strategy is crucial in PPIs in order for overcoming the energetical inferiority against the original, large-surface-based contact. The exception might be the biomolecule drugs like antibodies which recognized the protein...

Protein-protein interaction network is invaluable resource for the identification of a promising target for PPI drug research and development. Owing to the human genome sequencing and proteome analyses as well as the data science companies and organizations, we have rich access to PPI databases to figure out a candidate interaction to deeply investigate for a better treatment of diseases of worldwide interest. But still, it’s a kind of “mystery”...

Peptide-based molecules and peptides themselves, especially cyclic and natural peptides, have been approved for a variety of disease treatments including cancers.¹⁾ Anti-cancer peptides (ACPs) have long been investigated in mostly academic field and a number of natural ACPs have been disclosed so far.²⁾ ACPs are small peptide with a selective toxicity against cancer cells line a usual small-molecule-based or antibody-based anticancer agents...

PPI databases unambiguously expands our opportunity to figure out a fruit for a PPI drug target. Currently, more than twenty databases can be utilized for the sake of PPI research and predictions. One of the topmost databases on PPI is, generally speaking, STRING. PPI scientists usually takes STRING as one of the reliable, versatile and useful PPI database, but have you ever thought why STRING? Emerging PPI databases may also be worth looking at...

This review¹⁾ summarizes the recent status of peptide-based therapeutics research in the discovery stage and peptide related technologies in a simple fashion. It helps scientist in a variety of levels to achieve better understanding of peptide drug discovery issues as well. Peptides are among the classical and ubiquitous chemical types in the small-molecule world. Distinct and attractive nature of peptides...

Prediction of molecular interactions are becoming sophisticated and trustworthy and sometimes makes a contribution for decision making in drug discovery projects. Virtual screening of protein-ligand complexes has been the most focus area of in silico methodology to approach the protein of interest and used for selection of compounds to be assayed. However, the predicted docking...

Considerable efforts have been focused on cancer treatment for decades in a global sense. However, cancer is still a top target that necessitates us to deliver more effective and safer drugs to the patients. Here is a recent review on peptidomimetics in cancer targeting.¹⁾ This review would allow us better understanding of the potential of peptidomimetics in the field of cancer and also other diseases...

Bioisosteres are defined as “compounds or groups that possesses near-equal molecular shapes and volumes, approximately the same distribution of electrons, and which exhibit similar physical properties.”¹⁾ To say more simply, they are mimics of the original group. Hence, there is still a wide possibility of design and development of a new bioisostere for various functional groups...

Here is a review of 50 approved drugs in the US.¹⁾ In 2021, 29 small-molecule drugs appeared in the fields of oncologic, CNS, anti-infective etc.. This review is significantly stimulating for chemistry folks because the synthetic routes of small-molecule drugs are summarized in a simple fashion. Scientists would enjoy the art of synthetic schemes, which...