Like how artists uses paints, textures, and materials to create their artwork, nature “uses” molecules and their respective atoms to create the biological entities that we recognize around us. I’d like to begin a series of essays on the details of how the current understanding of chemistry relates to human emotion and psychology, and how […]
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In this post I’d like to discuss a natural product that is near and dear to my heart; the oil of the Copaiba genus of trees. The reason this natural product is special to me is because it’s mechanism of action was part of a side project I investigated as a graduate student. During that […]
One important class of proteins found in eukaryotic domain of biology is chaperonins. These proteins serve to assist the preparation of other proteins via assisted folding as well as other mechanisms. These types of proteins have emerged as potential targets for antifungal therapeutics since, without their function, many other essential cellular processes fail. A “new” […]
Today I will be discussing an interesting class of compounds referred to as racetams. Racetams are relatively simple molecules discovered over 60 years ago. Like many simple, aliphatic molecules with nitrogen incorporated, they have a distinct psychoactive effect. Looking at the physicochemical diversity among the five commercially available racetams I have studied, there is a […]
How a molecule interacts within a living organism is incredibly complicated. Even the simplest molecules can interact with over 25,000 protein products from genes (not including their splice variants) as well as a wide variety of lipids, sugars, nucleic acids, and their combinations distributed throughout the body. In a typical drug discovery effort, a narrow […]
I have always deeply believed that reading is the cornerstone of gaining knowledge. Through reading, we gain the wisdom and knowledge of others. I recently purchased a book titled “Scaffold hopping in medicinal chemistry” edited by Nathan Brown and published by Wiley VCH. It will be interesting to see my the change of my understanding […]
Most molecules relevant to life have chirality, a feature which means there are multiple geometric arrangements of an otherwise atomically identical compound. This feature gives a certain geometric asymmetry to molecules which may superficially look the same. Somewhere in the crucible of life, this asymmetry became systematic. Deoxyribose, ribose, lipids, and proteins took on a […]
I have now completed a 10.2 million compound virtual screen of FABP5, an incredibly important drug target for anti-inflammatory, anti-nociceptive, and anti-cancer medicinal development. I’m actually not a fan of this FABP5 model for several reasons. Firstly, the protein crystallized as a multimer with different conformations and binding modes of the ligand SB FI 26 […]
As I previously mentioned, I am interested in discovery of a new allosteric inhibitor of the Methionine tRNA synthetase of the tropical parasite Leishmania major. In order to achieve this goal, I have performed a virtual screen of the Leishmania major Methionyl tRNA synthetase protein (PDB ID 6SWX) at an allosteric site crystallized with an […]
When it comes to virtual screening , an important decision to make is which compounds to include in the study. The ZINC database has emerged as an immensely valuable tool for prioritizing and downloading specific compounds in computationally convenient forms. I am very impressed with the excellent organization, clear instruction, and overall reliability of the […]