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Specialty Chemistry Forums => Biochemistry and Chemical Biology Forum => Topic started by: Jhowa20 on August 28, 2015, 02:11:30 AM

Title: Biochemistry: Protease Inhibitor functional groups
Post by: Jhowa20 on August 28, 2015, 02:11:30 AM: Dear readers,

I'm currently studying functional groups (or structure-activity relationships), in particular that of protease inhibitors (PI). I'm exploring how the individual function groups can alter the effect that a PI can have on the human body. A problem has arised in which the complexity has increased and I am having troubles understanding these function groups. In example, how dose Darunavir function groups define how it functions.

My attempt at understanding is as follows:

1. Function groups are collectives of atoms that function in a particular way given their structure, and the nature of the atoms that make the molecule up (i.e. Carbon vs Oxygen).
2. Protease inhibitors have functional groups.

I am just confused. I don't mind doing the research myself, I just need a footing to start, would anyone be able to shed some light, or at least explain how I am suppose to start/begin explaining the functional groups of Darunavir.

Cheers
Title: Re: Biochemistry: Protease Inhibitor functional groups
Post by: kriggy on August 28, 2015, 03:29:34 AM: Well, you cant realy tell the efect of single functional group unless you have high amount of data - ie. different molecules and their known effects then you might be able to predict how it will behave.

Im not realy sure what is your question, are you asking what exactly is the function of those functional groups in given molecule (Darunavir as example)? Well, the best way is to look for crystal structure of darunavir in the cavity of PI so there you can see the interactions between the drug and enzyme. On Darunavir wikipedia page there is a picture / scheme of darunavir in the cavity of PI so you can see the hydrogen bonds and how it iteracts with the enzyme.
Some of the fuctional groups might be present not for the interaction with the enzyme but to improve the physical-chemical properties like pKa, water solubility, lipofility etc..

I suggest getting some medchem book you can find lot of information there
Title: Re: Biochemistry: Protease Inhibitor functional groups
Post by: Jhowa20 on August 28, 2015, 04:00:56 AM: Thanks for you response.

I am only new to biochemistry, so that may explain the lack of a direct question.

I was set a task in particular to describe the functional groups of a protease inhibitor, and its relationship to the HIV-protease. My question more or less was where do I begin.

I hope that makes sense.
Title: Re: Biochemistry: Protease Inhibitor functional groups
Post by: Babcock_Hall on August 28, 2015, 08:54:42 AM: I suggest you begin by listing the functional groups that are present in this inhibitor.
Title: Re: Biochemistry: Protease Inhibitor functional groups
Post by: Babcock_Hall on August 28, 2015, 06:17:19 PM: Assuming you have an aspartic protease, you might give some thought to how the inhibitor interacts with the aspartyl groups.