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Author Topic: Logic of making chemical compounds  (Read 853 times)

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Iamsorry21

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Logic of making chemical compounds
« on: March 21, 2017, 11:05:13 AM »

Dear all,
firstly I am sorry for below Q, I have no chemical background just we had discussion with friends and we found out below unclear to us so thank for patient and all answers.

Is it possible make chemical compound of reverse effect based on existing one ? For example I know that this substance/compound called "x" for example makes me happy, is it possible based on composition of X to make "Y" which willhave opposite effect  ?

That's it , thank you I just want to check the logic ...

Br..

A
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Arkcon

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Re: Logic of making chemical compounds
« Reply #1 on: March 21, 2017, 12:19:39 PM »

There's almost no way to answer a question as vague as yours.  But we can try to figure it out. 

You're asking for "logic" in chemistry, and the only way to properly perform chemistry if it follow chemical laws.  There's no "logical" way to make 2+2 equal 7, and there's no "logical" crime that isn't illegal.  So you're going to have to work harder with your definitions if you want any answer at all.

I'd like to ask you what chemical "makes" a person "happy."  That term is so vague it isn't even worth wondering if some other chemical worked opposite to that.
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hypervalent_iodine

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Re: Logic of making chemical compounds
« Reply #2 on: March 22, 2017, 04:28:46 AM »

I don't find the question to be that vague.

I believe it  is along the lines of, knowing the structural composition of some compound with some specific biological outcome, is it possible to use that structural information to design a compound with the exact opposite effect?

The simple answer is no, it isn't. The biological outcomes of a given compound once injested are because of the way that compound interacts with proteins and other structures in the body. There is no general method by which you could reasonably hope to "cancel out" that effect, if you could at all, since it depends on the nature of the interaction.
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Dan

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Re: Logic of making chemical compounds
« Reply #3 on: March 22, 2017, 05:08:57 AM »

The biological outcomes of a given compound once injested are because of the way that compound interacts with proteins and other structures in the body. There is no general method by which you could reasonably hope to "cancel out" that effect, if you could at all, since it depends on the nature of the interaction.

But by designing an inhibitor of the interaction, you can cancel the effect. This is the basis of much of med chem, hardly a far fetched concept.

So I would say the idea that you can use the structure of a molecule and how it interacts with a receptor to design another molecule to cancel its effect is a routine exercise in med chem. Blocking the signal that produces a certain effect may not produce the opposite effect though. For example, blocking happy signals may not make you sad, just less happy. If that makes sense, it depends on whether the opposite biological response is caused by lack of signal or different signal.
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hypervalent_iodine

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Re: Logic of making chemical compounds
« Reply #4 on: March 22, 2017, 05:43:29 AM »

The biological outcomes of a given compound once injested are because of the way that compound interacts with proteins and other structures in the body. There is no general method by which you could reasonably hope to "cancel out" that effect, if you could at all, since it depends on the nature of the interaction.


But by designing an inhibitor of the interaction, you can cancel the effect. This is the basis of much of med chem, hardly a far fetched concept.

So I would say the idea that you can use the structure of a molecule and how it interacts with a receptor to design another molecule to cancel its effect is a routine exercise in med chem. Blocking the signal that produces a certain effect may not produce the opposite effect though. For example, blocking happy signals may not make you sad, just less happy. If that makes sense, it depends on whether the opposite biological response is caused by lack of signal or different signal.

In theory you are correct. If only drug design were so routinely simple (or maybe not; I might be out of a job if it were.) I think what you describe would be considered a subset of ways you might try and target an enzyme for the purposes of inhibition. Consider for example that there is not just one mode of inhibition; you have competitive, non-competitive, uncompetitive, and various hybrids thereof.

I would further argue that library screening is probably used more routinely, since designing drugs in the way you describe would have to be based on information already known about an enzyme's function, it's substrate, the structure of the binding pocket, and the mechanism by which it reacts and binds the substrate. We don't know that much about the vast majority of proteins, hence my answer.

Also, as you say, designing an inhibitor against a particular process doesn't always give you the exact opposite effect. Beyond your own example, what if an enzyme's substrate was something as prevalent as, say, pyruvate?

In any case, I think I interpreted the question a little differently. An analogy by way of simple arithmetic: if I have some positive integer, I can effectively 'cancel it out' with another, negative integer of equal magnitude (as in, 1 + (-1) = 0). It's crude, but that's how I thought the OP was approaching the question. Based on that, my answer was generally no. It is, however, more complicated than that (as we have addressed).



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Dan

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Re: Logic of making chemical compounds
« Reply #5 on: March 22, 2017, 09:00:06 PM »

In theory you are correct. If only drug design were so routinely simple (or maybe not; I might be out of a job if it were.) I think what you describe would be considered a subset of ways you might try and target an enzyme for the purposes of inhibition. Consider for example that there is not just one mode of inhibition; you have competitive, non-competitive, uncompetitive, and various hybrids thereof.

I would further argue that library screening is probably used more routinely, since designing drugs in the way you describe would have to be based on information already known about an enzyme's function, it's substrate, the structure of the binding pocket, and the mechanism by which it reacts and binds the substrate. We don't know that much about the vast majority of proteins, hence my answer.

Also, as you say, designing an inhibitor against a particular process doesn't always give you the exact opposite effect. Beyond your own example, what if an enzyme's substrate was something as prevalent as, say, pyruvate?

In any case, I think I interpreted the question a little differently. An analogy by way of simple arithmetic: if I have some positive integer, I can effectively 'cancel it out' with another, negative integer of equal magnitude (as in, 1 + (-1) = 0). It's crude, but that's how I thought the OP was approaching the question. Based on that, my answer was generally no. It is, however, more complicated than that (as we have addressed).

These are excellent points, and I agree that we are interpreting the question differently. My point was that the basic concept described by the OP is not fundamentally completely wrong, just very underdeveloped. Of course the reality is far more complex and I'm glad you expanded on that.
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discodermolide

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Re: Logic of making chemical compounds
« Reply #6 on: March 23, 2017, 08:34:25 PM »

Search the terms receptor agonist and receptor antagonist and you will find your answer.
There are also many described methods of enzyme activation and inhibition using synthesised compounds.
Prof. Google is your friend.
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