A collection of problems about ATP site of Mur ligases

[Yuhang-CADD]

1 #6 Is it for sure that the amount of ATP in living cells is relatively larger than that of UMA? I could not find literature relevant.

If this is true, then the binding mode will be affected by the potential competitive inhibition and the effective dosage of such inhibitors will be large in order to achieve inhibition. So, what is the point of trying inhibitors targeting ATP site?

Could anyone help with this? Many thanks!

[drc007]

This is certainly an issue for any competitive inhibitor at the ATP binding site, the clinical dose will however depend on many factors. A very high affinity inhibitor would help, a slow off-rate would be an advantage, an extreme version would be a covalent inhibitor. A long half-life and distribution into the bacteria would be an advantage.

Similar issues arise with kinase inhibitors, however many make successful drugs.

[Yuhang-CADD]

This is certainly an issue for any competitive inhibitor at the ATP binding site, the clinical dose will however depend on many factors. A very high-affinity inhibitor would help, a slow off-rate would be an advantage, an extreme version would be a covalent inhibitor. A long half-life and distribution into the bacteria would be an advantage.

Similar issues arise with kinase inhibitors, however many make successful drugs.

Thank you so much for the guidance, it's a very clear explanation!

[Yuhang-CADD]

The average concentration of ATP in E. Coli was 1.54 mM.

For anyone who is interested in getting a quantitative perspective of ATP concentration in E. Coli bacterial cells, here is the reference that describes this in detail:

Yaginuma, H., Kawai, S., Tabata, K. et al. Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging. Sci Rep 4, 6522 (2014).

[Yuhang-CADD]

@drc007 I would really appreciate it if you could validate this for me!

According to the following paper, we know that ATP is the first substrate that binds to the Mur ligase domain (as an activator). https://doi.org/10.1021/bi970266r

Therefore, if we need to dock molecules at other active sites, we should preserve the ATP substrate while modelling. Am I right? Just in case anyone who is going to do CADD ignores this detail...

[chrisdowson1]

From Adrian

Hi,

The supposition is correct, in that for molecules that inhibit a Mur ligase by mimickry of the UDP substrate, the presence of ATP would be expected to be essential for binding of such an inhibitor.

Of course, that if the intention is to target ATP binding, then of course the modelling approach would require the adenine nucleotide binding sites to be empty.

Best Wishes, Adrian

Chris Dowson Professor of Microbiology Tel +44(0) 2476 523534 Fax +44(0)2476523568 Email c.g.dowson@warwick.ac.ukmailto:c.g.dowson@warwick.ac.uk Web page http://www2.warwick.ac.uk/fac/sci/lifesci/people/cdowson/ Citations http://scholar.google.co.uk/citations?user=MMn5etwAAAAJ&hl=en WAMIC Warwick Antimicrobial Interdisciplinary Centre https://www2.warwick.ac.uk/fac/cross_fac/wamic/ Warwick Antimicrobial Screening Facility https://warwick.ac.uk/fac/cross_fac/amrscreening/ Antibiotic Research UK https://www.antibioticresearch.org.uk

[cid:image001.png@01D6A09D.C9B12DF0]

From: Yuhang Wang notifications@github.com Reply to: opensourceantibiotics/murligase reply@reply.github.com Date: Monday, 12 October 2020 at 11:53 To: opensourceantibiotics/murligase murligase@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [opensourceantibiotics/murligase] A collection of problems about ATP site of Mur ligases (#23)

@drc007https://github.com/drc007 I would really appreciate it if you could validate this for me!

According to the following paper, we know that ATP is the first substrate that binds to the Mur ligase domain (as an activator). https://doi.org/10.1021/bi970266r

Therefore, if we need to dock molecules at other active sites, we should preserve the ATP substrate while modelling. Am I right? Just in case anyone who is going to do CADD ignores this detail...

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/opensourceantibiotics/murligase/issues/23#issuecomment-707046023, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALNDKBK3GF4RG3S5XIXIKDLSKLN23ANCNFSM4PN7NHRQ.

[Yuhang-CADD]

From Adrian Hi, The supposition is correct, in that for molecules that inhibit a Mur ligase by mimickry of the UDP substrate, the presence of ATP would be expected to be essential for binding of such an inhibitor. Of course, that if the intention is to target ATP binding, then of course the modelling approach would require the adenine nucleotide binding sites to be empty. Best Wishes, Adrian Chris Dowson Professor of Microbiology Tel +44(0) 2476 523534 Fax +44(0)2476523568 Email c.g.dowson@warwick.ac.ukmailto:c.g.dowson@warwick.ac.uk Web page http://www2.warwick.ac.uk/fac/sci/lifesci/people/cdowson/ Citations http://scholar.google.co.uk/citations?user=MMn5etwAAAAJ&hl=en WAMIC Warwick Antimicrobial Interdisciplinary Centre https://www2.warwick.ac.uk/fac/cross_fac/wamic/ Warwick Antimicrobial Screening Facility https://warwick.ac.uk/fac/cross_fac/amrscreening/ Antibiotic Research UK https://www.antibioticresearch.org.uk [cid:image001.png@01D6A09D.C9B12DF0] From: Yuhang Wang notifications@github.com Reply to: opensourceantibiotics/murligase reply@reply.github.com Date: Monday, 12 October 2020 at 11:53 To: opensourceantibiotics/murligase murligase@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [opensourceantibiotics/murligase] A collection of problems about ATP site of Mur ligases (#23) @drc007https://github.com/drc007 I would really appreciate it if you could validate this for me! According to the following paper, we know that ATP is the first substrate that binds to the Mur ligase domain (as an activator). https://doi.org/10.1021/bi970266r Therefore, if we need to dock molecules at other active sites, we should preserve the ATP substrate while modelling. Am I right? Just in case anyone who is going to do CADD ignores this detail... — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#23 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALNDKBK3GF4RG3S5XIXIKDLSKLN23ANCNFSM4PN7NHRQ.

Cheers! It's really helpful for everyone who might need this in the future!