Line notations for nucleic acids (both natural and therapeutic)

Line notations for nucleic acids (both natural and therapeutic)

Roger Sayle

Nextmove software, cambridge, uk

252nd ACS National Meeting, Philadelphia, PA, Wednesday 24th August 2016

overview

• This presentation provides an overview of efforts to update and extend the aging 1970 IUPAC/IUBMB recommendations on nucleic acid notations.

• Examples are given of representational challenges, literature precedents, and the relationship to HELM and Novartis’ sitrack representations.

• IUPAC-IUB Commission on Biochemical Nomenclature (CBN), “Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents”, http://www.chem.qmul.ac.uk/iupac/misc/naabb.html


Level 1: bioinformatics

• IUPAC70 defines condensed forms for DNA and RNA.

• dG-dA-dT-dC

– dGuo-P-dAdo-P-dThd-P-dCyd

– Gua-dRibf-P-Ade-dRibf-P-Thy-dRibf-P-Cyt-dRibf

– 2'-deoxy-guanylyl-(3'->5')-2'-deoxy-adenylyl-(3'->5')-thymidylyl-(3'->5')-2'-deoxy-cytidine

• G-A-T-C

– rGuo-P-rAdo-P-rUrd-P-rCyd

– Gua-Ribf-P-Ade-Ribf-P-Thy-Ribf-P-Cyt-Ribf

– guanylyl-(3'->5')-adenylyl-(3'->5')-uridylyl-(3'->5')-cytidine


Revision: carbohydrate suffix

• The first revision/tweak to IUPAC70 is better conform to IUPAC-IUBMB’s 1996 recommendations on Nomeclature of Carbohydrates, 2-CARB.

– It is understood that the rings are in pyranose form unless otherwise specified. -- 2-Carb-38.4

• Hence, Ribf is the preferred “canonical” form on output, to avoid ambiguity.

• For backward compatability, Rib is considered Ribf in nucleic acid sequences, but Ribp in carbohydrates.


Division of monomers

• Sugar and Splice represents nucleic acids as sequences of monomers, following the convention that the 5’ phosphate is associated with the sugar/base [this matches IUPAC and PDB].

• G-A-U-C is “rGuo”, “P-rAdo”, “P-rUrd”, “P-Cyd”.

• HELM currently disagrees, associating the 3’ PO3H2.

– RNA1{R(G)P.R(A)P.R(U)P.R(C)}$$$$

• Fortunately, the conventional form is accepted:

– RNA1{R(G).PR(A).PR(U).PR(C)}$$$$


The perception problem 1


Multiple tautomeric forms of guanine



Multiple protonation states of thymine



Multiple mesomeric forms of 7-methylguanine

Level 2: natural rna variants

• IUPAC70 provides the framework for handling the many “non-standard” RNA features often observed.

• Unusual bases:

– m2Gua, m3Ura, m5Cyt, m7Gua, hUra, Yra, Wyb, br5Ura, Hyp, Xan, etc.

• Unusual backbones:

– Ribf2Me, P-P-P-rAdo

• Sugar & Splice’s proposed syntax closely resembles that of the University of Albany’s RNA modification database, http://mods.rna.albany.edu/mods/


Iupac condensed for pdb4tna

• The perceived line notation/identifier for 4TNA is:

P-rGuo-P-rCyd-P-rGuo-P-rGuo-P-rAdo-P-rUrd-P-rUrd-P-rUrd-P-rAdo-P-m2Gua-Ribf-P-rCyd-P-rUrd-P-rCyd-P-rAdo-P-rGuo-P-hUra-Ribf-P-hUra-Ribf-P-rGuo-P-rGuo-P-rGuo-P-rAdo-P-rGuo-P-rAdo-P-rGuo-P-rCyd-P-m22Gua-Ribf-P-rCyd-P-rCyd-P-rAdo-P-rGuo-P-rAdo-P-Cyt-Ribf2Me-P-rUrd-P-Gua-Ribf2Me-P-rAdo-P-rAdo-P-Wyb(R)-Ribf-P-rAdo-P-rYrd-P-m5Cyt-Ribf-P-rUrd-P-rGuo-P-rGuo-P-rAdo-P-rGuo-P-m7Gua-Ribf-P-rUrd-P-rCyd-P-m5Cyt-Ribf-P-rUrd-P-rGuo-P-rUrd-P-rGuo-P-rThd-P-rYrd-P-rCyd-P-rGuo-P-m1Ade-Ribf-P-rUrd-P-rCyd-P-rCyd-P-rAdo-P-rCyd-P-rAdo-P-rGuo-P-rAdo-P-rAdo-P-rUrd-P-rUrd-P-rCyd-P-rGuo-P-rCyd-P-rAdo-P-rCyd-P-rCyd-P-rAdo


The 7-methylguanosine debate


m7Gua (Wikipedia) m7h8Gua (PDB’s 7MG)

m7Gua (Sigma-Aldrich)

Base stereochemistry


h56m5Ura h56m5Ura(S) PDB: QBT

h56m5Ura(R) PDB: PBT

h34Ura h34Ura(S) h34Ura(R) PDB: DDN

Level 3: nucleic therapeutics


• Non-standard phosphates

– Thiophosphates (sP)

• Non-standard sugars

– dRibf2F, L-Ribf (spiegelmer), Ribf2MeOEt, ddRibf, Araf, Araf2Me, dAraf2F

– Morpholino, tricyclo, lockedRibf, cEt constrained

• Non-standard topologies

– Head-to-Head, Tail-to-Tail and mixed sequences.

– Cyclic sequences.

Examples: arabinosyl nucleosides


• Clevudine m5Ura-dAraf2F

• Clofarabine cl2Ade-dAraf2F

• Cytarabine Cyt-Araf

• Fludarabine fl2Ade-Araf

• Nelarabine m6Gua-Araf

• Sorivudine brvin5Ura-Araf

• Vidarabine Ade-Araf

https://en.wikipedia.org/wiki/Arabinosyl_nucleosides

Mipomersen (kynamro)


• Gua-Ribf2MeOEt-sP-m5Cyt-Ribf2MeOt-sP-m5Cyt-Ribf2MeOEt-sP-m5Ura-Ribf2MeOEt-sP-m5Cyt-Ribf2MeOEt-sP-dAdo-sP-dGuo-sP-dThd-sP-m5Cyt-dRibf-sP-dThd-sP-dGuo-sP-m5Cyt-dRib-sP-dThd-sP-dThd-sP-m5Cyt-dRibf-sP-Gua-Ribf2MeOEt-sP-m5Cyt-Ribf2MeOEt-sP-Ade-Ribf2MeOEt-sP-m5Cyt-Rib2MeOEt-sP-m5Cyt-Rib2MeOEt

• The ChEMBL structure, CHEMBL2219536, is almost certainly wrong due to thiophosphate connectivity.

Thiophosphate stereochemistry

• Not only does ChEMBL get the thiophosphate connectivity wrong, but HELM ignores the influence of stereochemistry

– Hartmit Jahns, Jonathan Hall, et al. “Stereochemical Bias Introduced During RNA Synthesis Modulates the Activity of phosphorothioate siRNAs”, Nature Communications, Vol. 6, p. 6317, March 2015.

• Hence Sugar & Splice also supports RsP and SsP.

– For example, dC-RsP-dC has the SMILES string c1cn(c(=O)nc1N)[C@H]2C[C@@H]([C@H](O2)CO[P@](=S)(O)O[C@H]3C[C@@H](O[C@@H]3CO)n4ccc(nc4=O)N)O


On-going and future work

• Chemists continue to push back the boundaries of chemical space around nucleic acid therapeutics.

• NextMove Software endeavors to extend the state-of-the-art in nucleic acid perception, hopefully continuing to close the “RNA informatics gap”.


acknowledgements

• Joann Prescott-Roy, Novartis, Cambridge, MA.

• Evan Bolton, PubChem, NCBI, Bethesda, MD.

• Noel O’Boyle, NextMove Software, UK.

• Thank you for your time.


Pdb Nucleic acids

IUPAC/SnS PDB IUPAC/SnS PDB

P-dAdo _DA P-Wyb(R)-Ribf _YG

P-dCyd _DC P-m1Ade-Ribf 1MA

P-dGuo _DG P-m2Gua-Ribf 2MG

P-dThd _DT P-Thy-Ribf2Me 2MU

P-dUrd _DU P-m5Cyt-Ribf 5MC

P-rAdo __A P-m7Gua-Ribf 7MG

P-rCyd __C P-Ade-Ribf2Me A2M

P-rGuo __C P-m22Gua-Ribf M2G

P-rUrd __T P-Cyt-Ribf2Me OMC

P-rThd 5MU P-Gua-Ribf2Me OMG

P-rYrd PSU P-Ura-Ribf2Me OMU


pDB monosaccharides a-D- a-L- b-D- b-L-

allHexp AFD ALL

altHexp SHD

araHexp ARA ARB

araPenf BXY AHR BXX FUB

galHexp GLA GXL GAL

glcHexp GLC BGC

gulHexp GUP GL0

lyxHexp LDY

manHexp MAN BMA

ribHexp RIP

ribPenf RIB BDR

xylHexp XYS HSY XYP LXC

xylPenf XYZ


Line notations for nucleic acids (both natural and therapeutic)

Science

Transcript of Line notations for nucleic acids (both natural and therapeutic)