PPI Inhibitors Tripeptide Mimetics. Design of New Scaffolds. ChemDiv, Inc.
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1 PPI Inhiitors Tripeptide Mimetics. Design of ew Scffolds ChemDiv, Inc.
2 Frequency TRIPEPTIDE MTIFS in BILGY Three contiguous mino cids represent n optiml if not miniml size for iologicl signling [] Clerly not ll 8000 possile contiguous tripeptides re likely to hve iologicl importnce, ut sustntil numer of them ply significnt roles in iology 25 hevy toms (A) gve optiml lignd ffinity or mximl efficcy [] Given tht the verge numer of hevy (nonhydrogen) toms in the nturl mino cids is 8.3, three residues would on verge contriute 25 hevy toms umer of hevy toms Distriution of hevy toms in ll 8000 possile tripeptides The distriution of hevy toms cross ll 8000 possile tripeptides shows the pek of the distriution close to 25 hevy toms Tripeptide motifs represent potentilly importnt strting points for design of smll molecule iologicl modultors [] J Med Chem. 2011; 54: [] Bioorg Med Chem Lett. 2007; 17: 4258
3 BILGICALLY RELEVAT TRIPEPTIDE MTIFS Endogenous tripeptides include the following: (1) ECG (Glu-Cys-Gly) - (glutthione), ntioxidnt, cofctor; (2) EP (Glu-is-Pro) - stimultes pituitry glnd controlling thyroid-stimulting hormone secretion (3) FEG (Phe-Glu-Gly) - inhiition of nphylxis, nti-inflmmtory, modultes leukocyte dhesion (4) GK (Gly-is-Lys) - tissue remodeling nd wound heling (5) PLG (Pro-Leu-Gly) - modultor of the dopmine D2 receptor Tripeptide motifs in proteins include the following: (6) DLF/SLF (Asp<Ser>-Leu-Phe) - inhiition of β protein of cteril replisome, ntimicroil (7) ELR (Glu-Leu-Arg) - chemokine, growth fctor inding motif (8) GGQ (Gly-Cys-Gln) - relese fctor, stop codon recognition (9) GPE (Gly-Pro-Arg), neuroprotection (10) AV (is-al-vl) - cdherin motif, cell-cell interctions, nd dhesion (11) GK (is-gly-lys) - vitronectin inhiition (12) PQ (is-pro-gln) - streptvidin inding motif (13) KPV (Lys-Pro-Vl) - nti-inflmmtory properties (14) LDV (Leu-Asp-Vl) - vsculr cell dhesion molecule 1 (VCAM-1)/fironectin dhesion motif (15) RGD (Arg-Gly-Asp) - cell dhesion signl (16) SKL (Ser-Lys-Leu) - peroxisoml trgeting (17) KYL (Lys-Tyr-Leu) - vsoctive intestinl peptide (VIP) motif (18) RER (Arg-Glu-Arg) sapp motif, neuroprotection
4 Vsoctive Intestinl Peptide (VIP) Receptor on-peptide Antgonist Design Memer of the Secretin Fmily of Peptides Intercts with GPCRs: VPAC1 nd VPAC2. Diverse Ptho- Physiologicl Role cncer cell growth, dietes, septic shock CS []. [] J Phrmc Exp Ther. 2005; 315(1): 370
5 SDAVFTEYTKLRKQ Assessing the Lndscpe Known Led Compounds L K K G T LY KAA 2 -SDAVFTDYTRLRK 2 C-YRKKISELYKAAVE Ro (Preclinicl), Roche BAY (Preclinicl) Byer Trget: Prolems: Therpeutic Group: VPAC 2 gonist Poor iovilility nd stility Bronchodiltors, Chronic ostructive Pulmonry Diseses, tretment of Antillergy/ntisthmtic drugs VPAC 2 gonist Acts s insulin secretgogue - poor wter soluility nd short lifespn in vivo. Type 2 Dietes other ctive compounds re similr cyclic peptides, peptide frgments of VIP, or modified VIPs (Al/Gly replcements of key residues)
6 VIP nd Region Selected for Scffold Design tive VIP: S D A V F T D Y T R L R K Q M A V K K Y L S I L Steryl-K-K-Y-L: sme neurotrophic effects s entire 28- VIP [] Tripeptide Motifs Selected for Peptidomimetic Design: 2 2 KKY KYL [] PAS. 1999; 96: 4143
7 Selection of Smll Molecule Scffold Selected Trimers: K K Y K YL Studies hve shown residues in the -terminus re importnt for receptor inding: Lys 21 nd Leu 23 show high ffinity for VPAC 1 inding [1-3], wheres Tyr 22 nd Leu 23 re essentil for VPAC 2 inding [2,3]. 2 Constrined Peptidomimetic: Tetrhydroquinones Since Leu 23 is n importnt residue for inding oth receptors, concentrte scffold design on this end of tripeptide B B= Strong Bsic moieties [1] J Biol Chem. 2000; 275(31): [2] J Phrmcol Exp Ther. 2002; 303(2): 445 [3] Front Med Chem. 2005; 2: 393
8 Moleculr Docking of VIP nd the Core KYL Frgment Into the Active Site of hvpac1 A B (A) Moleculr docking of VIP into the -ted of hvpac1 receptor. VIP is represented in green, nd -ted is represented in lue. Red, side chins of Phe 6, Tyr 22, nd Asn 24 of VIP; yellow, trget residues of hvpac1 identified y photoffinity experiments nd Edmn degrdtion, i.e. Asp 107, Gly 116, nd Cys 122 (B) The criticl interctions etween KYL nd residues of hvpac1 ctive site
9 Proposl: Scffolds vip-1a & vip-1b for Synthesis of Discovery Lirry Source: 2 Introduce constrined quinone ring s peptide mimic, sic moieties for lysine replcement Lirries: Diverse sustituents looking t donting/withdrwing properties, -ond cceptor/ donors, soluility VIP-1 VIP-1 Exmples of molecules: 2 Cl SciFinder: o hits found Rexis: o hits found R1 =lkyl, ryl/hetryl mines, Strong ses:
10 Proposl: Scffolds vip-2a & vip-2b for Synthesis of Discovery Lirry Source: 2 Introduce constrined quinone ring s peptide mimic, sic moieties for lysine replcement Lirries: VIP-2 Diverse sustituents looking t donting/withdrwing properties, -ond cceptor/ donors, soluility VIP-2 Exmples of molecules: 2 SciFinder: o hits found Rexis: o hits found R1 =lkyl, ryl/hetryl mines Strong ses:
11 Moleculr Docking of Potentil Smll Molecule Inhiitors of hvpac1 Receptor from Discovery Lirries VIP-2 VIP2 exmple - Beige re designtes the mino cid residues importnt for VIP inding - The VLS ( penetrtion ) score is the mesure of lignd protein interction VLS scores tht re close to 0.0 re fvorle. Docking study ws performed using SurFlex Docking, Version 1.24 (BioPhrmics LLC)
12 Proposl: Scffolds vip-3a & vip-3b for Synthesis of Discovery Lirry Source: 2 R Introduce constrined 1 quinone ring s peptide mimic, sic moieties for lysine replcement Lirries: Diverse sustituents looking t donting/withdrwing properties, -ond cceptor/ donors, soluility VIP-3 VIP-3 R 3 R 3 Exmples of molecules: SciFinder: o hits found Rexis: o hits found R1 =lkyl, ryl/hetryl mines Strong ses:
13 Moleculr Docking of Potentil Smll Molecule Inhiitors of hvpac1 Receptor from Discovery Lirries VIP-3 VIP-3 exmple
14 Proposl: Scffold vip-4 for Synthesis of Discovery Lirry 2 Source: Introduce lrger, constrined quinone ring s peptide mimic, sic moieties for lysine replcement Lirries: R1 Diverse sustituents looking t donting/withdrwing properties, -ond cceptor/ donors, soluility VIP-4 Exmples of molecules: Me R1 =lkyl, ryl/hetryl mines, Strong ses: SciFinder: o hits found Rexis: o hits found
15 Moleculr Docking of Potentil Smll Molecule Inhiitors of hvpac1 Receptor from Discovery Lirries VIP-4 VIP-4 exmple
16 Selected VIP-Scffolds for Synthesis of Discovery Lirry Scffolds selected for synthesis possess: Proper sptil rrngement in the VIP inding site nd re ound to 2-4 mino cid residues criticl for complex formtion igh synthetic fesiility igh IP potentil Drug-like nd trctle VIP-2 VIP-2 VIP-3 VIP-3 R 3 R 3 R1 VIP-4
17 ther Tripeptide Mimetics. Design of ew Scffolds
18 PLG D r u g - l i k e n e s s S y n t h e t i c f e s i i l i t y ew Lirry (20-50 compounds) R1 R4 plg-01 Core lignment: Green strting PLG violet plg-01 scffold SYTETIC APPRAC to EW PLG-MIMETICS Design of ovel Scffolds - 1 modultor of the dopmine D2 receptor
19 SYTETIC APPRAC to EW PLG-MIMETICS Design of ovel Scffolds - 2 D r u g - l i k e n e s s PLG Unique vlidted chemistry 5 ew Lirry (20-50 compounds) R4 R1 plg-02 Core lignment: Green strting PLG violet plg-02 scffold
20 SYTETIC APPRAC to EW FEG-MIMETICS Design of ew Scffolds 2 FEG Inhiitor of nphylxis, nti-inflmmtory, modultes crdic leukocyte dhesion R1 feg R1 feg-02 F (Phe) - mimetic F (Phe) - mimetic E (Glu) - mimetic E (Glu) - mimetic
21 ther Peptidomimetics. Design of ew Scffolds
22 SYTETIC APPRAC to EW DI- & TRI-PEPTIDE MIMETICS ew Scffolds 1 R 2 R 2 3D
23 SYTETIC APPRAC to EW DI- & TRI-PEPTIDE MIMETICS ew Scffolds 2 X n R 3
24 SYTETIC APPRAC to EW DI- & TRI-PEPTIDE MIMETICS ew Scffolds 3 c d R 3 R 3 F R 1 R R 3 3 R1 R 3 R 3 R 4
Solutions In each case, the chirality center has the R configuration
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