The authors would like to thank Dr. Jumpei Morimoto and Dr. Todd Doran for valuable assistance. This work was supported by a contract from the NHLBI (NO1-HV-00242).

1. Basics of Split-and-pool Synthesis
In order to efficiently generate a large number of compounds on solid phase, split-and-pool synthesis is often employed as a general strategy. As shown in Figure 4, tentagel beads are first&#160;split into three portions. Each portion is reacted with a different reagent, generating the first residue on beads. After the first reaction, all three portions are pooled together, mixed, and then split again into three portions. Each portion will again react with a different reagent, generating the second residue on beads. After two split-and-pool steps, nine compounds are generated.
In sub-monomer synthesis, beads are first divided into several portions to react with different bromo acids in the presence of coupling reagent. After washing with solvent, all beads will be pooled together and mixed, then again divided into several portions to react with different primary amines. After amination, all beads are pooled together and washed thoroughly, completing a full monomer on each bead. This process can be repeated till desired diversity is reached.
2. Preparation of Acid Bromide from Natural Amino Acids
In sub-monomer synthesis, the synthesis of each monomer is divided into two separate steps: 1. coupling of acid bromide and 2. amination with primary amines (Figure 2). In order to synthesize a peptide tertiary amide, chiral acid bromides with side chains on the alpha carbon will be prepared from natural amino acids. Here we describe the method of transforming a natural amino acid into the corresponding acid bromide with high stereo fidelity. We use alanine as an example; other amino acids including serine, threonine, aspartic acid, glutamic acid, asparagine, glutamine, glycine, valine, isoleucine, phenylalanine can also be transformed into bromo acids under similar conditions. Note that some of the amino acids with functional groups like phenol, guanidine and amine need to be protected before the transformation. The reaction setup is shown in Figure 3.
Safety Precaution: For the following reactions involving HBr, NaNO2 and other corrosive/toxic chemicals, proper safety equipment like safety goggles, lab coat, and chemical resistant gloves are needed. All reactions should be performed in a fume hood by experienced chemist.
<ol>
	<li>Add 370 ml water into 630 ml 48% HBr solution to prepare a 1 L, 30% HBr solution. Add 500 ml ethylene glycol into a 1 L bath container; add dry ice to maintain the temperature at -10 &#176;C. Caution: 48% HBr solution is strongly acidic and corrosive, handle with care. Read the MSDS before use.</li>
	<li>Add D-alanine (8.9 g, 0.1 mol) and KBr (11.9 g, 0.1 mol) to a 250 ml three-neck round bottom flask with a magnetic stir bar. Add 100 ml, and the 30% HBr prepared in the previous step. Put the flask in the ethylene glycol bath prepared in step 2.1 and keep the temperature at -10 &#176;C. Bubble argon through a long needle from the bottom of the flask for 10 min as shown in Figure 3. Stir the solution with the magnetic stir bar at 300 rpm.</li>
	<li>Dissolve NaNO2 (8.28 g, 0.12 mol) in a 100 ml beaker with 20 ml water. Add the solution into the pressure equalizing dropping funnel and seal the dropping funnel with a septum. Slowly turn on the valve of the dropping funnel and let the NaNO2 solution drop into the flask. Control the valve to adjust the dripping rate to approximately 2 drops per sec. Keep the stirring at 300 rpm and keep the argon bubbling&#160;from the bottom of the flask. The flask should be kept in ethylene glycol bath at -10 &#176;C until all NaNO2 is added. Caution: This step generates heat and gas during the addition of NaNO2 solution. Dripping rate should be carefully controlled and the whole system should be open through the argon outlet.</li>
	<li>Keep stirring for 3 more hr&#160;and let the temperature warm up from -10 &#176;C to room temperature. The resulting solution should be clear to light yellow;&#160;if the color is too dark, apply vacuum to remove the excess nitrogen oxides and possible Br2 generated during the reaction.</li>
	<li>Extract the product from the solution with 3x 35 ml&#160;diethyl ether&#160;using an extracting funnel. Combine the organic phase and wash it with saturated brine. The organic phase can also be washed with a small amount of NaHCO3 prior to washing with brine to remove the color if it is dark. Dry the organic phase over Na2SO4 for 6 hr.</li>
	<li>Filter out the Na2SO4 and evaporate the solvent under vacuum, crude product should be obtained as clear to pale yellow oil. Crude product can be further purified by distillation at 115 &#176;C, 3 mm Hg, or by silica column with 3:1 hexane:ethyl acetate.</li>
	<li>Pure product is obtained as clear oil, 6.6 g (yield 74%), density = 1.69 g/ml, [&#945;]D20 = +24&#176; (methanol), 1H NMR (400 MHz, CDCl3) &#948; 4.41 (q, J = 7.0 Hz, 1H), 1.86 (d, J = 7.0 Hz, 3H). In the case of (S)-2-bromopropanoic acid-d4 (prepared from d4-L-alanine), pure product is obtained as clear oil, yield 78%, density = 1.72 g/ml, [&#945;]D20&#160;= -19&#176; (methanol). 1H NMR, no significant H signal is observed. ESI-MS- [M-1]-&#160;= 155.1 (expected 154.97). For (S)-2-bromo-4-methylpentanoic acid (prepared from L-leucine using the same procedure) pure product is obtained as clear oil, yield 89%, [&#945;]D20&#160;= +37&#176; (methanol), 1H NMR (400 MHz, CDCl3) &#948; 4.30 (t, J = 7.7 Hz, 1H), 1.94 (dd, J = 10.8, 3.9 Hz, 2H), 1.81 (tt, J = 13.2, 6.5 Hz, 1H), 0.96 (dd, J = 18.2, 6.6 Hz, 7H). In the case of (S)-2-bromo-3-phenylpropanoic acid (prepared from L-phenylalanine using the same procedure) pure product is obtained as pale yellow oil, yield 72%, [&#945;]D20&#160;= +17&#176; (methanol), 1H NMR (400 MHz, CDCl3) &#948; 7.38 &#8211; 7.19 (m, 5H), 4.42 (dd, J = 8.1, 7.3 Hz, 1H), 3.47 (dd, J = 14.2, 8.2 Hz, 1H), 3.25 (dd, J = 14.2, 7.2 Hz, 1H).</li>
</ol>
3. Isotopic Labeling of Alanine Using Transaminase
In combinatorial library synthesis, especially in the split-and-pool synthesis of one-bead one-compound (OBOC) libraries, the amount of compound that can be obtained from each bead is relatively small. (Typically 1 pmol to 10 nmol). Additionally, mass spectrometry is widely used for the identification and characterization of the final compound due to its high sensitivity. In order to use mass spectrometry to determine the absolute stereochemistry at the chiral centers of the final PTA products, bromo acid enantiomers should be isotopically labeled before use. Here we describe the method of using transaminase and D2O to label L-alanine.
<ol>
	<li>Dissolve L-alanine (300 mg, 3.36 mmol) with 10 ml of D2O in a 50 ml polyethylene tube. Add &#945;-ketoglutarate (10 mg, 0.068 mmol) as co-substrate. Warm up the tube to 37 &#176;C and adjust the pD to 8.5-8.7 using a 1 M NaOD soution. Note: pD is determined by pH test strips. Traditional electro pH meter equipped with glass electrode selective for H+ may give incorrect read out for D+.</li>
	<li>Add alanine transaminase (0.1 mg, EC 2.6.1.2 from pig heart, Roche Diagnostics, Indianapolis, IN) to the pD 8.5 - 8.7, 37 &#176;C solution prepared from previous step. Put the tube in a 37 &#176;C incubator and incubate it overnight with mild shaking, 10 to 30 rpm is preferred.</li>
	<li>After overnight incubation, take 0.5 ml of the D2O solution and check the reaction progress by 1H-NMR. All proton signals of alanine, &#948; 3.76 (q, J = 7.2 Hz, 1H), 1.46 (d, J = 7.3 Hz, 3H), 1H NMR 400 MHz, should be greatly suppressed due to deuteration. More than 98% of the proton should be exchanged to deuterium as described previously23. Note: D2O can be partially recovered by distillation if the reaction is performed on large scale (&#62;200 ml D2O). Normally, 60% to 80% of D2O can be distilled from the solution.</li>
	<li>Freeze the above solution with liquid nitrogen and lyophilize it using a lyophilizer to obtain white deuterated L-alanine powder.</li>
</ol>
4. Synthesis of Peptoid Linker Region
The linker region is not required for PTA library synthesis. However, in order to avoid the high background in the lower molecular weight range (100-600) of MALDI mass spectroscopy and to improve the ionization of the compounds, a peptoid linker with multiple polar residues is often used. This peptoid linker can be synthesized through standard peptoid synthesis procedure. Here we will synthesize a pentamer of N-methoxyethyl glycine as the linker (as shown in Figure 5).
<ol>
	<li>Swell 90 &#956;m Tentagel beads with RAM linker (1 g, 0.27 mmol/g) in 10 ml DMF for 3 hr&#160;in a 12 ml syringe reactor with mild shaking.</li>
	<li>Drain the DMF from the reactor and add 10 ml 20% piperidine DMF solution to deprotect the fmoc group from the Rink amide linker. Shake the beads with 20% piperidine solution for 30 min. Wash with DMF 5x&#160;to remove all piperidine.</li>
	<li>Take a few beads out from the syringe and test it with chloranil test. Beads should turn dark brown (chloranil test positive for primary amine) if fmoc is successfully deprotected.</li>
	<li>Prepare the following solutions: 1. 20 ml, 2 M bromoacetic acid/DMF solution; 2. 20 ml, 2 M DIC/DMF solution; 3. 10 ml, 1 M methoxylethylamine/DMF solution.</li>
	<li>Add 5 ml of 2 M bromoacetic acid/DMF solution to the beads, shake gently. Then add 5 ml of 2 M DIC/DMF solution to the beads; seal the syringe with the plunger and put it on the shaker. Shake for 10 min.</li>
	<li>Wash the beads with DMF thoroughly. Add 2 ml of 1 M methoxyethylamine/DMF solution prepared from step 4.4 to the beads. Seal the syringe with the plunger and shake it on the shaker for 30 min.</li>
	<li>Wash the beads with DMF 5x. Check a few beads with chloranil test, if positive (beads turn blue), then continue to the next step. Otherwise, repeat step 4.6.</li>
	<li>Repeat steps 4.5 to 4.7, 4x&#160;to complete the pentamer.</li>
</ol>
5. Split-and-pool Synthesis of PTA Library with (R)- and (S)-2-bromopropionic Acids
Here we describe the synthesis of a small PTA library with a theoretical diversity of 9,261 compounds using the 1 g&#160;of beads from step 4.8. Note that a 90 &#181;m tentagel bead contains approximately 2.9 million beads per gram; therefore the redundancy of the library will be 2.9 x 106 / 9,261 = 312 copies. We will use bromoacetic acid, (R)-2-bromopropanoic and isotopic labeled (S)-2-bromopropanoic acid-d4 as the acids, and 7 different amines (A1 ~ A7, see Figure 5 for details) for amination. Syringe reactors and a vacuum manifold will be used to perform the synthesis.
<ol>
	<li>Add 10 ml of 1:1 DCM:DMF to the syringe from step 4.8; use a 1,000 &#956;l pipette with a truncated pipette tip to split all 1 g&#160;beads evenly into three 5 ml syringe reactors. Label them as B (bromoacetic acid), R ((R)-2-bromopropanoic) and S ((S)-2-bromopropanoic acid-d4). Wash all 3 syringes with DCM 3x, and wash syringes labeled with R and S with anhydrous THF 3x, wash syringe labeled with B with DMF 3x.</li>
	<li>Syringe R and S. BTC coupling of bromopropanoic acid.
	<ol>
		<li>Prepare a fresh BTC/THF solution. Add approximately 200 mg of BTC into the vial in a fume hood, seal it with the cap. Weigh the amount of BTC in the vial. Calculate the amount of solvent needed and add anhydrous THF into the vial to make a 20 mg/ml BTC/THF solution.</li>
		<li>Prepare the bromo acids/BTC mixture. Add (R)-2-bromopropanoic acid (89 &#956;l, 0.95 mmol) and (S)-2-bromopropanoic acid-d4 (89 &#956;l, 0.95 mmol) in two small vials separately. To each vial, add 5 ml of the above 20 mg/ml BTC/THF solution. Seal the two vials and put them in -20 &#176;C freezer for 20 min.</li>
		<li>Add 1,125 &#956;l, 2:1 THF/DIPEA (750 &#956;l THF, 375 &#956;l DIPEA, 2.2 mmol) to syringe R and S separately. Mix the beads with the pipette tip. Let them sit for 5 min.</li>
		<li>Take the two cooled bromo acids/BTC mixtures from step 5.2.2, add 2,4,6-Trimethylpyridine (356 &#956;l, 2.7 mmol) to each vials. White precipitates will form immediately. Apply the corresponding suspension directly to the basified beads (syringe R and S in step 5.2.3) as soon as possible and then put them on a shaker to shake under 120 rpm for 2 hr. 
		Note: The solution in the syringe reactors should be a pale yellowish suspension during the whole course of the reaction. A darker color is an indication of excessive heat released during the initial addition of the acid chloride solution. This can be solved by further cooling down or dilute the bromo acids/BTC mixture.</li>
	</ol>
	</li>
	<li>Syringe B. Bromoacetic acid coupling with DIC
	<ol>
		<li>Prepare a fresh 20 ml, 2 M bromoacetic acid/DMF solution. Prepare a 20 ml, 2 M DIC/DMF solution.</li>
		<li>Add 2&#160;ml of 2 M bromoacetic acid/DMF solution to syringe B, shake gently. Add 2&#160;ml of 2 M DIC/DMF solution to syringe B, shake gently.</li>
		<li>Put syringe B on the same shaker as syringe R and S, shake it for 2 hr. Note that the coupling reaction of bromoacetic acid /DIC is done within 30 min; prolonged reaction time is for the convenience of split-and-pool synthesis.</li>
	</ol>
	</li>
	<li>After 2 hr, take syringe R, S and B from the shaker. Wash all three syringes thoroughly with DCM&#160;5x. Then wash with DMF 5x. Note that syringe R and S cannot be washed with DMF before being washed with DCM or THF first.</li>
	<li>Pool all the beads from syringes R, S and B into one 12 ml syringe reactor. Wash all the beads with DMF 5x.</li>
	<li>Add 10 ml of 1:1 DCM:DMF to the syringe; use a 1,000 &#956;l pipette with a truncated pipette tip to split all the beads evenly into 7 individual 2 ml syringes, label them as A1-A7.</li>
	<li>Amination. Prepare 10 ml, 2 M primary amine/DMF solutions for each of the 7 amines listed in Figure 5. Add 5 ml of each amine solution to the corresponding syringe A1-A7. Incubate all 7 syringes in a 60 &#176;C incubator with shaking overnight.</li>
	<li>After incubation, wash all beads thoroughly with DMF.&#160; Take a few of beads from each syringe and check with chloranil test. If the beads turn green (positive) within 3 min, proceed with next step. If negative, repeat step 5.7 for the negative syringes.</li>
	<li>Repeat steps 5.1 to 5.8 2x to complete the trimer. Optional step: After each cycle, we recommend to check the synthesis quality by mass spectroscopy as described below. All 9,261 compounds are now synthesized on tentagel beads as OBOC library.</li>
	<li>Mass spectroscopic confirmation of PTAs. 
	PTAs are highly structured oligomers and possess many common features of N-methylated peptides. One of the common problems of solid phase synthesis of N-methylated peptides is the acid degradation during TFA cleavage. To suppress acid degradation, cleavage of molecules like cyclosporine from solid support is often carried out under low temperature. We compared various cleaving conditions for cleaving different PTA molecules from the solid support. We found that, generally, low temperature and reduced TFA concentration could effectively suppress acid degradation and provide purer compounds.
	<ol>
		<li>Prepare 10 ml 1:1 TFA/DCM solution in a 15 ml tube. Seal the tube and put it in a -20 &#176;C freezer for 20 min.</li>
		<li>Wash the beads that need to be cleaved with DCM 5x. Shake the beads in DCM for 15 min and wash the beads again with DCM 5x.</li>
		<li>Drain the DCM from the syringe. Use a light microscope and a pipette with truncated tip to transfer each individual bead into a 96-well plate, one bead per well.</li>
		<li>Cover the 96-well plate with a cover slip. Put the plate in a -20 &#176;C freezer for 15 min.</li>
		<li>Take the cooled 1:1 TFA/DCM solution from step 5.10.1 and add 20 &#956;l to each of the wells that contains a bead. Put the cover slip back and put the 96-well plate on a shaker in the -20 &#176;C fridge.</li>
		<li>Shake for 20 min. Take the 96-well plate out and peel off the cover slip. Blow-dry the TFA/DCM from each well by blowing air or argon over it. If more than 10 beads are cleaved, a speedvac can be used to dry the TFA/DCM from the whole plate. Note that at this point, not all of the compounds are cleaved off the beads, but the cleaved compounds should be more than enough to perform the mass spectroscopy analysis.</li>
		<li>Add 20 &#956;l 6:4 ACN:H2O solution to dissolve the cleaved compounds from each well. Spot 0.6 &#956;l of each compound solution together with 0.6 &#956;l CHCA MALDI matrix on the MALDI plate.</li>
		<li>Use MALDI mass spectrometry to determine the molecular weight and sequence (MS/MS) of each compound.</li>
	</ol>
	</li>
</ol>
6. Chloranil Test
<ol>
	<li>Prepare the following reagents fresh for each test. Solution A: 2% Chloranil (CAS: 118-75-2) in DMF. Solution B: 2% acetaldehyde (CAS: 75-07-0) in DMF.</li>
	<li>Mix 100 &#956;l of solution A with 100 &#956;l of solution B before the test in a 1.5 ml tube; drop the beads in and gently shake. If the beads turn blue within 5 min, it indicates the presence of secondary amine on the surface of the beads. Primary amines give a dark brown color instead of turning blue.</li>
</ol>

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E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extraordinarily+robust+polyproline+type+I+peptoid+helices+generated+via+the+incorporation+of+alpha-chiral+aromatic+N-1-naphthylethyl+side+chains.">Extraordinarily robust polyproline type I peptoid helices generated via the incorporation of alpha-chiral aromatic N-1-naphthylethyl side chains.</a> J Am Chem Soc. 133, 15559-15567 (2011).</li><li>Huang, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+threaded+loop+conformation+adopted+by+a+family+of+peptoid+nonamers.">A threaded loop conformation adopted by a family of peptoid nonamers.</a> Journal of the American Chemical Society. 128, 1733-1738 (2006).</li><li>Lee, J. H., Kim, H. S., Lim, H. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+Facile+Solid-Phase+Synthesis+of+Conformationally+Constrained+Bicyclic+Peptoids.">Design and Facile Solid-Phase Synthesis of Conformationally Constrained Bicyclic Peptoids.</a> Organic Letters. 13, 5012-5015 (2011).</li><li>Gao, Y., Kodadek, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synthesis+and+Screening+of+Stereochemically+Diverse+Combinatorial+Libraries+of+Peptide+Tertiary+Amides.">Synthesis and Screening of Stereochemically Diverse Combinatorial Libraries of Peptide Tertiary Amides.</a> Chem Biol. 20, 360-369 (2013).</li><li>Urban, J., Vaisar, T., Shen, R., Lee, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lability+of+N-alkylated+peptides+towards+TFA+cleavage.">Lability of N-alkylated peptides towards TFA cleavage.</a> Int J Pept Protein Res. 47, 182-189 (1996).</li><li>Rzuczek, S. G., Gao, Y., Tang, Z., Thornton, C. A., Kodadek, T., Disney, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Features+of+Modularly+Assembled+Compounds+That+Impart+Bioactivity+Against+an+RNA+Target.">Features of Modularly Assembled Compounds That Impart Bioactivity Against an RNA Target.</a> ACS Chemical Biology. 8 (10), 2312-2321 (2013).</li><li>Thern, B., Rudolph, J., Jung, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Triphosgene+as+highly+efficient+reagent+for+the+solid-phase+coupling+of+N-alkylated+amino+acids&#8212;total+synthesis+of+cyclosporin+O.">Triphosgene as highly efficient reagent for the solid-phase coupling of N-alkylated amino acids&#8212;total synthesis of cyclosporin O.</a> Tetrahedron Letters. 43, 5013-5016 (2002).</li><li>Sleebs, M. M., Scanlon, D., Karas, J., Maharani, R., Hughes, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Total+Synthesis+of+the+Antifungal+Depsipeptide+Petriellin+A.">Total Synthesis of the Antifungal Depsipeptide Petriellin A.</a> J Org Chem. 76, 6686-6693 (2011).</li><li>Vaisar, T., Urban, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gas-phase+fragmentation+of+protonated+mono-N-methylated+peptides.+Analogy+with+solution-phase+acid-catalyzed+hydrolysis.">Gas-phase fragmentation of protonated mono-N-methylated peptides. Analogy with solution-phase acid-catalyzed hydrolysis.</a> Journal of Mass Spectrometry. 33, 505-524 (1998).</li><li>Creighton, C. J., Romoff, T. T., Bu, J. H., Goodman, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanistic+studies+of+an+unusual+amide+bond+scission.">Mechanistic studies of an unusual amide bond scission.</a> Journal of the American Chemical Society. 121, 6786-6791 (1999).</li><li>Sewald, N., Sewald, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient,+racemization-free+peptide+coupling+of+N-alkyl+amino+acids+by+using+amino+acid+chlorides+generated+in+situ--total+syntheses+of+the+cyclopeptides+cyclosporin+O+and+omphalotin+A.">Efficient, racemization-free peptide coupling of N-alkyl amino acids by using amino acid chlorides generated in situ--total syntheses of the cyclopeptides cyclosporin O and omphalotin A.</a> Angewandte Chemie (International ed. in English). 41, 4661-4663 (2002).</li><li>Astle, J. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Seamless+Bead+to+Microarray+Screening:+Rapid+Identification+of+the+Highest+Affinity+Protein+Ligands+from+Large+Combinatorial+Libraries.">Seamless Bead to Microarray Screening: Rapid Identification of the Highest Affinity Protein Ligands from Large Combinatorial Libraries.</a> Chem Biol. 17, 38-45 (2010).</li><li>Strohalm, M., Kavan, D., Novak, P., Volny, M., Havlicek, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=mMass+3:+a+cross-platform+software+environment+for+precise+analysis+of+mass+spectrometric+data.">mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data.</a> Anal Chem. 82, 4648-4651 (2010).</li></ol>

The authors declare that they have no competing financial interests.

Peptide tertiary amides (PTAs) are a superfamily of peptidomimetic oligomers. Besides the well-studied peptides, peptoids and N-methylated peptides, a large portion of compounds within this family remains understudied, majorly due to lack of synthetic method to access general N-alkylated peptides. Here we describe an efficient method to synthesize PTAs with chiral building blocks derived from amino acids. Previously, we have reported to use a new sub-monomer route to synthesis libraries of PTA molecules23. We ...

Peptidomimetics are compounds that mimic the structure of natural peptides. They are designed to retain the bioactivity while overcoming some of the problems associated with natural peptides, including cell permeability and stability against proteolysis1-3. Due to the oligomeric nature of these compounds, large synthetic libraries can be readily accessed through monomeric or sub-monomeric synthetic routes4-7. One of the most studied classes of peptidomimetics is&#160;peptoids. Peptoids are oligomers of N-alkylated glycines that can be synthesized easily using a sub-monomer strategy8,9. Many useful protein ligands have been successfully identified from screening large synthetic peptoid libraries against protein targets1,10-14. Nonetheless, &#8220;hits&#8221; identified from peptoid libraries rarely archive very high affinity towards protein targets1,10-14,22. One major difference between peptoids and natural peptides is that most of the peptoids generally lack the ability to form secondary structure due to the lack of chiral centers and conformational constraints. In order to solve this problem, multiple strategies were developed over the past decade, largely focusing on the modification of side chains contained on the main chain nitrogen atoms15-22. Recently, we have developed a new synthetic route to introduce natural amino acid side chains onto a peptoid backbone to create peptide tertiary amides23.
Peptide tertiary amides (PTAs) are a super family of peptidomimetics that include but are not limited to peptides (R2&#160;= H), peptoids (R1&#160;= H) and N-methylated peptides (R1&#160;&#8800; H, R2&#160;= Me). (See Figure 1) Our synthetic route employs naturally occurring amino acids as the source of chirality and side chains on the &#945;-carbon, and commercially available primary amines to provide N-substitutions. Therefore, a larger chemical space than that of simple peptides, peptoids or N-methylated peptides can be explored. Circular dichroism spectra have shown that PTA molecules are highly structured in solution. Characterization of one of the PTA-protein complexes clearly shows that the conformational constraints of PTA are required for binding. Recently, we have also discovered that some of the PTA molecules possess improved cell permeability than their peptoid and peptide counterparts. We believe that these PTA libraries can be a good source of high-affinity ligands for protein targets. In this paper, we will discuss the synthesis of a sample one-bead one-compound (OBOC) PTA library in details along with some improved conditions for the coupling and cleavage of these compounds.

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			<td></td>
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			<td></td>
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			<td height="21" style="height:21px;width:249px;">Syringe reactor</td>
			<td style="width:169px;">INTAVIS&#160;</td>
			<td style="width:160px;">Reaction Column</td>
			<td>3ml, 5ml, 10ml, 20ml</td>
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			<td height="21" style="height:21px;width:249px;">Vacuum manifold&#160;</td>
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			<td>Vac-Man</td>
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</table>

split-and-pool synthesis and characterization of peptide tertiary amide library

Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid phase by using combinatorial chemistry. One of the most well studied classes of peptidomimetics is peptoids. Peptoids are easy to synthesize and have been shown to be proteolysis-resistant and cell-permeable. Over the past decade, many useful protein ligands have been identified through screening of peptoid libraries. However, most of the ligands identified from peptoid libraries do not display high affinity, with rare exceptions. This may be due, in part, to the lack of chiral centers and conformational constraints in peptoid molecules. Recently, we described a new synthetic route to access peptide tertiary amides (PTAs). PTAs are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. With side chains on both &#945;-carbon and main chain nitrogen atoms, the conformation of these molecules are greatly constrained by sterical hindrance and allylic 1,3 strain. (Figure 1) Our study suggests that these PTA molecules are highly structured in solution and can be used to identify protein ligands. We believe that these molecules can be a future source of high-affinity protein ligands. Here we describe the synthetic method combining the power of both split-and-pool and sub-monomer strategies to synthesize a sample one-bead one-compound (OBOC) library of PTAs.

Here we show three representative MALDI spectrums from a PTA trimer with linker. As shown in Figure 6A, when cleaved under room temperature using 50% TFA/DCM solution, significant degradation is observed. In Figure 6A, peak 593 and 484 correspond to the linker and the PTA trimer respectively, show that the whole molecule was successfully synthesized on bead but degraded during cleavage. When cleaved under low temperature condition as described above, the amount of TFA-induced degradation...

Watch this Scientific Journal Video about Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library at JoVE.com

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Peptide tertiary amides (PTAs) are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. Here we describe a synthetic method which combines&#160;both split-and-pool and sub-monomer strategies to synthesize a one-bead one-compound library of PTAs.

Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid ...

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Chemistry

Unit 1

Carboxylic Acid Derivatives

SCIENTISTS IN ACTION

18.0K Views.  The Scripps Research Institute.  אורגני חיבור פפטיד שיישונים (PTAs) הוא superfamily של peptidomimetics שכולל, אך אינם מוגבלים לפפטידים, peptoids ופפטידים מפוגלים-N. כאן אנו מתארים שיטה סינתטית המשלבת את שניהם מפוצלת וברכה ואסטרטגיות תת מונומר לסנתז ספרייה חד מתחם אחד אגל PTAs. 

Video: Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Nucleoside Triphosphates - From Synthesis to Biochemical Characterization

The traditional strategy for the introduction of chemical functionalities is the use of solid-phase synthesis by appending suitably modified phosphoramidite precursors to the nascent chain. However, the conditions used during the synthesis and the restriction to rather short sequences hamper the applicability of this methodology. On the other hand, modified nucleoside triphosphates are activated building blocks that have been employed for the mild introduction of numerous functional groups into nucleic acids, a strategy that paves the way for the use of modified nucleic acids in a wide-ranging palette of practical applications such as functional tagging and generation of ribozymes and DNAzymes. One of the major challenges resides in the intricacy of the methodology leading to the isolation and characterization of these nucleoside analogues.
	
	In this video article, we present a detailed protocol for the synthesis of these modified analogues using phosphorous(III)-based reagents. In addition, the procedure for their biochemical characterization is divulged, with a special emphasis on primer extension reactions and TdT tailing polymerization. This detailed protocol will be of use for the crafting of modified dNTPs and their further use in chemical biology.

The protocol described herein aims to explain and abridge the numerous obstacles in the way of the intricate route leading to modified nucleoside triphosphates. Consequently, this protocol facilitates both the synthesis of these activated building-blocks and their availability for practical applications.

The  traditional strategy for the introduction of chemical functionalities is the  use of solid-phase synthesis by appending suitably modified ...

Amide Coupling Reaction for the Synthesis of Bispyridine-based Ligands and Their Complexation to Platinum as Dinuclear Anticancer Agents

Amide coupling reactions can be used to synthesize bispyridine-based ligands for use as bridging linkers in multinuclear platinum anticancer drugs. Isonicotinic acid, or its derivatives, are coupled to variable length diaminoalkane chains under an inert atmosphere in anhydrous DMF or DMSO with the use of a weak base, triethylamine, and a coupling agent, 1-propylphosphonic anhydride. The products precipitate from solution upon formation or can be precipitated by the addition of water. If desired, the ligands can be further purified by recrystallization from hot water. Dinuclear platinum complex synthesis using the bispyridine ligands is done in hot water using transplatin. The most informative of the chemical characterization techniques to determine the structure and gross purity of both the bispyridine ligands and the final platinum complexes is 1H NMR with particular analysis of the aromatic region of the spectra (7-9 ppm). The platinum complexes have potential application as anticancer agents and the synthesis method can be modified to produce trinuclear and other multinuclear complexes with different hydrogen bonding functionality in the bridging ligand.

This protocol describes the use of amide coupling reactions of isonicotinic acid and diaminoalkanes to form bridging ligands suitable for use in the synthesis of multinuclear platinum complexes, which combine aspects of the anticancer drugs BBR3464 and picoplatin.

Amide coupling reactions can be used to synthesize bispyridine-based ligands for use as bridging linkers in multinuclear platinum anticancer drugs. ...

Synthesis and Characterization of Functionalized Metal-organic Frameworks

Metal-organic frameworks have attracted extraordinary amounts of research attention, as they are attractive candidates for numerous industrial and technological applications. Their signature property is their ultrahigh porosity, which however imparts a series of challenges when it comes to both constructing them and working with them. Securing desired MOF chemical and physical functionality by linker/node assembly into a highly porous framework of choice can pose difficulties, as less porous and more thermodynamically stable congeners (e.g., other crystalline polymorphs, catenated analogues) are often preferentially obtained by conventional synthesis methods. Once the desired product is obtained, its characterization often requires specialized techniques that address complications potentially arising from, for example, guest-molecule loss or preferential orientation of microcrystallites. Finally, accessing the large voids inside the MOFs for use in applications that involve gases can be problematic, as frameworks may be subject to collapse during removal of solvent molecules (remnants of solvothermal synthesis). In this paper, we describe synthesis and characterization methods routinely utilized in our lab either to solve or circumvent these issues. The methods include solvent-assisted linker exchange, powder X-ray diffraction in capillaries, and materials activation (cavity evacuation) by supercritical CO2 drying. Finally, we provide a protocol for determining a suitable pressure region for applying the Brunauer-Emmett-Teller analysis to nitrogen isotherms, so as to estimate surface area of MOFs with good accuracy.

Synthesis, activation, and characterization of intentionally designed metal-organic framework materials is challenging, especially when building blocks are incompatible or unwanted polymorphs are thermodynamically favored over desired forms. We describe how applications of solvent-assisted linker exchange, powder X-ray diffraction in capillaries and activation via supercritical CO2 drying, can address some of these challenges.

Metal-organic frameworks have attracted extraordinary amounts of research attention, as they are attractive candidates for numerous industrial and ...

The Synthesis, Characterization and Reactivity of a Series of Ruthenium N-triphosPh Complexes

Herein we report the synthesis of a tridentate phosphine ligand N(CH2PPh2)3 (N-triphosPh) (1) via a phosphorus based Mannich reaction of the hydroxylmethylene phosphine precursor with ammonia in methanol under a nitrogen atmosphere. The N-triphosPh ligand precipitates from the solution after approximately 1 hr of reflux and can be isolated analytically pure via simple cannula filtration procedure under nitrogen. Reaction of the N-triphosPh ligand with [Ru3(CO)12] under reflux affords a deep red solution that show evolution of CO gas on ligand complexation. Orange crystals of the complex [Ru(CO)2{N(CH2PPh2)3}-&#954;3P] (2) were isolated on cooling to RT. The 31P{1H} NMR spectrum showed a characteristic single peak at lower frequency compared to the free ligand. Reaction of a toluene solution of complex 2 with oxygen resulted in the instantaneous precipitation of the carbonate complex [Ru(CO3)(CO){N(CH2PPh2)3}-&#954;3P] (3) as an air stable orange solid. Subsequent hydrogenation of 3 under 15 bar of hydrogen in a high-pressure reactor gave the dihydride complex [RuH2(CO){N(CH2PPh2)3}-&#954;3P] (4), which was fully characterized by X-ray crystallography and NMR spectroscopy. Complexes 3 and 4 are potentially useful catalyst precursors for a range of hydrogenation reactions, including biomass-derived products such as levulinic acid (LA). Complex 4 was found to cleanly react with LA in the presence of the proton source additive NH4PF6 to give [Ru(CO){N(CH2PPh2)3}-&#954;3P{CH3CO(CH2)2CO2H}-&#954;2O](PF6) (6).

The Synthesis, Characterization and Reactivity of a Series of Ruthenium N-triphosPh Complexes

Ruthenium phosphine complexes are widely used for homogeneous catalytic reactions such as hydrogenations. The synthesis of a series of novel tridentate ruthenium complexes bearing the N-triphos ligand N(CH2PPh2)3 is reported. Additionally, the stoichiometric reaction of a dihydride Ru&#8211;N-triphos complex with levulinic acid is described.

Herein we report the synthesis of a tridentate phosphine ligand N(CH2PPh2)3 (N-triphosPh) (1) via a phosphorus based Mannich reaction of the ...

Synthesis, Characterization, and Functionalization of Hybrid Au/CdS and Au/ZnS Core/Shell Nanoparticles

Plasmonic nanoparticles are an attractive material for light harvesting applications due to their easily modified surface, high surface area and large extinction coefficients which can be tuned across the visible spectrum. Research into the plasmonic enhancement of optical transitions has become popular, due to the possibility of altering and in some cases improving photo-absorption or emission properties of nearby chromophores such as molecular dyes or quantum dots. The electric field of the plasmon can couple with the excitation dipole of a chromophore, perturbing the electronic states involved in the transition and leading to increased absorption and emission rates. These enhancements can also be negated at close distances by energy transfer mechanism, making the spatial arrangement of the two species critical. Ultimately, enhancement of light harvesting efficiency in plasmonic solar cells could lead to thinner and, therefore, lower cost devices. The development of hybrid core/shell particles could offer a solution to this issue. The addition of a dielectric spacer between a gold nanoparticles and a chromophore is the proposed method to control the exciton plasmon coupling strength and thereby balance losses with the plasmonic gains. A detailed procedure for the coating of gold nanoparticles with CdS and ZnS semiconductor shells is presented. The nanoparticles show high uniformity with size control in both the core gold particles and shell species allowing for a more accurate investigation into the plasmonic enhancement of external chromophores.

The synthesis of uniform gold nanoparticles coated with semiconductor shells of CdS or ZnS is performed. The semiconductor coating is conducted by first depositing a silver sulfide shell and exchanging the silver cations for zinc or cadmium cations.

Plasmonic nanoparticles are an attractive material for light harvesting applications due to their easily modified surface, high surface area and large ...

Development of a Backbone Cyclic Peptide Library as Potential Antiparasitic Therapeutics Using Microwave Irradiation

Protein-protein interactions (PPIs) are intimately involved in almost all biological processes and are linked to many human diseases. Therefore, there is a major effort to target PPIs in basic research and in the pharmaceutical industry. Protein-protein interfaces are usually large, flat, and often lack pockets, complicating the discovery of small molecules that target such sites. Alternative targeting approaches using antibodies have limitations due to poor oral bioavailability, low cell-permeability, and production inefficiency.
Using peptides to target PPI interfaces has several advantages. Peptides have higher conformational flexibility, increased selectivity, and are generally inexpensive. However, peptides have their own limitations including poor stability and inefficiency crossing cell membranes. To overcome such limitations, peptide cyclization can be performed. Cyclization has been demonstrated to improve peptide selectivity, metabolic stability, and bioavailability. However, predicting the bioactive conformation of a cyclic peptide is not trivial. To overcome this challenge, one attractive approach it to screen a focused library to screen in which all backbone cyclic peptides have the same primary sequence, but differ in parameters that influence their conformation, such as ring size and position.
We describe a detailed protocol for synthesizing a library of backbone cyclic peptides targeting specific parasite PPIs. Using a rational design approach, we developed peptides derived from the scaffold protein Leishmania receptor for activated C-kinase (LACK). We hypothesized that sequences in LACK that are conserved in parasites, but not in the mammalian host homolog, may represent interaction sites for proteins that are critical for the parasites&#39; viability. The cyclic peptides were synthesized using microwave irradiation to reduce reaction times and increase efficiency. Developing a library of backbone cyclic peptides with different ring sizes facilitates a systematic screen for the most biological active conformation. This method provides a general, fast, and facile way to synthesize cyclic peptides.

A simple and general method for the synthesis of cyclic peptides using microwave irradiation is outlined. This procedure enables the synthesis of backbone cyclic peptides with a collection of different conformations while retaining the side chains and the pharmacophoric moieties., and therefore, allows to screen for the bioactive conformation.

Protein-protein interactions (PPIs) are intimately involved in almost all biological processes and are linked to many human diseases. Therefore, there is ...

Synthesis and Characterization of Supramolecular Colloids

Control over colloidal assembly is of utmost importance for the development of functional colloidal materials with tailored structural and mechanical properties for applications in photonics, drug delivery and coating technology. Here we present a new family of colloidal building blocks, coined supramolecular colloids, whose self-assembly is controlled through surface-functionalization with a benzene-1,3,5-tricarboxamide (BTA) derived supramolecular moiety. Such BTAs interact via directional, strong, yet reversible hydrogen-bonds with other identical BTAs. Herein, a protocol is presented that describes how to couple these BTAs to colloids and how to quantify the number of coupling sites, which determines the multivalency of the supramolecular colloids. Light scattering measurements show that the refractive index of the colloids is almost matched with that of the solvent, which strongly reduces the van der Waals forces between the colloids. Before photo-activation, the colloids remain well dispersed, as the BTAs are equipped with a photo-labile group that blocks the formation of hydrogen-bonds. Controlled deprotection with UV-light activates the short-range hydrogen-bonds between the BTAs, which triggers the colloidal self-assembly. The evolution from the dispersed state to the clustered state is monitored by confocal microscopy. These results are further quantified by image analysis with simple routines using ImageJ and Matlab. This merger of supramolecular chemistry and colloidal science offers a direct route towards light- and thermo-responsive colloidal assembly encoded in the surface-grafted monolayer.

A protocol for the synthesis and characterization of colloids coated with supramolecular moieties is described. These supramolecular colloids undergo self-assembly upon the activation of the hydrogen-bonds between the surface-anchored molecules by UV-light.

Control over colloidal assembly is of utmost importance for the development of functional colloidal materials with tailored structural and mechanical ...

Synthesis and Characterization of Fe-doped Aluminosilicate Nanotubes with Enhanced Electron Conductive Properties

The goal of the protocol is to synthesize Fe-doped aluminosilicate nanotubes of the imogolite type with the formula (OH)3Al2-xFexO3SiOH. Doping with Fe aims at lowering the band gap of imogolite, an insulator with the chemical formula (OH)3Al2O3SiOH, and at modifying its adsorption properties towards azo-dyes, an important class of organic pollutants of both wastewater and groundwater.
Fe-doped nanotubes are obtained in two ways: by direct synthesis, where FeCl3 is added to an aqueous mixture of the Si and Al precursors, and by post-synthesis loading, where preformed nanotubes are put in contact with a FeCl3&#8226;6H2O aqueous solution. In both synthesis methods, isomorphic substitution of Al3+ by Fe3+ occurs, preserving the nanotube structure. Isomorphic substitution is indeed limited to a mass fraction of ~1.0% Fe, since at a higher Fe content (i.e., a mass fraction of 1.4% Fe), Fe2O3 clusters form, especially when the loading procedure is adopted. The physicochemical properties of the materials are studied by means of X-ray powder diffraction (XRD), N2 sorption isotherms at -196 &#176;C, high resolution transmission electron microscopy (HRTEM), diffuse reflectance (DR) UV-Vis spectroscopy, and &#950;-potential measurements. The most relevant result is the possibility to replace Al3+ ions (located on the outer surface of the nanotubes) by post-synthesis loading on preformed imogolite without perturbing the delicate hydrolysis equilibria occurring during nanotube formation. During the loading procedure, an anionic exchange occurs, where Al3+ ions on the outer surface of the nanotubes are replaced by Fe3+ ions. In Fe-doped aluminosilicate nanotubes, isomorphic substitution of Al3+ by Fe3+ is found to affect the band gap of doped imogolite. Nonetheless, Fe3+ sites on the outer surface of nanotubes are able to coordinate organic moieties, like the azo-dye Acid Orange 7, through a ligand-displacement mechanism occurring in an aqueous solution.

Here, we present a protocol to synthesize and characterize Fe-doped aluminosilicate nanotubes. The materials are obtained by either sol-gel synthesis upon addition of FeCl3&#8226;6H2O to the mixture containing the Si and Al precursors or by post-synthesis ionic exchange of preformed aluminosilicate nanotubes.

The goal of the protocol is to synthesize Fe-doped aluminosilicate nanotubes of the imogolite type with the formula (OH)3Al2-xFexO3SiOH. Doping with Fe ...

Facile Protocol for the Synthesis of Self-assembling Polyamine-based Peptide Amphiphiles (PPAs) and Related Biomaterials

Polyamine-based Peptide Amphiphiles (PPAs) are a new class of self-assembling amphiphilic biomaterials-related to the peptide amphiphiles (PAs). Traditional PAs possess charged amino acids as solubilizing groups (lysine, arginine), which are directly connected to a lipid segment or can contain a linker region made of neutral amino acids. Tuning the peptide sequence of PAs can yield diverse morphologies. Similarly, PPAs possess a hydrophobic segment and neutral amino acids, but also contain polyamine molecules as water solubilizing (hydrophilic) groups. As is the case with PAs, PPAs can also self-assemble into diverse morphologies, including small rods, twisted nano-ribbons, and fused nano-sheets, when dissolved in water. However, the presence of both primary and secondary amines on a single polyamine molecule poses a significant challenge when synthesizing PPAs. In this paper, we show a simple protocol, based on literature precedents, to achieve a facile synthesis of PPAs using solid phase peptide synthesis (SPPS). This protocol can be extended to the synthesis of PAs and other similar systems. We also illustrate the steps that are needed for cleavage from the resin, identification, and purification.

Facile Protocol for the Synthesis of Self-assembling Polyamine-based Peptide Amphiphiles PPAs and Related Biomaterials

The synthesis of polyamine-based peptide amphiphiles (PPAs) is a significant challenge due to the presence of multiple amine nitrogens, which requires judicious use of protecting groups to mask these reactive functionalities. In this paper, we describe a facile method for the preparation of these new class of self-assembling molecules.

Polyamine-based Peptide Amphiphiles (PPAs) are a new class of self-assembling amphiphilic biomaterials-related to the peptide amphiphiles (PAs). ...

Synthesis and Characterization of 1,2-Dithiolane Modified Self-Assembling Peptides

This report focuses on the synthesis of an N-terminus 1,2-dithiolane modified self-assembling peptide and the characterization of the resulting self-assembled supramolecular structures. The synthetic route takes advantage of solid-phase peptide synthesis with the on-resin coupling of the dithiolane precursor molecule, 3-(acetylthio)-2-(acetylthiomethyl)propanoic acid, and the microwave-assisted thioacetate deprotection of the peptide N-terminus before final cleavage from the resin to yield the 1,2-dithiolane modified peptide. After the high-performance liquid chromatography (HPLC) purification of the 1,2-dithiolane peptide, derived from the nucleating core of the A&#946; peptide associated with Alzheimer&#39;s disease, the peptide is shown to self-assemble into cross-&#946; amyloid fibers. Protocols to characterize the amyloid fibers by Fourier-transform infrared spectroscopy (FT-IR), circular dichroism spectroscopy (CD) and transmission electron microscopy (TEM) are presented. The methods of N-terminal modification with a 1,2-dithiolane moiety to well-characterized self-assembling peptides can now be explored as model systems to develop post-assembly modification strategies and explore dynamic covalent chemistry on supramolecular peptide nanofiber surfaces.

A protocol for the synthesis of a 1,2-dithiolane modified peptide and the characterization of the supramolecular structures resulting from the peptide self-assembly.