We thank the Engineering and Physical Sciences Research Council (EPSRC) for financial support (HLB). We also thank Srid&#233;vi Maalika Ramanoudjame for her assistance during the filming of this procedure.

1. Solid-phase Synthesis of Peptoids
NOTE: Peptoids are synthesized manually using the submonomer procedure of solid-phase peptoid synthesis. This method allows high coupling efficiency and good final product yields. Synthesis on solid-phase also allows excess reactants to be removed easily at the end of each step and the method has been modified here to allow different functionalized cationic monomers (i.e., arginine-type and lysine-type residues) to be included within the same sequence.1,2
<ol>
	<li>Synthesis of a linear peptoid 
	Caution: Carry out safety assessments before starting synthesis. Carry out all reactions in a fume hood and wear adequate personal protective equipment as appropriate (i.e., disposable nitrile gloves, safety glasses and a lab coat). Take particular care when using the following reagents and solvents. Dimethylformamide (DMF) is a suspected teratogen and dichloromethane (DCM) is a carcinogen. N,N&#39;-diisopropylcarbodiimide (DIC) and piperidine are hazardous to eyes, skin, via respiratory inhalation and may cause skin sensitization. Hydrazine is a suspected carcinogen, fatal if inhaled and causes severe burns to skin or eyes. Bromoacetic acid is also hazardous to skin, eyes and the respiratory tract and may cause burns upon contact. Trifluoroacetic acid (TFA) is a volatile liquid and can cause severe burns so handle with care. Heavy duty gloves are recommended.
	<ol>
		<li>Add 0.12 g Fmoc-protected Rink Amide resin (0.1 mmol, typical loading 0.7 mmol/g) to a capped 20 ml polypropylene reaction vessel with two frits. Add 5 ml dimethylformamide (DMF) to swell the resin and leave the vessel to stand for at least 60 minutes at room temperature. Drain the DMF using a solid-phase extraction vacuum platform.</li>
		<li>To deprotect the Fmoc group on the swollen resin, add 2 ml piperidine solution (20% in DMF v/v). Place the vessel on a shaker platform at room temperature (450 rpm) and shake for 5 min. Remove the solution via vacuum station.
		<ol>
			<li>Repeat Fmoc deprotection with 2 ml piperidine solution and shake for 15 min at room temperature. Drain the solution as before.</li>
		</ol>
		</li>
		<li>Wash the resin by adding 2 ml DMF and mixing the resin for 30 sec. Drain the DMF and repeat three more times.</li>
		<li>For the acetylation, add 1 ml of bromoacetic acid solution (0.6 M in DMF) and 0.2 ml N,N&#39;-diisopropylcarbodiimide solution (DIC, 50% in DMF v/v). Leave reaction vessel to shake for 20 min at room temperature. Drain the solution and wash the resin with 2 ml DMF three times.</li>
		<li>For the displacement, add 1 ml of amine solution (1.5 M in DMF). Shake the resin for 60 min at room temperature. Drain the solution and wash the resin with 2 ml DMF three times.
		<ol>
			<li>To add an arginine-type monomer, follow step 1.7. Depending upon the desired peptoid sequence, different amines will be added.</li>
		</ol>
		</li>
		<li>Repeat steps 1.1.4 and 1.1.5.</li>
		<li>To include a guanidine functionalized monomer (i.e., NArg), add 1 ml of unprotected diamine solution (1.5 M in DMF) to the resin and shake for 60 min at room temperature.
		<ol>
			<li>Drain the solution and wash the resin with 2 ml DMF three times.</li>
			<li>Add 2-acetyldimedone (0.2 g, 1 mmol in 0.5 ml DMF, 10 equivalents) to add the Dde group to the free primary amine and shake for 60 min at room temperature. Drain the solution and wash the resin with 2 ml DMF three times.</li>
		</ol>
		</li>
		<li>Continue submonomer synthesis as in 1.1.4 to 1.1.7 until the desired sequence is made. Add 2 ml DMF to wash the resin and repeat three times.</li>
		<li>To deprotect the Dde group on resin, add 4 ml 2% hydrazine solution (in DMF v/v) and shake for 3 min at room temperature. Drain the solution and repeat three times.</li>
		<li>Drain the solution and wash the resin with 2 ml DMF three times.</li>
		<li>Add pyrazole-1-carboxamidine (6 equivalents per free amine, i.e., per NArg monomers, in the minimum volume of DMF) and N,N-diisopropylethylamine or DIPEA (6 equivalents per free amine) and shake at room temperature for 60 min.</li>
		<li>Drain the solution and wash the resin with 2 ml dichloromethane three times. Leave the resin to dry in air for 10 min then the resin can be stored until cleavage (section 2).</li>
		<li>To pause the synthesis, wash the resin with 2 ml DMF three times. Add 2 ml DMF, stopper the synthesis vessel and leave at room temperature in a fume hood. 
		NOTE: The synthesis may be paused after any displacement step (except the second displacement step as diketopiperazines may be formed).</li>
	</ol>
	</li>
	<li>Side-chain deprotection and cleavage from resin
	<ol>
		<li>Undertake a test cleave to check the progress of synthesis (purity and mass) at any point during synthesis after the displacement steps, addition or removal of Dde-protecting group or after the final sequence has been made.
		<ol>
			<li>Transfer approximately 10 resin beads from the reaction vessel into a new 8 ml polypropylene fritted cartridge.</li>
			<li>Add 1 ml of trifluoroacetic acid cleavage cocktail (containing 95% TFA, 2.5% H2O, 2.5% triisopropylsilane) and shake for 90 min at room temperature.</li>
			<li>Filter the TFA cleavage cocktail from the resin using the fritted reaction vessel into a 10 ml round bottomed flask.</li>
			<li>Evaporate the cleavage cocktail using a rotary evaporator and redissolve the resulting oil in 1 ml acetonitrile/water for submission to LC-MS or analytical HPLC.</li>
		</ol>
		</li>
		<li>For the final cleavage: in the same fritted polypropylene reaction cartridge used for synthesis, add 4 ml of the TFA cleavage cocktail (95% TFA, 2.5% H2O, 2.5% triisopropylsilane) and cover the vessel. Shake for 90 min at room temperature.</li>
		<li>Filter the TFA cleavage cocktail from the resin using the fritted reaction vessel into a 50 ml round bottomed flask.</li>
		<li>Evaporate the cleavage cocktail using a rotary evaporator. After the TFA has been removed, the product should be obtained as an oil. To aid TFA removal from this crude oil, add 2 ml anhydrous diethyl ether and the peptoid should precipitate.
		<ol>
			<li>Either remove the diethyl ether via pipette and discard or evaporate using a rotary evaporator. Repeat diethyl ether precipitation three times.</li>
		</ol>
		</li>
		<li>Dissolve the crude peptoid in 10 ml acetonitrile/acidified water solution (50% acetonitrile, 0.1% TFA in water v/v). Transfer to a pre-weighed container, freeze at 20 &#176;C and lyophilize to a dry powder.</li>
	</ol>
	</li>
</ol>
2. Characterization and Purification
NOTE: The peptoid synthesis can be monitored and the final peptoid assessed via analytical reverse-phase HPLC using a C18 column and electrospray liquid-chromatography mass spectrometry (LC-MS). All HPLC solvents of solvents for LC-MS should be freshly prepared.
<ol>
	<li>Analytical HPLC
	<ol>
		<li>Weigh 1 mg of peptoid in a small glass vial. Add the minimum volume of acetonitrile to dissolve and dilute to 1 ml with water. Ensure that the peptoid has completely dissolved.</li>
		<li>Inject 10 &#181;l to analytical HPLC (suggested gradient 0 - 100% solvent B over 30 min, where solvent A = 95% water, 5% acetonitrile, 0.05% TFA and solvent B = 95% acetonitrile, 5% water, 0.03% TFA), as per manufacturer&#39;s instructions.</li>
		<li>Visualize UV spectrum at 220 nm.</li>
	</ol>
	</li>
	<li>ESI LC-MS
	<ol>
		<li>Make 1 mg/ml peptoid solution as in step 2.1.1.</li>
		<li>Inject 1 &#181;l to electrospray LC-MS to determine if the molecular weight of the target peptoid is present, using manufacturer&#39;s instructions.</li>
		<li>Check the target mass of the peptoid sequence using a peptoid calculator, as per instructions on the calculator. 26 This web utility also allows the assignment of any deletion/addition products seen in the mass spectrum.26</li>
	</ol>
	</li>
	<li>Preparative reverse phase HPLC
	<ol>
		<li>Dissolve crude peptoids into 2 ml acidified water/acetonitrile (95% water, 5% MeCN, 0.1% TFA) and purify by preparative RP-HPLC using manufacturer&#39;s protocol. Determine the gradient by the elution time obtained from analytical HPLC and the amount injected will depend upon the column dimensions.</li>
		<li>Visualize using a detector set at 220 nm.</li>
		<li>Collect fractions in 15 ml centrifuge tubes, freeze at 20 &#176;C and lyophilize.</li>
		<li>Re-analyze fractions using LC-MS and analytical HPLC according to manufacturer&#39;s protocol. Recombine purified fractions.</li>
	</ol>
	</li>
</ol>
3. Biological Testing against Leishmania mexicana Parasites
Caution: Safety assessments must be carried out before starting synthesis. Leishmania mexicana is classified a hazard group 2 pathogen in the U.K. and adequate control measures must be in place prior to starting testing. All work must be carried out in a class 2 microbiological safety cabinet and adequate personal protective equipment worn as appropriate (i.e., nitrile gloves, safety glasses and a lab coat).
<ol>
	<li>Subculture of parasites
	<ol>
		<li>Defrost 1 ml -150 &#176;C frozen stock Leishmania mexicana M379 by placing vial in a 37 &#176;C water bath for 30 sec.</li>
		<li>Transfer the stock solution to 10 ml Schneider&#39;s Insect medium (at pH 7.0 supplemented with 15% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin) in a 25 cm3 cell culture flask with a non-vented cap.</li>
		<li>Incubate at 26 &#176;C for 72 hr.</li>
		<li>Examine parasites under microscope (400X magnification) to check condition. They should be insect stage promastigotes, procyclic forms in log phase with many dividing cells.</li>
		<li>Maintain procyclic promastigotes by sub-culturing parasites to a concentration of 5 x 105 parasites/ml every three days. Count cells using a Neubauer improved hemocytometer.</li>
	</ol>
	</li>
	<li>Transformation of L. mexicana insect stage into mammalian stage axenic amastigote form 27
	<ol>
		<li>Day 0: Prepare 10 ml culture of log stage parasites at 5 x 105 parasites/ml in Schneider&#39;s Insect medium (at pH 7.0 supplemented with 15% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin) in a 25 cm3 cell culture flask with a non-vented cap.</li>
		<li>Incubate at 26 &#176;C for 48 hr.</li>
		<li>Day 3: Transfer 10 ml culture to a 50 ml centrifuge tube and centrifuge at 447 x g for 5 min.</li>
		<li>Pour off old medium and add 10 ml Schneider&#39;s Insect medium (at pH 5.5 supplemented with 20% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin). Gently resuspend the pellet of parasites in the new medium using a pipette.</li>
		<li>Count the number of parasites using a Neubauer improved hemocytometer. Dilute to a concentration of 5 x 105 parasites/ml with pH 5.5 medium and transfer to a 25 cm3 cell culture flask.</li>
		<li>Incubate at 26 &#176;C for approximately 6 days.</li>
		<li>Day 9: Examine parasites under a microscope (400X). They should be in the non-replicating, infectious metacyclic promastigote stage.</li>
		<li>Count the number of parasites using a Neubauer improved hemocytometer. Dilute to a concentration of 5 x 105 parasites/ml with pH 5.5 medium.</li>
		<li>Remove 10 ml of cell culture and transfer to cell culture flask. Incubate at 32 &#176;C for 5 days.</li>
		<li>Day 14: Check appearance of parasites under the microscope (400X). They should be in the pathogenic amastigote stage, lacking the flagellum characteristic of promastigotes, and ready for assay.</li>
	</ol>
	</li>
	<li>Cytotoxicity assay on L. mexicana axenic amastigotes. 
	NOTE: The biological testing of peptoids uses high-throughput assays carried out in 96 well plates. This protocol describes the testing of L. mexicana axenic amastigotes, but identical assays can also be carried out on the promastigote stage parasites in appropriate media. Compounds are incubated with parasites at concentrations from 3 - 100 &#181;M for 60 min and then incubated for 24 hr following a 10-fold dilution. Results are gained by measuring the fluorescence of wells after incubation with Resazurin-based cell viability solution (e.g., alamarBlue).
	<ol>
		<li>Prepare compound stock solutions. Weigh out 1 mg of the final purified peptoid product using an analytical balance. Add the appropriate volume of molecular biology grade dimethylsulphoxide (DMSO) to a concentration of 5 mM. Make 6 &#181;l aliquots and freeze at -20 &#176;C.</li>
		<li>Prepare compound solutions on 96 well plates (a recommended plate layout can be seen in the results section, Figure 6) in triplicate from 100 to 3 &#181;M. Add 2 &#181;l of 5 mM stock solution of each compound in the top row (i.e., A). Add 48 &#181;l fresh Schneider&#39;s Insect medium (at pH 5.5 and 20% fetal bovine serum (FBS), 1% penicillin/streptomycin(P/S)) to top row using a multi-channel pipette. Add 25 &#181;l Schneider&#39;s Insect medium to all other rows (B - F).
		<ol>
			<li>Carry out a serial dilution by pipetting 25 &#181;l solution from the top row. Add to the row below and mix. Carry out dilutions until the last row, where the last 25 &#181;l solution should be discarded.</li>
			<li>Use amphotericin B (5 mM stocks) as a positive control and DMSO (2% solution) as a negative control in triplicate.</li>
		</ol>
		</li>
		<li>Prepare parasite solution: transfer culture to a 50 ml centrifuge tube and centrifuge at 447 x g for 5 min. Pour off old medium and add 10 ml Schneider&#39;s Insect medium (at pH 5.5 and 20% FBS, 1% P/S).</li>
		<li>Gently dissolve the pellet of parasites in the new medium using a pipette and count using a Neubauer improved hemocytometer. Dilute culture to 8 x 106 parasites/ml.</li>
		<li>Add 25 &#181;l L. mexicana culture to each well. Incubate plates for 60 min at 32 &#176;C.</li>
		<li>Remove plate from the incubator and remove 40 &#181;l solution from each well.</li>
		<li>Add 90 &#181;l fresh medium and incubate for 24 hr at 32 &#176;C.</li>
		<li>Add 10 &#181;l Resazurin-based cell viability solution to each well. Incubate for 4 hr at 32 &#176;C.</li>
		<li>Measure the fluorescence using a plate reader (&#955;ex = 540 nm, &#955;em = 600 nm), as per manufacturer&#39;s instructions. Analyze data by removing average background (from medium only wells) and comparing the fluorescence of wells after normalization with respect to the DMSO controls.</li>
	</ol>
	</li>
</ol>

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J., Ruchala, P., Hong, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Roles+of+Arginine+and+Lysine+Residues+in+the+Translocation+of+a+Cell-Penetrating+Peptide+from+(13)C,+(31)P+and+(19)F+Solid-State+NMR.">Roles of Arginine and Lysine Residues in the Translocation of a Cell-Penetrating Peptide from (13)C, (31)P and (19)F Solid-State NMR.</a> Biochem. 48, 4587-4595 (2009).</li><li>Andreev, 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=Guanidino+groups+greatly+enhance+the+action+of+antimicrobial+peptidomimetics+against+bacterial+cytoplasmic+membranes.">Guanidino groups greatly enhance the action of antimicrobial peptidomimetics against bacterial cytoplasmic membranes.</a> BBA Biomembranes. 1838, 2492-2502 (2014).</li><li>Foged, C., 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=Cellular+uptake+and+membrane-destabilising+properties+of+alpha-peptide/beta-peptoid+chimeras:+lessons+for+the+design+of+new+cell-penetrating+peptides.">Cellular uptake and membrane-destabilising properties of alpha-peptide/beta-peptoid chimeras: lessons for the design of new cell-penetrating peptides.</a> BBA Biomembranes. 1778, 2487-2495 (2008).</li><li>Vedel, L., 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=Antiplasmodial+and+prehemolytic+activities+of+alpha-peptide-beta-peptoid+chimeras.">Antiplasmodial and prehemolytic activities of alpha-peptide-beta-peptoid chimeras.</a> Chem Bio Chem. 8, 1781-1784 (2007).</li><li>Lear, S., Cobb, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pep-Calc.com:+a+set+of+web+utilities+for+the+calculation+of+peptide+and+peptoid+properties+and+automatic+mass+spectral+peak+assignment.">Pep-Calc.com: a set of web utilities for the calculation of peptide and peptoid properties and automatic mass spectral peak assignment.</a> J Computer-Aided Mol Des. , 1-7 (2016).</li><li>Bates, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complete+developmental+cycle+of+Leishmania+mexicana+in+axenic+culture.">Complete developmental cycle of Leishmania mexicana in axenic culture.</a> Parasitol. 108, 1-9 (1994).</li><li>Gossage, S. M., Rogers, M. E., Bates, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two+separate+growth+phases+during+the+development+of+Leishmania+in+sand+flies:+implications+for+understanding+the+life+cycle.">Two separate growth phases during the development of Leishmania in sand flies: implications for understanding the life cycle.</a> Int J Parasitology. 33, 1027-1034 (2003).</li><li>Seo, J., Lee, B. C., Zuckermann, R. N., Ducheyne, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Comp Biomaterials. 2, 53-76 (2011).</li><li>Nash, I. A., Bycroft, B. W., Chan, W. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dde+-+A+selective+primary+amine+protecting+group:+A+facile+solid+phase+synthetic+approach+to+polyamine+conjugates.">Dde - A selective primary amine protecting group: A facile solid phase synthetic approach to polyamine conjugates.</a> Tetrahedron Lett. 37, 2625-2628 (1996).</li><li>Culf, A. S., Ouellette, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Solid-phase+synthesis+of+N-substituted+glycine+oligomers+(alpha-peptoids)+and+derivatives.">Solid-phase synthesis of N-substituted glycine oligomers (alpha-peptoids) and derivatives.</a> Molecules. 15, 5282-5335 (2010).</li><li>Tran, H., Gael, S. L., Connolly, M. D., Zuckermann, R. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Solid-phase+Submonomer+Synthesis+of+Peptoid+Polymers+and+their+Self-Assembly+into+Highly-Ordered+Nanosheets.">Solid-phase Submonomer Synthesis of Peptoid Polymers and their Self-Assembly into Highly-Ordered Nanosheets.</a> J Vis Exp. , e3373 (2011).</li><li>Burkoth, T. S., Fafarman, A. T., Charych, D. H., Connolly, M. D., Zuckermann, R. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Incorporation+of+unprotected+heterocyclic+side+chains+into+peptoid+oligomers+via+solid-phase+submonomer+synthesis.">Incorporation of unprotected heterocyclic side chains into peptoid oligomers via solid-phase submonomer synthesis.</a> J. Am. Chem. Soc. 125, 8841-8845 (2003).</li><li>Nakayama, G. R., Caton, M. C., Nova, M. P., Parandoosh, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assessment+of+the+Alamar+Blue+assay+for+cellular+growth+and+viability+in+vitro.">Assessment of the Alamar Blue assay for cellular growth and viability in vitro.</a> J Immunol Methods. 204, 205-208 (1997).</li></ol>

The authors have nothing to disclose.

Peptoids are increasingly being studied within the chemical biology and medicinal chemistry fields in applications such as novel therapeutics3-5, cell delivery agents18,20 and diagnostic tools.29 Typically, these sequences are cationic to provide a degree of selectivity for the pathogen over mammalian cells, the ability to penetrate through cell membranes and also aid solubility in aqueous systems. There are numerous examples of cationic peptoids that contain solely lysine- or arginine-mimetic residues in the literature. However, to date, the synthesis of peptoids that contain both of these cationic residues in the same sequence has been hindered by lack of a suitable synthetic procedure. The protocol described here allows mixed cationic peptoids to be synthesized in an efficient manner and is highly desirable as it offers a route to modulate the biological and chemical properties of amphipathic peptoids.
Our method uses an adaptation to the commonly used submonomer peptoid synthesis and permits the addition of both lysine- and arginine-type monomers within the same sequence. It uses room temperature couplings and established protecting group chemistry so it is anticipated that this method will be useful for the majority of research groups. To add orthogonal protection for the arginine-type residue, an unprotected diamine is added under standard displacement conditions and then protected in a 60-minute coupling with Dde-OH. A variety of diamines can be used which allows side chains from 2 carbons to 6 carbons long to be installed, i.e., 1,2-diaminoethane to 1,6-diaminohexane respectively. The protecting Dde-OH dissolves well in DMF and is a very efficient and selective protecting group for primary amines. The Dde-protection group leaves secondary amines unaffected, e.g., the unprotected N terminus of peptoid chain.30 One limitation is that all of the synthesis was undertaken manually; however, it is anticipated that the coupling conditions developed make the method amenable for use with automated peptide/peptoid synthesizers.
The on resin deprotection of the Dde-groups is undertaken using a 2% hydrazine solution in DMF to leave free amines that can be guanidinylated on resin using pyrazole-1-carboxamidine. Six equivalents of the pyrazole-1-carboxamidine and six equivalents of DIPEA are used per free amine on the resin (i.e., six equivalents for each NArg type monomer to be installed). Again, this reaction is also efficient and the pyrazole-1-carboxamidine reagent has good solubility in DMF. Completion of the reaction is typically seen via LC-MS after 60 minutes at room temperature.
Due to the versatility of the submonomer method, a wide variety of primary amines can be used in the displacement step so conditions may need to be optimized to increase coupling efficiency and overall product yields or purity.31 For the sequences discussed above, no special conditions were necessary for successful couplings. However, longer displacement times or higher amine concentrations could be used for problematic displacements (i.e., for poorly nucleophilic or sterically bulky amines). Some amines may not be completely soluble in DMF, in which case it is recommended to dissolve these in N-methyl-2-pyrrolidone (NMP), or other appropriate solvents for solid-phase reactions instead as in a previous comprehensive method for submonomer synthesis of peptoids.32 To incorporate monomers that contain unprotected heteroatoms in the side chains, acetylation using chloroacetic acid has been shown to be effective by other groups.33 Additionally, other resins may be used with this method to yield peptoids with different C terminal functionalization. Wang resins and 2-chlorotrityl chloride resins are routinely used in the submonomer synthesis of peptoids. For example, this method has been successfully used with 2-chlorotrityl chloride resin in our group.2 Different solid supports will require a different loading procedure to Rink Amide discussed here (dependent on the specific resin used) so this should be checked with the literature prior to synthesis.
Similar to peptide synthesis, the conditions for final cleavage of the peptoid off resin can also be optimized for the specific sequence. In this protocol, a TFA cleavage cocktail was used (with triisopropylsilane and water as scavengers). The peptoids presented here contained only Boc protection which is a reasonably acid labile group. To ensure complete deprotection of sequences with a greater proportion of protected residues or less acid labile protecting groups, longer cleavage times may be necessary (i.e., cleavage times in excess of 2 hours are recommended for sequences that contain Pbf or tertiary-butyl ester protected groups). Alternative scavengers can also be used for specialized side chains (for example, ethanedithiol or 2-mercaptoethanol are often used in peptides that have sulphur containing side chains like cysteine or methionine).
The biological assay presented is a standard cytotoxicity test which can be altered to suit different cell lines. It is important to note that each 96-well plate should contain sufficient controls to allow confidence in the results obtained. In this case, amphotericin B is used as a positive control as it is a known drug used to treat the disease and DMSO is used as a negative control as this is the solvent used to make compound stocks for the assay. If other cell lines are being used, alternative, suitable controls should be obtained and validated before use. L. mexicana is incubated with the peptoid at concentrations between 100 and 2 &#181;M for one hour, and then the parasite/peptoid solution is diluted by a factor of ten for overnight incubation (i.e., wells initially with 100 &#181;M peptoid stock are diluted to 10 &#181;M).
The cell viability reagent is added to each well (10% of total well volume) at the end of the assay. A visible color change is seen between wells with viable parasites (pink), control wells with no viable parasites (blue) and a spectrum between with intermediate numbers of viable parasites. The fluorescence is proportional to the number of living cells and corresponds to the metabolic activity of the cells; resazurin dye (non-fluorescent) is converted to the fluorescent resorufin by reduction reactions in metabolically active cells.34 In this assay, the incubation time with the cell viability reagent has been optimized for L. mexicana. Incubation times with the viability reagent will vary for plates seeded at different cell concentrations or with different cell lines (for example this method can also be used with mammalian cells). Dependent on the exact plate reader used, considerations need to be made before fluorescence measurements are taken. Any air bubbles in wells should be removed to ensure accurate readings can be taken. Some plate readers read from the bottom of plates, in which case flat bottomed 96 well plates should be used. Other machines may read from the top of the plate, so the lid of the plate should be removed before measurement.
Finally, in the future, this protocol may be compatible with automated synthesizers that are capable of making many sequences in parallel. Additionally, the synthesis of cyclic peptoids is also possible using this method. This protocol should provide researchers with a practical synthetic procedure that can be used to access novel peptoid scaffolds with both lysine- and arginine-type monomers, which may be of use in many applications, including materials or medicinal fields.

Peptoids (or poly-N-substituted glycines) are a class of peptide-mimetics that offer similar properties to peptides and as such are increasingly being investigated for medicinal and materials applications. In peptides, the side chain of each amino acid is connected to the &#945;-carbon of the amide backbone; in peptoids the side chains are shifted onto the nitrogen atom of the backbone. Crucially, this gives peptoids greater resistance to proteolysis.
Peptoids are commonly synthesized using the submonomer method pioneered by Zuckermann et al., where peptoid monomers can be built by sequential haloacetylation of an amine functionality attached to a solid support and subsequent displacement of the halogen using a primary amine.1 Our group has recently developed an adaptation to this submonomer method to allow lysine- and arginine-type peptoid residues to be included within the same peptoid sequence for the first time.2 This manual solid-phase approach to peptoid synthesis uses commercially available reagents and common laboratory equipment, making it accessible for the majority of laboratories. Peptoids have been shown to have promising activities against a wide range of Gram negative bacteria, Gram positive bacterial and fungal species that are comparable to many known antimicrobial peptides.3-9
In our work, peptoids have been used as novel anti-infective compounds for treatment of the neglected tropical disease leishmaniasis.5,10 Leishmaniasis is endemic in more than 80 countries worldwide and it is estimated that over 12 million people are infected globally.11 The disease is caused by protozoan parasites that are transmitted by the bite of a sandfly. Leishmania species can cause cutaneous leishmaniasis, a condition that leads to scarring and damage to mucous membranes, or the life-threatening visceral leishmaniasis, which causes fatal organ damage. No vaccine is currently available for this disease and existing treatments rely on a small number of drugs that have severe side effects. In addition, resistance to existing drugs is an emerging and serious problem so new treatments are desperately needed to effectively treat leishmaniasis in the future.12-16
In these antimicrobial applications, peptoids are often designed to be amphipathic with a mixture of cationic and hydrophobic monomers.3,4 This can give peptoids a degree of selectivity towards bacterial cells, reduce toxicity to mammalian cells, and to improve their activity as molecular transporters.17-20 The majority of the anti-infective peptoids in the literature contain cationic side chains that are exclusively comprised of either amino functionalized lysine-type monomers or arginine-type residues. Peptide-peptoid chimeras, where the cationic chains are comprised of the amino acids lysine or arginine, have also been synthesized to examine the effect of cationic groups on activity and toxicity.21-25
Poly-lysine peptoids can be easily synthesized using commercially available Boc-protected amines. The poly-arginine peptoids reported can be made using a method which uses pyrazole-1-carboxamidine as a guanidinylation agent.18 However, this can only be undertaken after the peptoid has been cleaved from the resin and Boc protection on side chains removed, so every lysine-type residue within the sequence is transformed into an arginine residue. In an effort to fine tune the chemical and biological properties of the compounds, we developed a method that allows dual cationic functionality (e.g., NLys and NArg) to be included in any given peptoid sequence for the first time.2
Herein, we describe the synthesis, purification and characterization of two novel peptoids that contain both lysine- and arginine-type residues in the same sequence. The method uses orthogonal N-Boc and N-Dde protection on resin with pyrazole-1-carboxamidine as a guanidinylation reagent. The biological evaluation of these peptoids is also described in cytotoxicity assays against Leishmania mexicana, the causative agent of cutaneous leishmaniasis. This provides a practical method to access peptoids with dual cationic functionality and to assess their biological activity. It is expected that this method will aid the synthesis of amphipathic peptoids by the peptoid community in the future.

<table border="0" cellpadding="0" cellspacing="0" width="2269">
	<tbody>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Polypropylene solid phase extraction cartridges with two frits</td>
			<td style="width:144px;">Crawford Scientific</td>
			<td style="width:119px;">12131017 and 12131015</td>
			<td style="width:1791px;">20 mL and 6 mL cartridges used in this preparation</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Trifluoroacetic acid</td>
			<td style="width:144px;">Tokyo Chemical Industry (Europe)</td>
			<td style="width:119px;">T0431-100g</td>
			<td>&#62;98%; CAUTION can cause severe burns and respiratory irritation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">N-N&#39;-diisopropylcarbodiimide</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>38370-100ML</td>
			<td>&#62;98%; CAUTION hazardous to eyes, skin and via respiratory inhalation, may also cause sensitisation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Dimethylformamide</td>
			<td style="width:144px;">Fischer Scientific</td>
			<td align="right" style="width:119px;">10346180</td>
			<td>HPLC grade; CAUTION suspected teratogen</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Acetonitrile</td>
			<td style="width:144px;">Fischer Scientific</td>
			<td align="right" style="width:119px;">10407440</td>
			<td>HPLC grade</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Dichloromethane</td>
			<td style="width:144px;">Fischer Scientific</td>
			<td align="right" style="width:119px;">10354263</td>
			<td>99.8%; CAUTION suspected carcinogen</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Bromacetic acid</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>17000-100G</td>
			<td>&#62;99%; ; CAUTION causes burns and hazardous to skin, eyes and respiratory tract</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">(S)-(-)-alpha methylbenzylamine</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>115568-100G</td>
			<td>98%; CAUTION harmful if swallowed, toxic in contact with skin, causes severe skin burns and eye damage, used to synthesise the Nspe monomer</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">N-Boc 1,4 diaminobutane</td>
			<td style="width:144px;">Tokyo Chemical Industry (Europe)</td>
			<td style="width:119px;">A1373-25g</td>
			<td>&#62;98%; CAUTION causes severe skin burns and eye damage, used to synthesise the NLys monomer</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">N-Boc 1,2 diaminoethane</td>
			<td style="width:144px;">Tokyo Chemical Industry (Europe)</td>
			<td>A1371-25g</td>
			<td>&#62;97%; CAUTION causes severe skin burns and eye damage, used to synthesise the Nae monomer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">1,2 diaminobutane</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>D13208-100G</td>
			<td>99%; CAUTION flammable liquid and vapour, harmful if swallowed or inhaled, toxic in contact with skin, causes severe skin burns and eye damage, used in the synthesis of the NhArg monomer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">1,4 diaminoethane</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>03550-250ML</td>
			<td>&#62;99.5%; CAUTION flammable liquid and vapour, harmful if swallowed or inhaled, toxic in contact with skin, causes severe skin burns and eye damage, used in the synthesis of the NnArg monomer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">1H-pyrazole-1-carboxamidine HCl</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>402516-10G</td>
			<td>as HCl salt; CAUTION harmful if swallowed and may cause an allergic skin reaction, causes serious eye damage</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Hydrazine monohydrate</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>207942-5G</td>
			<td>reagent grade; CAUTION suspected carcinogen, fatal if inhaled and causes severe burns to skin and eyes</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">2-acetyl dimedone</td>
			<td style="width:144px;">Novabiochem</td>
			<td align="right">8510150005</td>
			<td>Dde-OH</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Rink Amide resin</td>
			<td style="width:144px;">Novabiochem</td>
			<td align="right">8551190005</td>
			<td>100-200 mesh, high loading&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Piperidine</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>411027-1L</td>
			<td>&#62;99.5%, a controlled substance, so adequate permission must be obtained before purchase; CAUTION highly flammable liquid and vapour, harmful if swallowed and toxic in contact with skin or if inhaled, causes severe skin burns and eye damage, harmful to aquatic life with long lasting effects</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Triisopropylsilane</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>233781-50G</td>
			<td>98%; CAUTION flammable liquid and vapour, causes skin irritation and serious eye irritation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">alamarBlue</td>
			<td style="width:144px;">ThermoFischer&#160;</td>
			<td style="width:119px;">DAL1025</td>
			<td>Not classified as hazardous</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Schneider&#39;s Insect Medium</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>S9895-1L</td>
			<td>Powdered, medium must be made prior to use following manafacturers instructions; allow to warm to room temperature before use in biological assays</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">96 well plates</td>
			<td style="width:144px;">VWR</td>
			<td style="width:119px;">734-1793</td>
			<td>Flat bottom (to allow fluorescence measurement from the bottom), tissue-culture treated</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Solvent reservoirs</td>
			<td style="width:144px;">VWR</td>
			<td>613-1182</td>
			<td>Used with multi channel pipette</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Multi channel pipette</td>
			<td style="width:144px;">Eppendorf</td>
			<td align="right" style="width:119px;">3122000043</td>
			<td style="width:1791px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Pipette tips</td>
			<td style="width:144px;">Starlab Group</td>
			<td>S1111-3810, S1113-1810, S1111-6810</td>
			<td>Volume of tip dependent on pipette used. 10 &#181;L, 10 - 200 &#181;L and 1000 &#181;L recommended for assays</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">25 cm3 cell culture flasks</td>
			<td style="width:144px;">VWR</td>
			<td style="width:119px;">734-2312</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">50 mL centrifuge tubes</td>
			<td style="width:144px;">VWR</td>
			<td style="width:119px;">525-0791</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;width:216px;">dimethylsulphoxide (molecular biology grade)</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>D8418-50ML</td>
			<td>Not classified as hazardous</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Heat Inactivated Fetal Bovine Serum</td>
			<td style="width:144px;">ThermoFischer&#160;</td>
			<td style="width:119px;">10082139-100mL</td>
			<td>Gibco</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Penicillin/Streptomycin</td>
			<td style="width:144px;">ThermoFischer&#160;</td>
			<td style="width:119px;">15140148-20mL</td>
			<td style="width:1791px;">Abbreviation: P/S</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Amphotericin B</td>
			<td style="width:144px;">Sigma Aldrich</td>
			<td>46006-100mg</td>
			<td>Amphotericin B trihydrate, VetranalTM analytical standard</td>
		</tr>
	</tbody>
</table>

an efficient method for the synthesis of peptoids with mixed lysine-type/arginine-type monomers and evaluation of their anti-leishmanial activity

This protocol describes the manual solid-phase synthesis of linear peptoids that contain two differently functionalized cationic monomers. In this procedure amino functionalized 'lysine' and guanido functionalized 'arginine' peptoid monomers can be included within the same peptoid sequence. This procedure uses on-resin (N-(1-(4,4-dimethyl-2,6-dioxocyclohexylidene)ethyl) or Dde protection, orthogonal conditions to the Boc protection of lysine monomers. Subsequent deprotection allows an efficient on-resin guanidinylation reaction to form the arginine residues. The procedure is compatible with the commonly used submonomer method of peptoid synthesis, allowing simple peptoids to be made using common laboratory equipment and commercially available reagents. The representative synthesis, purification and characterization of two mixed peptoids is described. The evaluation of these compounds as potential anti-infectives in screening assays against Leishmania mexicana is also described. The protozoan parasite L. mexicana is a causative agent of cutaneous leishmaniasis, a neglected tropical disease that affects up to 12 million people worldwide.

As a representative result, the synthesis and characterization of two 12 residue peptoids containing two lysine-type monomers and two-arginine type monomers each will be described. The subsequent results from cytotoxicity assay are also shown.
Two peptoids [(NnArgNspeNspe)(NaeNspeNspe)]2 (a) and [(NhArgNspeNspe)(NLysNspeNspe)]2 (b) were synthesized using 120 mg Rink Amide resin each (loading = 0.79 mmol/g). All acetylation and displacement steps were carried out as described above, with all reagents purchased commercially. For these residues, the following amines were used in the displacement step: Nspe (S)-(-)-&#945;-methylbenzylamine, Nae N-(tert-butoxycarbonyl)-1,2-diaminoethane, NLys N-(tert-butoxycarbonyl)-1,4-diaminobutane. For the arginine derivative residues, the following unprotected diamines were coupled: NhArg 1,4-diaminobutane or NnArg 1,2-diaminoethane, followed by on-resin protection with 2-acetyldimedone (Dde-OH). After the entire sequence had been synthesized, hydrazine deprotection of the Dde yields free amines to guanidinylate.
<img alt="Figure 1" src="/files/ftp_upload/54750/54750fig1.jpg" /> 
Figure 1. Peptoid structures (a) [(NnArgNspeNspe)(NaeNspeNspe)]2 and (b)&#160;[(NhArgNspeNspe)(NLysNspeNspe)]2. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54750/54750fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/54750/54750fig2.jpg" /> 
Figure 2. The method used to synthesize mixed arginine/lysine peptoids.&#160;i. Standard displacement step in the submonomer method with diamine; ii. Addition of Dde-OH, 90 minutes to protect free amine; iii. Further additions to extend the peptoid chain using the submonomer method; iv. Deprotection of Dde using 2% hydrazine in DMF; v. Guanidinylation of free amine on resin with pyrazole-1-carboxamidine and DIPEA in DMF; vi. Acidic cleavage from the resin and deprotection of Boc groups. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54750/54750fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Following cleavage from the resin and lyophilization, the crude products were obtained as white powders: (a) 154 mg, (b) 163 mg. Products were purified via RP-HPLC as described with maximum 50 mg injections using a LC pump with a UV-vis detector (&#955; = 250 nm) on an analytical column, 250 mm x 10 mm, 5 &#181;m; flow rate = 2 ml/min. Fractions corresponding to the target mass were combined and obtained as white powders: (a) 54 mg (b) 65 mg, final yields of approximately 30% for fractions &#62;90% pure.
The final compound identities after purification were confirmed by LC-MS (see Figure 3) using a triple quadrupole mass spectrometer equipped with an UPLC and a photodiode array detector. Accurate mass spectrometry was undertaken using the same spectrometer on the [M+2H]2+ ions. The following calculated and observed masses were found in close agreement (Figure 4): (a) calculated = 896.0026 amu, observed = 896.0038 amu; (b) calculated = 952.0691 amu, observed = 952.0730 amu.
<img alt="Figure 3" src="/files/ftp_upload/54750/54750fig3.jpg" /> 
Figure 3. LC-MS for purified peptoids. (a) m/z = 1,792 and (b) m/z = 1,903. Where the top is TIC, middle LC-MS spectrum, bottom UV chromatogram at 220 nm. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54750/54750fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" src="/files/ftp_upload/54750/54750fig4.jpg" /> 
Figure 4. Accurate mass spectrometry data for peptoids (a) and (b). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54750/54750fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Product purity was assessed using an analytical RP-HPLC (LC pump with a UV-vis detector on an analytical column, 4.6 mm x 100 mm, 3.5 &#181;m; flow rate = 1 ml/min), and visualized at 220 nm, the absorbance of amide backbone. Figure 5a and 5b shows that the compounds are homogeneous.
<img alt="Figure 5" src="/files/ftp_upload/54750/54750fig5.jpg" /> 
Figure 5. Analytical HPLC for the purified peptoids (a) and (b). There is a gradient 0-100% B over 30 minutes, column oven at 40 &#176;C (A = 95% H2O, 5% MeCN, 0.05% TFA; B = 95% MeCN, 5% H2O, 0.03% TFA). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54750/54750fig5large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The purified peptoids (a) and (b) were tested in cytotoxicity assays against L. mexicana axenic amastigotes. Frozen stocks of L. mexicana were defrosted and transformed to the amastigote stage ready for the assay. 72 hours after defrosting, the parasites should be insect stage promastigotes in their procyclic form, in log phase with many dividing cells. At this stage the parasites can be transformed into the amastigote stage using the pH and temperature shift described.27 At Day 9 of the transformation, the parasites will be in the non-replicating infectious metacyclic promastigote stage. Finally at Day 14, the parasites should be in the pathogenic amastigote stage where parasites lack the characteristic flagella of the promastigotes.28
5 mM stock solutions of the compounds were made in cell culture grade DMSO and tested in triplicates on a minimum of two occasions to ensure a robust data set was collected. A representative 96-well plate plan is shown in Figure 6. At the end of the assay, the cell viability reagent was added to each well and the fluorescence was measured as described to calculate the viability of parasites at each concentration tested (see Figure 7). ED50 values were calculated as peptoid (a) &#62;100 &#181;M and peptoid (b) 37 &#181;M respectively. The error bars plotted, show the variation between wells as a standard deviation and it can be seen that these are reasonable for most bars.
<img alt="Figure 6" src="/files/ftp_upload/54750/54750fig6.jpg" /> 
Figure 6. Representative 96 well plate plan for a cytotoxicity assay on 2 peptoid solutions (including positive and negative controls). med+ = medium (Schneider&#39;s Insect Medium, pH 5.5, 20% FBS, 1% P/S). L. mex. = 8 x 106/ml parasite culture in med+. AmphoB = 5 mM in DMSO. Peptoid = 5 mM stock solution in DMSO. Empty wells should contain sterile water. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54750/54750fig6large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 7" src="/files/ftp_upload/54750/54750fig7.jpg" /> 
Figure 7. Results from cytotoxicity assay against L. mexicana axenic amastigote parasites using peptoid (a) and (b).&#160;It can be seen that the peptoid (b) is more effective than peptoid (a) at reducing the percentage of viable parasites, with both compounds having a dose dependent effect. The error bars plotted show the variation between wells as a standard deviation. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54750/54750fig7large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about An Efficient Method for the Synthesis of Peptoids with Mixed Lysine-type/Arginine-type Monomers and Evaluation of Their Anti-leishmanial Activity at JoVE.com

An Efficient Method for the Synthesis of Peptoids with Mixed Lysine-type/Arginine-type Monomers and Evaluation of Their Anti-leishmanial Activity

A protocol to synthesize peptoids with mixed cationic functionality in the same sequence is presented (lysine- and arginine-type monomers). Subsequent testing of these compounds against Leishmania mexicana, the protozoan parasites that cause cutaneous leishmaniasis, is also described.

This protocol describes the manual solid-phase synthesis of linear peptoids that contain two differently functionalized cationic monomers. In this ...

an-efficient-method-for-synthesis-peptoids-with-mixed-lysine

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JoVE Journal

Biochemistry

12.0K Views.  Durham University. A protocol to synthesize peptoids with mixed cationic functionality in the same sequence is presented (lysine- and arginine-type monomers). Subsequent testing of these compounds against Leishmania mexicana, the protozoan parasites that cause cutaneous leishmaniasis, is also described.

Video: An Efficient Method for the Synthesis of Peptoids with Mixed Lysine-type/Arginine-type Monomers and Evaluation of Their Anti-leishmanial Activity

Preparation and In Vivo Use of an Activity-based Probe for N-acylethanolamine Acid Amidase

Activity-based protein profiling (ABPP) is a method for the identification of an enzyme of interest in a complex proteome through the use of a chemical probe that targets the enzyme&#39;s active sites. A reporter tag introduced into the probe allows for the detection of the labeled enzyme by in-gel fluorescence scanning, protein blot, fluorescence microscopy, or liquid chromatography-mass spectrometry. Here, we describe the preparation and use of the compound ARN14686, a click chemistry activity-based probe (CC-ABP) that selectively recognizes the enzyme N-acylethanolamine acid amidase (NAAA). NAAA is a cysteine hydrolase that promotes inflammation by deactivating endogenous peroxisome proliferator-activated receptor (PPAR)-alpha agonists such as palmitoylethanolamide (PEA) and oleoylethanolamide (OEA). NAAA is synthesized as an inactive full-length proenzyme, which is activated by autoproteolysis in the acidic pH of the lysosome. Localization studies have shown that NAAA is predominantly expressed in macrophages and other monocyte-derived cells, as well as in B-lymphocytes. We provide examples of how ARN14686 can be used to detect and quantify active NAAA ex vivo in rodent tissues by protein blot and fluorescence microscopy.

Preparation and In Vivo Use of an Activity-based Probe for N-acylethanolamine Acid Amidase

Here, we describe the preparation and use of an activity-based probe (ARN14686, undec-10-ynyl-N-[(3S)-2-oxoazetidin-3-yl]carbamate) that allows for the detection and quantification of the active form of the proinflammatory enzyme N-acylethanolamine acid amidase (NAAA), both in vitro and ex vivo.

Activity-based protein profiling (ABPP) is a method for the identification of an enzyme of interest in a complex proteome through the use of a chemical ...

A Facile and Efficient Approach for the Production of Reversible Disulfide Cross-linked Micelles

Nanomedicine is an emerging form of therapy that harnesses the unique properties of particles that are nanometers in scale for biomedical application. Improving drug delivery to maximize therapeutic outcomes and to reduce drug-associated side effects are some of the cornerstones of present-day nanomedicine. Nanoparticles in particular have found a wide application in cancer treatment. Nanoparticles that offer a high degree of flexibility in design, application, and production based on the tumor microenvironment are projected to be more effective with rapid translation into clinical practice. The polymeric micellar nano-carrier is a popular choice for drug delivery applications.
In this article, we describe a simple and effective protocol for synthesizing drug-loaded, disulfide cross-linked micelles based on the self-assembly of a well-defined amphiphilic linear-dendritic copolymer (telodendrimer, TD). TD is composed of polyethylene glycol (PEG) as the hydrophilic segment and a thiolated cholic acid cluster as the core-forming hydrophobic moiety attached stepwise to an amine-terminated PEG using solution-based peptide chemistry. Chemotherapy drugs, such as paclitaxel (PTX), can be loaded using a standard solvent evaporation method. The O2-mediated oxidation was previously utilized to form intra-micellar disulfide cross-links from free thiol groups on the TDs. However, the reaction was slow and not feasible for large-scale production. Recently, an H2O2-mediated oxidation method was explored as a more feasible and efficient approach, and it was 96 times faster than the previously reported method. Using this approach, 50 g of PTX-loaded, disulfide cross-linked nanoparticles have been successfully produced with narrow particle size distribution and high drug loading efficiency. The stability of the resulting micelle solution is analyzed using disrupting conditions such as co-incubation with a detergent, sodium dodecyl sulfate, with or without a reducing agent. The drug-loaded, disulfide cross-linked micelles demonstrated less hemolytic activity when compared to their non-cross-linked counterparts.

To deliver cancer drugs to tumor sites with high specificity and reduced side effects, new methods based on nanoparticles are required. Here, we describe disulfide cross-linked micelles that can be easily prepared by hydrogen peroxide-mediated oxidation and are able to dissociate efficiently under a reducing tumor environment to release payloads.

Nanomedicine is an emerging form of therapy that harnesses the unique properties of particles that are nanometers in scale for biomedical application. ...

An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Plant seeds accumulate large amounts of storage reserves comprising biodegradable organic matter. Humans rely on seed storage reserves for food and as industrial materials. Gene expression profiles are powerful tools for investigating metabolic regulation in plant cells. Therefore, detailed, accurate gene expression profiles during seed development are required for crop breeding. Acquiring highly purified RNA is essential for producing these profiles. Efficient methods are needed to isolate highly purified RNA from seeds. Here, we describe a method for isolating RNA from seeds containing large amounts of oils, proteins, and polyphenols, which have inhibitory effects on high-purity RNA isolation. Our method enables highly purified RNA to be obtained from seeds without the use of phenol, chloroform, or additional processes for RNA purification. This method is applicable to Arabidopsis, rapeseed, and soybean seeds. Our method will be useful for monitoring the expression patterns of low level transcripts in developing and mature seeds.

We have succeeded in establishing a method for RNA isolation from plant seeds containing large amounts of oils, proteins, and polyphenols, which have inhibitory effects on high-purity RNA isolation. Our method is suitable for monitoring the expression of genes with low level transcripts in seeds.

Plant seeds accumulate large amounts of storage reserves comprising biodegradable organic matter. Humans rely on seed storage reserves for food and as ...

Synthesis of 1,2-Azaborines and the Preparation of Their Protein Complexes with T4 Lysozyme Mutants

We describe a general synthesis of 1,2-azaborines using standard air-free techniques and protein complex preparation with T4 lysozyme mutants by vapor diffusion. Oxygen- and moisture-sensitive compounds are prepared and isolated under an inert atmosphere (N2) using either a vacuum gas manifold or a glove box. As an example of azaborine synthesis, we demonstrate the synthesis and purification of the volatile N-H-B-ethyl-1,2-azaborine by a five-step sequence involving distillation and column chromatography for the isolation of products. T4 lysozyme mutants L99A and L99A/M102Q are expressed with Escherichia coli RR1 strain. Standard protocols for chemical cell lysis followed by purification using carboxymethyl ion exchange column affords protein of sufficiently high purity for crystallization. Protein crystallization is performed in various concentrations of precipitant at different pH ranges using the hanging drop vapor diffusion method. Complex preparation with the small molecules is carried out by vapor diffusion method under an inert atmosphere. X-ray diffraction analysis of the crystal complex provides unambiguous structural evidence of binding interactions between the protein binding site and 1,2-azaborines.

A protocol for the synthesis of 1,2-azaborines and the preparation of their protein complexes with T4 lysozyme mutants is presented.

We describe a general synthesis of 1,2-azaborines using standard air-free techniques and protein complex preparation with T4 lysozyme mutants by vapor ...

Rab10 Phosphorylation Detection by LRRK2 Activity Using SDS-PAGE with a Phosphate-binding Tag

Mutations in leucine-rich repeat kinase 2 (LRRK2) have been shown to be linked with familial Parkinson&#39;s disease (FPD). Since abnormal activation of the kinase activity of LRRK2 has been implicated in the pathogenesis of PD, it is essential to establish a method to evaluate the physiological levels of the kinase activity of LRRK2. Recent studies revealed that LRRK2 phosphorylates members of the Rab GTPase family, including Rab10, under physiological conditions. Although the phosphorylation of endogenous Rab10 by LRRK2 in cultured cells could be detected by mass spectrometry, it has been difficult to detect it by immunoblotting due to the poor sensitivity of currently available phosphorylation-specific antibodies for Rab10. Here, we describe a simple method of detecting the endogenous levels of Rab10 phosphorylation by LRRK2 based on immunoblotting utilizing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) combined with a phosphate-binding tag (P-tag), which is N-(5-(2-aminoethylcarbamoyl)pyridin-2-ylmetyl)-N,N&#39;,N&#39;-tris(pyridin-2-yl-methyl)-1,3-diaminopropan-2-ol. The present protocol not only provides an example of the methodology utilizing the P-tag but also enables the assessment of how mutations as well as inhibitor treatment/administration or any other factors alter the downstream signaling of LRRK2 in cells and tissues.

The present study describes a simple method of detecting endogenous levels of Rab10 phosphorylation by leucine-rich repeat kinase 2.

Mutations in leucine-rich repeat kinase 2 (LRRK2) have been shown to be linked with familial Parkinson&#39;s disease (FPD). Since abnormal activation of ...

Highly Sensitive and Quantitative Detection of Proteins and Their Isoforms by Capillary Isoelectric Focusing Method

Immunoblotting has become a routine technique in many laboratories for protein characterization from biological samples. The following protocol provides an alternative strategy, capillary isoelectric focusing (cIEF), with many advantages compared to conventional immunoblotting. This is an antibody-based, automated, rapid, and quantitative method in which a complete western blotting procedure takes place inside an ultrathin capillary. This technique does not require a gel to transfer to a membrane, stripping of blots, or x-ray films, which are typically required for conventional immunoblotting. Here, proteins are separated according to their charge (isoelectric point; pI), using less than a microliter (400 nL) of total protein lysate. After electrophoresis, proteins are immobilized onto the capillary walls by ultraviolet light treatment, followed by primary and secondary (horseradish peroxidase (HRP) conjugated) antibody incubation, whose binding is detected through enhanced chemiluminescence (ECL), generating a light signal that can be captured and recorded by a charge-coupled device (CCD) camera. The digital image can be analyzed and quantified (peak area) using software. This high throughput procedure can handle 96 samples at a time; is highly sensitive, with protein detection in the picogram range; and produces highly reproducible results because of automation. All of these aspects are extremely valuable when the quantity of samples (e.g., tissue samples and biopsies) is a limiting factor. The technique has wider applications as well, including screening of drugs or antibodies, biomarker discovery, and diagnostic purposes.

Capillary isoelectric focusing is an antibody-based, ultrasensitive, high throughput technique, enabling detailed characterization of proteins and their isoforms from extremely small biological samples. The following describes a protocol for detection and quantification of specific proteins and their isoforms in an automated and robotized manner.

Immunoblotting has become a routine technique in many laboratories for protein characterization from biological samples. The following protocol provides ...

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be greatly facilitated by the production of milligram amounts of pure, folded ligand binding domains. Attempts to heterologously express periplasmic ligand binding domains of bacterial chemoreceptors in Escherichia coli (E. coli) often result in their targeting into inclusion bodies. Here, a method is presented for protein recovery from inclusion bodies, its refolding and purification, using the periplasmic dCACHE ligand binding domain of Campylobacter jejuni (C. jejuni) chemoreceptor Tlp3 as an example. The approach involves expression of the protein of interest with a cleavable His6-tag, isolation and urea-mediated solubilisation of inclusion bodies, protein refolding by urea depletion, and purification by means of affinity chromatography, followed by tag removal and size-exclusion chromatography. The circular dichroism spectroscopy is used to confirm the folded state of the pure protein. It has been demonstrated that this protocol is generally useful for production of milligram amounts of dCACHE periplasmic ligand binding domains of other bacterial chemoreceptors in a soluble and crystallisable form.

A procedure is presented for the refolding of the dCACHE periplasmic ligand binding domain of Campylobacter jejuni chemoreceptor Tlp3 from inclusion bodies and the purification to yield milligram quantities of protein.

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be ...

Enrichment of Native Lipoprotein Particles with microRNA and Subsequent Determination of Their Absolute/Relative microRNA Content and Their Cellular Transfer Rate

Lipoprotein particles are predominately transporters of lipids and cholesterol in the bloodstream. Furthermore, they contain small amounts of strands of noncoding microRNA (miRNA). In general, miRNA alters the protein expression profile due to interactions with messenger-RNA (mRNA). Thus, knowledge of the relative and absolute miRNA content of lipoprotein particles is essential to estimate the biological effect of cellular particle uptake. Here, a quantitative real-time polymerase chain reaction (qPCR)-based protocol is presented to determine the absolute miRNA content of lipoprotein particles&#8212;exemplified shown for native and miRNA-enriched lipoprotein particles. The relative miRNA content is quantified using multiwell microfluidic array cards. Furthermore, this protocol allows scientists to estimate the cellular miRNA and, thus, the lipoprotein particle uptake rate. A significant increase of the cellular miRNA level is observable when using high-density lipoprotein (HDL) particles artificially loaded with miRNA, whereas incubation with native HDL particles yields no significant effect due to their rather low miRNA content. In contrast, the cellular uptake of low-density lipoprotein (LDL) particles&#8212;neither with native miRNA nor artificially loaded with it&#8212;did not alter the cellular miRNA level.

Here, a quantitative real-time polymerase chain reaction-based protocol is presented for the determination of the native micro-RNA content (absolute/relative) of lipoprotein particles. In addition, a method for increasing the micro-RNA level, as well as a method for determining the cellular uptake rate of lipoprotein particles, is demonstrated.

Lipoprotein particles are predominately transporters of lipids and cholesterol in the bloodstream. Furthermore, they contain small amounts of strands of ...

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Chromatin is a higher-order structure that packages eukaryotic DNA. Chromatin undergoes dynamic alterations according to the cell cycle phase and in response to environmental stimuli. These changes are essential for genomic integrity, epigenetic regulation, and DNA metabolic reactions such as replication, transcription, and repair. Chromatin assembly is crucial for chromatin dynamics and is catalyzed by histone chaperones. Despite extensive studies, the mechanisms by which histone chaperones enable chromatin assembly remains elusive. Moreover, the global features of nucleosomes organized by histone chaperones are poorly understood. To address these problems, this work describes a unique single-molecule imaging technique named DNA curtain, which facilitates the investigation of the molecular details of nucleosome assembly by histone chaperones. DNA curtain is a hybrid technique that combines lipid fluidity, microfluidics, and total internal reflection fluorescence microscopy (TIRFM) to provide a universal platform for real-time imaging of diverse protein-DNA interactions.Using DNA curtain, the histone chaperone function of Abo1, the Schizosaccharomyces pombe bromodomain-containing AAA+ ATPase, is investigated, and the molecular mechanism underlying histone assembly of Abo1 is revealed. DNA curtain provides a unique approach for studying chromatin dynamics.

DNA curtain, a high-throughput single-molecule imaging technique, provides a platform for real-time visualization of diverse protein-DNA interactions. The present protocol utilizes the DNA curtain technique to investigate the biological role and molecular mechanism of Abo1, a Schizosaccharomyces pombe bromodomain-containing AAA+ ATPase.

Chromatin is a higher-order structure that packages eukaryotic DNA. Chromatin undergoes dynamic alterations according to the cell cycle phase and in ...

A Nanobar-Supported Lipid Bilayer System for the Study of Membrane Curvature Sensing Proteins in vitro

Membrane curvature plays important roles&#160;in various essential processes of cells, such as cell migration, cell division, and vesicle trafficking. It is not only passively generated by cellular activities, but also actively regulates protein interactions and is involved in many intracellular signaling. Thus, it is of great value to examine the role of membrane curvature in regulating the distribution and dynamics of proteins and lipids. Recently, many techniques have been developed to study the relationship between the curved membrane and protein in vitro. Compared to traditional techniques, the newly developed nanobar-supported lipid bilayer (SLB) offers both high-throughput and better accuracy in membrane curvature generation by forming a continuous lipid bilayer on patterned arrays of nanobars with a pre-defined membrane curvature and local flat control. Both the lipid fluidity and protein sensitivity to curved membranes can be quantitatively characterized using fluorescence microscopy imaging. Here, a detailed procedure on how to form a SLB on fabricated glass surfaces containing nanobar arrays&#160;and the characterization of curvature-sensitive proteins on such SLB are introduced. In addition, protocols for nanochip reusing and image processing are covered. Beyond the nanobar-SLB, this protocol is readily applicable to all types of nanostructured glass chips for curvature sensing studies.

A Nanobar-Supported Lipid Bilayer System for the Study of Membrane Curvature Sensing Proteins in vitro

Here, a nanobar-supported lipid bilayer system is developed to provide a synthetic membrane with a defined curvature that enables the characterization of proteins with curvature sensing ability in vitro.

Membrane curvature plays important roles&#160;in various essential processes of cells, such as cell migration, cell division, and vesicle trafficking. It ...