Thiol | EPFL Graph Search

In organic chemistry, a thiol ('θaɪɒl; ), or thiol derivative, is any organosulfur compound of the form , where R represents an alkyl or other organic substituent. The functional group itself is referred to as either a thiol group or a sulfhydryl group, or a sulfanyl group. Thiols are the sulfur analogue of alcohols (that is, sulfur takes the place of oxygen in the hydroxyl () group of an alcohol), and the word is a blend of "thio-" with "alcohol". Many thiols have strong odors resembling that of garlic or rotten eggs. Thiols are used as odorants to assist in the detection of natural gas (which in pure form is odorless), and the "smell of natural gas" is due to the smell of the thiol used as the odorant. Thiols are sometimes referred to as mercaptans (mərˈkæptæn) or mercapto compounds, a term introduced in 1832 by William Christopher Zeise and is derived from the Latin mercurio captāns ('capturing mercury') because the thiolate group () bonds very strongly with mercury compounds.

New methods for developing (bi)cyclic peptides by phage display

Camille Villequey

Cyclic peptide ligands are a promising molecular format for the development of therapeutics. They combine some of the advantages of large protein therapeutics (high affinity and specificity) and of small molecule drugs (accessibility to chemical synthesis and low immunogenicity). With phage display, large combinatorial libraries of more than one billion mono- and polycyclic peptides can be developed and screened against virtually any target. During phage affinity selections, the physical link between phenotype (encoded peptide) and genotype (phage DNA) allows the identification of enriched peptide binders by sequencing of the phage vector DNA. Based on these concepts, our laboratory has established a robust chemistry in which phage displayed peptides containing two or three cysteines are cyclized or bi-cyclized with thiol-reactive linkers. This procedure has been generally applied for the isolation of potent and selective (bi)cyclic peptide ligands with therapeutic potential. The isolation of binders with optimal properties is highly dependent on the possibility to generate (bi)cyclic peptide libraries with high structural diversity and on the ability to thoroughly decode the phage selection output. In my PhD work, I developed new methods to generate large and structurally diverse libraries and to decode more efficiently phage selected peptides. In my first project, I explore the cyclization of peptides with two chemical bridges as a method to provide rapid access to phage-encoded libraries with high scaffold diversity. To this end, a range of twelve structurally diverse chemicals were tested for thiol-reactivity and phage compatibility. Subsequently, peptide libraries of the format XCXnCXnCX (X = random amino acid, C = cysteine, n = 3 or 4) were cyclized with six of these chemical linkers and panned against the protease plasma kallikrein. The selection yielded inhibitors with remarkable affinity (sub-nM KI), target selectivity (>1000-fold) and proteolytic stability (t1/2 in plasma > 3 days) despite a relatively small molecular mass (~ 1200 Da). In the second project, I developed phage-encoded libraries of small cyclic peptides in order to identify ligands that have the potential to be orally absorbed. A major challenge for the generation of such library is the usually low diversity of compounds due to the limited number of amino acids. In this work, we addressed this limitation by taking advantage of a recently discovered peptide cyclization reaction in which the thiol of a cysteine is ligated with the N-terminal amino group using a chemical reagent. We applied this strategies to two phage-encoded peptide libraries of four and five amino acids (XXXC and XXXXC) that were cyclized with eight chemical linkers yielding a collection of more than 1.3 million compounds. Panning the libraries against the two disease targets plasma kallikrein and coagulation factor XIa yielded ligands with single-digit micromolar affinity. In a third project, I developed a strategy to bypass the bacterial infection step in phage display. Bacterial infection is usually crucial for the propagation and identification of enriched clones by DNA sequencing. However, mutations or chemical modifications of the phage coat proteins, sometimes lead to decreased infection rates and therefore compromise the entire procedure. Consequently, there is an interest for developing methods in which this step could be completely omitted.

EPFL2017

A new non-toxic chemically cross-linked ELP hydrogel for in situ protein delivery

Karine Ciapala

Proteins play an essential role in all biological processes and have been attracting more and more attention as drug candidates due to their high specificity and activity. However, their use as therapeutics has been seriously held back given that their ability to be effectively and conveniently delivered is problematic. Indeed, simple oral administration is ineffective since proteins are degraded in the digestive tract. Until now, these therapeutic agents were delivered by infusions or frequent injections. But this causes serious problems, as the compound does not get delivered in a prolonged continuous manner. Additionally, injections are also problematic as patients are reluctant to use needles unless there illness is life threatening. That is why focus has grown over the last years on developing novel delivery systems for proteins. Amongst the various types of delivery systems that exist, hydrogel based ones are very promising, as they possess remarkable biomimetic properties. The hydrogels that are chemically cross-linked are stronger than their counterparts, the physical hydrogels. An appealing approach to protein delivery that is more and more sought is to form the hydrogel in situ from an injected aqueous polymer solution and to use the formed gel as a depot for the sustained release of the protein. Oxygen sensitive gellation is an interesting stimulus to form these gels, but has not been successfully developed, as the gelling kinetics are too slow. Therefore, research groups have turned to the use of toxic chemicals to speed up the reaction. Elastin-like poylpeptides (ELP) are artificial biopolymers that are composed of a pentapeptide repeat. This repeat consists of Val-Pro-Gly-Xaa-Gly, where Xaa denotes a guest residue. An interesting characteristic of ELPs is that they are thermally responsive. Meaning, that when in solution they go through a lower critical solution temperature (LCST) transition. Below their LCST they are soluble in water and above their LCST they are insoluble. ELPs are well suited for drug delivery applications for many reasons such as their biocompatibility. The ELP that is studied is ELP9 Gel. Its guest residues are Val, Ala and Cys in a ratio of 1:14:1 respectively. As this ELP has cysteines it has the capacity to form a gel via cross-linking of the thiols groups by oxidation. The rheological tests that were carried out showed that this ELP9 Gel has all the characteristics of a gel. Furthermore, its gelling kinetics were greatly increased by heating it, but still remain too long for in situ applications. This suggests that the LCST behaviour of ELPs seems to play some role in favouring the cross-linking. But further controls remain to be done to confirm this hypothesized tandem process. A delivery strategy that involved this ELP9 Gel and Blue Fluorescent Proteins (BFP) with added cysteines was not successful as the molecular biology to obtain the modified proteins failed. However, the elaboration of a fusion peptide between Glucagon-Like-Peptide-1 (GLP-1) and ELP9 Gel was accomplished. The preliminary activity assay showed a reduced activity in comparison to the GLP-1 peptide alone. Unfortunately this ELP9 Gel has a setback due to its slow gelling time. Therefore, before continuing the research on the delivery strategies, it would be wiser to create a better ELP. If a new ELP with a higher cysteine concentration and lower transition temperature can be created, its gelling kinetics may be favourable for in situ protein delivery applications and thus, a chemically cross-linked hydrogel that does not require any toxic cross-linker would be available. This would be a big step in creating a very robust hydrogel for protein delivery applications but also for tissue regeneration

2009

Stability and physical properties of alkylsilane and alkylphosphonate self-assembled monolayer (SAM) films on metal oxide substrates characterized at the micro- and nanoscale

Enamul Hoque

Self-assembled monolayer (SAM) films have attracted immense attention for both fundamental and applied research. A SAM is composed of a large number of molecules with a head group that chemisorbs onto a substrate, a tail group that interacts with the outer surface of the film, and a spacer (backbone) chain group that connects the head and tail groups resulting in a coating. Interactions between spacer groups of different molecules, such as van der Waals forces and/or hydrogen bonding, hasten SAM film formation and contribute to its stability. In this dissertation, SAM and thin films have been formed onto copper and aluminum oxide surfaces by reaction with 1H,1H,2H,2H-perfluorodecyldimethylchlorosilane (PFMS), 1H,1H,2H,2H-perfluorodecyltrichlorosilane (PFTS), 1H,1H,2H,2H-perfluorodecylphosphonic acid (PFDP), octylphosphonic acid (OP), decylphosphonic acid (DP), and octadecylphosphonic acid (ODP). The properties and stability of the films were investigated employing complementary surface analysis techniques: X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), friction force microscopy (FFM), a derivative of AFM, contact angle measurements (CAMs), and Fourier transform infrared reflection/absorption spectroscopy (FT-IRRAS). The perfluoroalkylsilane SAM on Cu is found to be extremely hydrophobic typically having sessile drop static contact angles of more than 130° for pure water and a surface energy of 14 mJ/m2 (mN/m). FFM showed a significant reduction in the adhesive force and friction coefficient of PFMS modified Cu (PFMS/Cu) compared to unmodified Cu. Treatment by exposure to harsh conditions showed that PFMS/Cu SAM can withstand boiling nitric acid (pH=1.8), boiling water, and warm sodium hydroxide (pH=12, 60 °C) solutions for at least 30 minutes. Furthermore, no SAM degradation was observed when PFMS/Cu was exposed to warm nitric acid solution for up to 70 min at 60 °C or 50 min at 80 °C. XPS and FT-IRRAS data reveal a coordination of the PFMS silicon (Si) atom with a cuprate (CuO) molecule present on the oxidized copper substrate. The data give good evidence that the stability of the SAM film on the PFMS modified oxidized Cu surface is largely due to the formation of a siloxy-copper (-Si-O-Cu-) bond via a condensation reaction between silanol (-Si-OH) and copper hydroxide (CuOH). For a PFTS modified Cu surface (PFTS/Cu), the sessile drop static contact angle of pure water has been measured to be more than 125° and the surface energy to be typically less than 16 mJ/m2. Stability tests show that the PFTS/Cu film can survive in boiling pure water for one hour, boiling nitric acid (pH 1.5 or 1.8) for 30 minutes, sodium hydroxide solution (pH 12, 70 °C) for 30 minutes, and autoclave conditions (steam at 134 °C and 3 atmospheres) for 15 minutes. The more commonly used self-assembled monolayer (SAM) modifications of Cu surfaces, e.g. thiol compounds, are significantly less stable than PFTS/Cu. Extremely hydrophobic (low surface energy) and stable PFMS/Cu SAMs and PFTS/Cu films could be useful as corrosion inhibitors in micro/nanoelectronic devices and/or as promoters for anti-wetting, low adhesion surfaces or drop-wise condensation on heat exchange surfaces. XPS analysis confirmed the presence of perfluorinated and non-perfluorinated alkylphosphonate molecules on the PFDP, DP, and ODP SAMs deposited at the aluminum oxide coated silicon (Al/Si) surfaces. The sessile drop static contact angle of pure water on PFDP SAMs was typically more than 130° and on DP and ODP typically more than 125° indicating that the phosphonic acid SAMs reacted with Al samples were very hydrophobic. The surface roughness for PFDP/Al, DP/Al, ODP/Al, and bare Al was approximately 35 nm, as determined by AFM. The surface energy for PFDP/Al was determined to be approximately 11 mJ/m2 by the Zisman plot method compared to 21 mJ/m2 and 20 mJ/m2 for DP/Al and ODP/Al, respectively. PFDP/Al gave the lowest adhesion and friction force while bare Al gave the highest. The adhesion and friction forces for ODP/Al and DP/Al SAMs were in between. ODP, DP, and OP SAMs have been studied in detail on relatively flat aluminum oxide surfaces. The rms surface roughness for ODP/Al, DP/Al, OP/Al, and bare Al was less than 15 nm, as determined by AFM. The sessile drop static contact angle of pure water on ODP/Al and DP/Al was typically more than 115° and on OP/Al typically less than 105°. The surface energy for ODP/Al and DP/Al was determined to be approximately 21 mJ/m2 and 22 mJ/m2, respectively, compared to 26 mJ/m2 for OP/Al. ODP/Al and OP/Al were studied by FFM to better understand their micro-/nano-tribological properties. ODP/Al gave the lowest coefficient of friction values while bare Al gave the highest. The adhesion forces for ODP/Al and OP/Al were comparable. The chemical stability of ODP/Al, PFDP/Al, DP/Al, OP/Al, and PFMS/Al SAMs has been inspected by exposure to warm nitric acid (pH 1.8, 30 min, 60-95 °C). The XPS data and stability against harsh chemical conditions indicate that a type of bond forms between a phosphonic acid (PA) or silane molecule and the oxidized Al surface. Stability tests using warm nitric acid (pH 1.8, 30 min, 60-95 °C) show ODP/Al SAMs to be most stable followed by PFDP/Al, DP/Al, PFMS/Al, and OP/Al SAMs. For PFTS/Al, stability tests demonstrate that modified aluminum is able to survive exposure to warm nitric acid (pH = 1.8, 60 °C, 30 min) indicating some degree of robustness. Hydrophobic, low adhesion, and robust aluminum surfaces have useful applications for micro/nano-electromechanical systems (MEMS/NEMS), such as digital micro-mirror devices (DMDs). These studies are expected to aid in the design and selection of proper lubricants for MEMS/NEMS.

EPFL2007