Colloidal gold

From Wikipedia, the free encyclopedia

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

 

Suspensions of gold nanoparticles of various sizes. The size difference causes the difference in colors.

Colloidal gold is a sol or colloidal suspension of nanoparticles of gold in a fluid, usually water. The colloid is usually either an intense red colour (for spherical particles less than 100 nm) or blue/purple (for larger spherical particles or nanorods). Due to their optical, electronic, and molecular-recognition properties, gold nanoparticles are the subject of substantial research, with many potential or promised applications in a wide variety of areas, including electron microscopy, electronics, nanotechnology, materials science, and biomedicine.

The properties of colloidal gold nanoparticles, and thus their potential applications, depend strongly upon their size and shape. For example, rodlike particles have both a transverse and longitudinal absorption peak, and anisotropy of the shape affects their self-assembly.

History

This cranberry glass bowl was made by adding a gold salt (probably gold chloride) to molten glass.

Used since ancient times as a method of staining glass colloidal gold was used in the 4th-century Lycurgus Cup, which changes color depending on the location of light source.

During the Middle Ages, soluble gold, a solution containing gold salt, had a reputation for its curative property for various diseases. In 1618, Francis Anthony, a philosopher and member of the medical profession, published a book called Panacea Aurea, sive tractatus duo de ipsius Auro Potabili (Latin: gold potion, or two treatments of potable gold). The book introduces information on the formation of colloidal gold and its medical uses. About half a century later, English botanist Nicholas Culpepper published book in 1656, Treatise of Aurum Potabile, solely discussing the medical uses of colloidal gold.

In 1676, Johann Kunckel, a German chemist, published a book on the manufacture of stained glass. In his book Valuable Observations or Remarks About the Fixed and Volatile Salts-Auro and Argento Potabile, Spiritu Mundi and the Like, Kunckel assumed that the pink color of Aurum Potabile came from small particles of metallic gold, not visible to human eyes. In 1842, John Herschel invented a photographic process called chrysotype (from the Greek χρῡσός meaning "gold") that used colloidal gold to record images on paper.

Modern scientific evaluation of colloidal gold did not begin until Michael Faraday's work in the 1850s. In 1856, in a basement laboratory of Royal Institution, Faraday accidentally created a ruby red solution while mounting pieces of gold leaf onto microscope slides. Since he was already interested in the properties of light and matter, Faraday further investigated the optical properties of the colloidal gold. He prepared the first pure sample of colloidal gold, which he called 'activated gold', in 1857. He used phosphorus to reduce a solution of gold chloride. The colloidal gold Faraday made 150 years ago is still optically active. For a long time, the composition of the 'ruby' gold was unclear. Several chemists suspected it to be a gold tin compound, due to its preparation. Faraday recognized that the color was actually due to the miniature size of the gold particles. He noted the light scattering properties of suspended gold microparticles, which is now called Faraday-Tyndall effect.

In 1898, Richard Adolf Zsigmondy prepared the first colloidal gold in diluted solution. Apart from Zsigmondy, Theodor Svedberg, who invented ultracentrifugation, and Gustav Mie, who provided the theory for scattering and absorption by spherical particles, were also interested in the synthesis and properties of colloidal gold.

With advances in various analytical technologies in the 20th century, studies on gold nanoparticles has accelerated. Advanced microscopy methods, such as atomic force microscopy and electron microscopy, have contributed the most to nanoparticle research. Due to their comparably easy synthesis and high stability, various gold particles have been studied for their practical uses. Different types of gold nanoparticle are already used in many industries, such as electronics.

Physical properties

Optical

The variation of scattering cross section of 100 nm-radius gold nanoparticle vs. the wavelength

Colloidal gold has been used by artists for centuries because of the nanoparticle’s interactions with visible light. Gold nanoparticles absorb and scatter light resulting in colours ranging from vibrant reds (smaller particles) to blues to black and finally to clear and colorless (larger particles), depending on particle size, shape, local refractive index, and aggregation state. These colors occur because of a phenomenon called localized surface plasmon resonance (LSPR), in which conduction electrons on the surface of the nanoparticle oscillate in resonance with incident light.

Effect of size

As a general rule, the wavelength of light absorbed increases as a function of increasing nano particle size. For example, pseudo-spherical gold nanoparticles with diameters ~ 30 nm have a peak LSPR absorption at ~530 nm.

Effect of local refractive index

Changes in the apparent color of a gold nanoparticle solution can also be caused by the environment in which the colloidal gold is suspended. The optical properties of gold nanoparticles depends on the refractive index near the nanoparticle surface, therefore both the molecules directly attached to the nanoparticle surface (i.e. nanoparticle ligands) and/or the nanoparticle solvent both may influence observed optical features. As the refractive index near the gold surface increases, the NP LSPR will shift to longer wavelengths In addition to solvent environment, the extinction peak can be tuned by coating the nanoparticles with non-conducting shells such as silica, bio molecules, or aluminium oxide.

Effect of aggregation

When gold nano particles aggregate, the optical properties of the particle change, because the effective particle size, shape, and dielectric environment all change.

Medical research

Electron microscopy

Main article: Immunogold labelling

Colloidal gold and various derivatives have long been among the most widely used labels for antigens in biological electron microscopy. Colloidal gold particles can be attached to many traditional biological probes such as antibodies, lectins, superantigens, glycans, nucleic acids, and receptors. Particles of different sizes are easily distinguishable in electron micrographs, allowing simultaneous multiple-labelling experiments.

In addition to biological probes, gold nanoparticles can be transferred to various mineral substrates, such as mica, single crystal silicon, and atomically flat gold(III), to be observed under atomic force microscopy (AFM).

Drug delivery system

Gold nanoparticles can be used to optimize the biodistribution of drugs to diseased organs, tissues or cells, in order to improve and target drug delivery. Nanoparticle-mediated drug delivery is feasible only if the drug distribution is otherwise inadequate. These cases include drug targeting of unstable (proteins, siRNA, DNA), delivery to the difficult sites (brain, retina, tumors, intracellular organelles) and drugs with serious side effects (e.g. anti-cancer agents). The performance of the nanoparticles depends on the size and surface functionalities in the particles. Also, the drug release and particle disintegration can vary depending on the system (e.g. biodegradable polymers sensitive to pH). An optimal nanodrug delivery system ensures that the active drug is available at the site of action for the correct time and duration, and their concentration should be above the minimal effective concentration (MEC) and below the minimal toxic concentration (MTC).

Gold nanoparticles are being investigated as carriers for drugs such as Paclitaxel. The administration of hydrophobic drugs require molecular encapsulation and it is found that nanosized particles are particularly efficient in evading the reticuloendothelial system.

Tumor detection

In cancer research, colloidal gold can be used to target tumors and provide detection using SERS (surface enhanced Raman spectroscopy) in vivo. These gold nanoparticles are surrounded with Raman reporters, which provide light emission that is over 200 times brighter than quantum dots. It was found that the Raman reporters were stabilized when the nanoparticles were encapsulated with a thiol-modified polyethylene glycol coat. This allows for compatibility and circulation in vivo. To specifically target tumor cells, the polyethylenegylated gold particles are conjugated with an antibody (or an antibody fragment such as scFv), against, e.g. epidermal growth factor receptor, which is sometimes overexpressed in cells of certain cancer types. Using SERS, these pegylated gold nanoparticles can then detect the location of the tumor.

Gold nanoparticles accumulate in tumors, due to the leakiness of tumor vasculature, and can be used as contrast agents for enhanced imaging in a time-resolved optical tomography system using short-pulse lasers for skin cancer detection in mouse model. It is found that intravenously administrated spherical gold nanoparticles broadened the temporal profile of reflected optical signals and enhanced the contrast between surrounding normal tissue and tumors.

Tumor targeting via multifunctional nanocarriers. Cancer cells reduce adhesion to neighboring cells and migrate into the vasculature-rich stroma. Once at the vasculature, cells can freely enter the bloodstream. Once the tumor is directly connected to the main blood circulation system, multifunctional nanocarriers can interact directly with cancer cells and effectively target tumors.

Gene therapy

Gold nanoparticles have shown potential as intracellular delivery vehicles for siRNA oligonucleotides with maximal therapeutic impact.

Multifunctional siRNA-gold nanoparticles with several biomolecules: PEG, cell penetration and cell adhesion peptides and siRNA. Two different approaches were employed to conjugate the siRNA to the gold nanoparticle: (1) Covalent approach: use of thiolated siRNA for gold-thiol binding to the nanoparticle; (2) Ionic approach: interaction of the negatively charged siRNA to the modified surface of the AuNP through ionic interactions.

Gold nanoparticles show potential as intracellular delivery vehicles for antisense oligonucleotides (single and double stranded DNA) by providing protection against intracellular nucleases and ease of functionalization for selective targeting.

Photothermal agents

Gold nanorods are being investigated as photothermal agents for in-vivo applications. Gold nanorods are rod-shaped gold nanoparticles whose aspect ratios tune the surface plasmon resonance (SPR) band from the visible to near-infrared wavelength. The total extinction of light at the SPR is made up of both absorption and scattering. For the smaller axial diameter nanorods (~10 nm), absorption dominates, whereas for the larger axial diameter nanorods (>35 nm) scattering can dominate. As a consequence, for in-vivo studies, small diameter gold nanorods are being used as photothermal converters of near-infrared light due to their high absorption cross-sections. Since near-infrared light transmits readily through human skin and tissue, these nanorods can be used as ablation components for cancer, and other targets. When coated with polymers, gold nanorods have been observed to circulate in-vivo with half-lives longer than 6 hours, bodily residence times around 72 hours, and little to no uptake in any internal organs except the liver.

Despite the unquestionable success of gold nanorods as photothermal agents in preclinical research, they have yet to obtain the approval for clinical use because the size is above the renal excretion threshold. In 2019, the first NIR-absorbing plasmonic ultrasmall-in-nano architecture has been reported, and jointly combine: (i) a suitable photothermal conversion for hyperthermia treatments, (ii) the possibility of multiple photothermal treatments and (iii) renal excretion of the building blocks after the therapeutic action.

Radiotherapy dose enhancer

Considerable interest has been shown in the use of gold and other heavy-atom-containing nanoparticles to enhance the dose delivered to tumors. Since the gold nanoparticles are taken up by the tumors more than the nearby healthy tissue, the dose is selectively enhanced. The biological effectiveness of this type of therapy seems to be due to the local deposition of the radiation dose near the nanoparticles. This mechanism is the same as occurs in heavy ion therapy.

Detection of toxic gas

Researchers have developed simple inexpensive methods for on-site detection of hydrogen sulfide H
₂S present in air based on the antiaggregation of gold nanoparticles (AuNPs). Dissolving H
₂S into a weak alkaline buffer solution leads to the formation of HS-, which can stabilize AuNPs and ensure they maintain their red color allowing for visual detection of toxic levels of H
₂S.

Gold nanoparticle based biosensor

Gold nanoparticles are incorporated into biosensors to enhance its stability, sensitivity, and selectivity. Nanoparticle properties such as small size, high surface-to-volume ratio, and high surface energy allow immobilization of large range of biomolecules. Gold nanoparticle, in particular, could also act as "electron wire" to transport electrons and its amplification effect on electromagnetic light allows it to function as signal amplifiers. Main types of gold nanoparticle based biosensors are optical and electrochemical biosensor.

Optical biosensor

Gold nanoparticle-based (Au-NP) biosensor for Glutathione (GSH). The AuNPs are functionalised with a chemical group that binds to GSH and makes the NPs partially collapse, and thus change colour. The exact amount of GSH can be derived via UV-vis spectroscopy through a calibration curve.

Gold nanoparticles improve the sensitivity of optical sensor by response to the change in local refractive index. The angle of the incidence light for surface plasmon resonance, an interaction between light wave and conducting electrons in metal, changes when other substances are bounded to the metal surface. Because gold is very sensitive to its surroundings' dielectric constant, binding of an analyte would significantly shift gold nanoparticle's SPR and therefore allow more sensitive detection. Gold nanoparticle could also amplify the SPR signal. When the plasmon wave pass through the gold nanoparticle, the charge density in the wave and the electron I the gold interacted and resulted in higher energy response, so called electron coupling. Since the analyte and bio-receptor now bind to the gold, it increases the apparent mass of the analyte and therefore amplified the signal. These properties had been used to build DNA sensor with 1000-fold sensitive than without the Au NP. Humidity sensor was also built by altering the atom interspacing between molecules with humidity change, the interspacing change would also result in a change of the Au NP's LSPR.

Electrochemical biosensor

Electrochemical sensor convert biological information into electrical signals that could be detected. The conductivity and biocompatibility of Au NP allow it to act as "electron wire". It transfers electron between the electrode and the active site of the enzyme. It could be accomplished in two ways: attach the Au NP to either the enzyme or the electrode. GNP-glucose oxidase monolayer electrode was constructed use these two methods. The Au NP allowed more freedom in the enzyme's orientation and therefore more sensitive and stable detection. Au NP also acts as immobilization platform for the enzyme. Most biomolecules denatures or lose its activity when interacted with the electrode. The biocompatibility and high surface energy of Au allow it to bind to a large amount of protein without altering its activity and results in a more sensitive sensor. Moreover, Au NP also catalyzes biological reactions. Gold nanoparticle under 2 nm has shown catalytic activity to the oxidation of styrene.

Immunological biosensor

Gold nanoparticles have been coated with peptides and glycans for use in immunological detection methods. The possibility to use glyconanoparticles in ELISA was unexpected, but the method seems to have a high sensitivity and thus offers potential for development of specific assays for diagnostic identification of antibodies in patient sera.

Thin films

Gold nanoparticles capped with organic ligands, such as alkanethiol molecules, can self-assemble into large monolayers (>cm${\displaystyle ^{2}}$). The particles are first prepared in organic solvent, such as chloroform or toluene, and are then spread into monolayers either on a liquid surface or on a solid substrate. Such interfacial thin films of nanoparticles have close relationship with Langmuir-Blodgett monolayers made from surfactants.

The mechanical properties of nanoparticle monolayers have been studied extensively. For 5 nm spheres capped with dodecanethiol, the Young's modulus of the monolayer is on the order of GPa. The mechanics of the membranes are guided by strong interactions between ligand shells on adjacent particles. Upon fracture, the films crack perpendicular to the direction of strain at a fracture stress of 11 ${\displaystyle \pm }$ 2.6 MPa, comparable to that of cross-linked polymer films. Free-standing nanoparticle membranes exhibit bending rigidity on the order of 10${\displaystyle ^{5}}$ eV, higher than what is predicted in theory for continuum plates of the same thickness, due to nonlocal microstructural constraints such as nonlocal coupling of particle rotational degrees of freedom. On the other hand, resistance to bending is found to be greatly reduced in nanoparticle monolayers that are supported at the air/water interface, possibly due to screening of ligand interactions in a wet environment.

Surface chemistry

In many different types of colloidal gold syntheses, the interface of the nanoparticles can display widely different character – ranging from an interface similar to a self-assembled monolayer to a disordered boundary with no repeating patterns. Beyond the Au-Ligand interface, conjugation of the interfacial ligands with various functional moieties (from small organic molecules to polymers to DNA to RNA) afford colloidal gold much of its vast functionality.

Ligand exchange/functionalization

After initial nanoparticle synthesis, colloidal gold ligands are often exchanged with new ligands designed for specific applications. For example, Au NPs produced via the Turkevich-style (or Citrate Reduction) method are readily reacted via ligand exchange reactions, due to the relatively weak binding between the carboxyl groups and the surfaces of the NPs. This ligand exchange can produce conjugation with a number of biomolecules from DNA to RNA to proteins to polymers (such as PEG) to increase biocompatibility and functionality. For example, ligands have been shown to enhance catalytic activity by mediating interactions between adsorbates and the active gold surfaces for specific oxygenation reactions. Ligand exchange can also be used to promote phase transfer of the colloidal particles. Ligand exchange is also possible with alkane thiol-arrested NPs produced from the Brust-type synthesis method, although higher temperatures are needed to promote the rate of the ligand detachment. An alternative method for further functionalization is achieved through the conjugation of the ligands with other molecules, though this method can cause the colloidal stability of the Au NPs to breakdown.

Ligand removal

In many cases, as in various high-temperature catalytic applications of Au, the removal of the capping ligands produces more desirable physicochemical properties. The removal of ligands from colloidal gold while maintaining a relatively constant number of Au atoms per Au NP can be difficult due to the tendency for these bare clusters to aggregate. The removal of ligands is partially achievable by simply washing away all excess capping ligands, though this method is ineffective in removing all capping ligand. More often ligand removal achieved under high temperature or light ablation followed by washing. Alternatively, the ligands can be electrochemically etched off.

Surface structure and chemical environment

The precise structure of the ligands on the surface of colloidal gold NPs impact the properties of the colloidal gold particles. Binding conformations and surface packing of the capping ligands at the surface of the colloidal gold NPs tend to differ greatly from bulk surface model adsorption, largely due to the high curvature observed at the nanoparticle surfaces. Thiolate-gold interfaces at the nanoscale have been well-studied and the thiolate ligands are observed to pull Au atoms off of the surface of the particles to for “staple” motifs that have significant Thiyl-Au(0) character. The citrate-gold surface, on the other hand, is relatively less-studied due to the vast number of binding conformations of the citrate to the curved gold surfaces. A study performed in 2014 identified that the most-preferred binding of the citrate involves two carboxylic acids and the hydroxyl group of the citrate binds three surface metal atoms.

Health and safety

See also: Health and safety hazards of nanomaterials and Nanotoxicology

As gold nanoparticles (AuNPs) are further investigated for targeted drug delivery in humans, their toxicity needs to be considered. For the most part, it is suggested that AuNPs are biocompatible,^{[citation needed]} but the concentrations at which they become toxic needs to be determined, and if those concentrations fall within the range of used concentrations. Toxicity can be tested in vitro and in vivo. In vitro toxicity results can vary depending on the type of the cellular growth media with different protein compositions, the method used to determine cellular toxicity (cell health, cell stress, how many cells are taken into a cell), and the capping ligands in solution. In vivo assessments can determine the general health of an organism (abnormal behavior, weight loss, average life span) as well as tissue specific toxicology (kidney, liver, blood) and inflammation and oxidative responses. In vitro experiments are more popular than in vivo experiments because in vitro experiments are more simplistic to perform than in vivo experiments.

Toxicity and hazards in synthesis

While AuNPs themselves appear to have low or negligible toxicity, and the literature shows that the toxicity has much more to do with the ligands rather than the particles themselves, the synthesis of them involves chemicals that are hazardous. Sodium borohydride, a harsh reagent, is used to reduce the gold ions to gold metal. The gold ions usually come from chloroauric acid, a potent acid. Because of the high toxicity and hazard of reagents used to synthesize AuNPs, the need for more “green” methods of synthesis arose.

Toxicity due to capping ligands

Some of the capping ligands associated with AuNPs can be toxic while others are nontoxic. In gold nanorods (AuNRs), it has been shown that a strong cytotoxicity was associated with CTAB-stabilized AuNRs at low concentration, but it is thought that free CTAB was the culprit in toxicity. Modifications that overcoat these AuNRs reduces this toxicity in human colon cancer cells (HT-29) by preventing CTAB molecules from desorbing from the AuNRs back into the solution. Ligand toxicity can also be seen in AuNPs. Compared to the 90% toxicity of HAuCl4 at the same concentration, AuNPs with carboxylate termini were shown to be non-toxic. Large AuNPs conjugated with biotin, cysteine, citrate, and glucose were not toxic in human leukemia cells (K562) for concentrations up to 0.25 M. Also, citrate-capped gold nanospheres (AuNSs) have been proven to be compatible with human blood and did not cause platelet aggregation or an immune response. However, citrate-capped gold nanoparticles sizes 8-37 nm were found to be lethally toxic for mice, causing shorter lifespans, severe sickness, loss of appetite and weight, hair discoloration, and damage to the liver, spleen, and lungs; gold nanoparticles accumulated in the spleen and liver after traveling a section of the immune system. There are mixed-views for polyethylene glycol (PEG)-modified AuNPs. These AuNPs were found to be toxic in mouse liver by injection, causing cell death and minor inflammation. However, AuNPs conjugated with PEG copolymers showed negligible toxicity towards human colon cells (Caco-2). AuNP toxicity also depends on the overall charge of the ligands. In certain doses, AuNSs that have positively-charged ligands are toxic in monkey kidney cells (Cos-1), human red blood cells, and E. coli because of the AuNSs interaction with the negatively-charged cell membrane; AuNSs with negatively-charged ligands have been found to be nontoxic in these species. In addition to the previously mentioned in vivo and in vitro experiments, other similar experiments have been performed. Alkylthiolate-AuNPs with trimethlyammonium ligand termini mediate the translocation of DNA across mammalian cell membranes in vitro at a high level, which is detrimental to these cells. Corneal haze in rabbits have been healed in vivo by using polyethylemnimine-capped gold nanoparticles that were transfected with a gene that promotes wound healing and inhibits corneal fibrosis.

Toxicity due to size of nanoparticles

Toxicity in certain systems can also be dependent on the size of the nanoparticle. AuNSs size 1.4 nm were found to be toxic in human skin cancer cells (SK-Mel-28), human cervical cancer cells (HeLa), mouse fibroblast cells (L929), and mouse macrophages (J774A.1), while 0.8, 1.2, and 1.8 nm sized AuNSs were less toxic by a six-fold amount and 15 nm AuNSs were nontoxic. There is some evidence for AuNP buildup after injection in in vivo studies, but this is very size dependent. 1.8 nm AuNPs were found to be almost totally trapped in the lungs of rats. Different sized AuNPs were found to buildup in the blood, brain, stomach, pancreas, kidneys, liver, and spleen.

Biosafety and biokinetics investigations on biodegradable ultrasmall-in-nano architectures have demonstrated that gold nanoparticles are able to avoid metal accumulation in organisms through escaping by the renal pathway.

Synthesis

Potential difference as a function of distance from particle surface.

Generally, gold nanoparticles are produced in a liquid ("liquid chemical methods") by reduction of chloroauric acid (H[AuCl
₄]). To prevent the particles from aggregating, stabilizing agents are added. Citrate acts both as the reducing agent and colloidal stabilizer.

They can be functionalized with various organic ligands to create organic-inorganic hybrids with advanced functionality.

Turkevich method

This simple method was pioneered by J. Turkevich et al. in 1951 and refined by G. Frens in the 1970s. It produces modestly monodisperse spherical gold nanoparticles of around 10–20 nm in diameter. Larger particles can be produced, but at the cost of monodispersity and shape. In this method, hot chloroauric acid is treated with sodium citrate solution, producing colloidal gold. The Turkevich reaction proceeds via formation of transient gold nanowires. These gold nanowires are responsible for the dark appearance of the reaction solution before it turns ruby-red.

Capping agents

A capping agent is used during nanoparticle synthesis to inhibit particle growth and aggregation. The chemical blocks or reduces reactivity at the periphery of the particle—a good capping agent has a high affinity for the new nuclei. Citrate ions or tannic acid function both as a reducing agent and a capping agent. Less sodium citrate results in larger particles.

Brust-Schiffrin method

This method was discovered by Brust and Schiffrin in the early 1990s, and can be used to produce gold nanoparticles in organic liquids that are normally not miscible with water (like toluene). It involves the reaction of a chlorauric acid solution with tetraoctylammonium bromide (TOAB) solution in toluene and sodium borohydride as an anti-coagulant and a reducing agent, respectively.

Here, the gold nanoparticles will be around 5–6 nm. NaBH₄ is the reducing agent, and TOAB is both the phase transfer catalyst and the stabilizing agent.

TOAB does not bind to the gold nanoparticles particularly strongly, so the solution will aggregate gradually over the course of approximately two weeks. To prevent this, one can add a stronger binding agent, like a thiol (in particular, alkanethiols), which will bind to gold, producing a near-permanent solution. Alkanethiol protected gold nanoparticles can be precipitated and then redissolved. Thiols are better binding agents because there is a strong affinity for the gold-sulfur bonds that form when the two substances react with each other. Tetra-dodecanthiol is a commonly used strong binding agent to synthesize smaller particles. Some of the phase transfer agent may remain bound to the purified nanoparticles, this may affect physical properties such as solubility. In order to remove as much of this agent as possible, the nanoparticles must be further purified by soxhlet extraction.

Perrault method

This approach, discovered by Perrault and Chan in 2009, uses hydroquinone to reduce HAuCl₄ in an aqueous solution that contains 15 nm gold nanoparticle seeds. This seed-based method of synthesis is similar to that used in photographic film development, in which silver grains within the film grow through addition of reduced silver onto their surface. Likewise, gold nanoparticles can act in conjunction with hydroquinone to catalyze reduction of ionic gold onto their surface. The presence of a stabilizer such as citrate results in controlled deposition of gold atoms onto the particles, and growth. Typically, the nanoparticle seeds are produced using the citrate method. The hydroquinone method complements that of Frens, as it extends the range of monodispersed spherical particle sizes that can be produced. Whereas the Frens method is ideal for particles of 12–20 nm, the hydroquinone method can produce particles of at least 30–300 nm.

Martin method

This simple method, discovered by Martin and Eah in 2010, generates nearly monodisperse "naked" gold nanoparticles in water. Precisely controlling the reduction stoichiometry by adjusting the ratio of NaBH₄-NaOH ions to HAuCl₄-HCl ions within the "sweet zone," along with heating, enables reproducible diameter tuning between 3–6 nm. The aqueous particles are colloidally stable due to their high charge from the excess ions in solution. These particles can be coated with various hydrophilic functionalities, or mixed with hydrophobic ligands for applications in non-polar solvents. In non-polar solvents the nanoparticles remain highly charged, and self-assemble on liquid droplets to form 2D monolayer films of monodisperse nanoparticles.

Nanotech studies

Bacillus licheniformis can be used in synthesis of gold nanocubes with sizes between 10 and 100 nanometres. Gold nanoparticles are usually synthesized at high temperatures in organic solvents or using toxic reagents. The bacteria produce them in much milder conditions.

Navarro et al. method

For particles larger than 30 nm, control of particle size with a low polydispersity of spherical gold nanoparticles remains challenging. In order to provide maximum control on the NP structure, Navarro and co-workers used a modified Turkevitch-Frens procedure using sodium acetylacetonate as the reducing agent and sodium citrate as the stabilizer.

Sonolysis

Another method for the experimental generation of gold particles is by sonolysis. The first method of this type was invented by Baigent and Müller. This work pioneered the use of ultrasound to provide the energy for the processes involved and allowed the creation of gold particles with a diameter of under 10 nm. In another method using ultrasound, the reaction of an aqueous solution of HAuCl₄ with glucose, the reducing agents are hydroxyl radicals and sugar pyrolysis radicals (forming at the interfacial region between the collapsing cavities and the bulk water) and the morphology obtained is that of nanoribbons with width 30–50 nm and length of several micrometers. These ribbons are very flexible and can bend with angles larger than 90°. When glucose is replaced by cyclodextrin (a glucose oligomer), only spherical gold particles are obtained, suggesting that glucose is essential in directing the morphology toward a ribbon.

Block copolymer-mediated method

An economical, environmentally benign and fast synthesis methodology for gold nanoparticles using block copolymer has been developed by Sakai et al. In this synthesis methodology, block copolymer plays the dual role of a reducing agent as well as a stabilizing agent. The formation of gold nanoparticles comprises three main steps: reduction of gold salt ion by block copolymers in the solution and formation of gold clusters, adsorption of block copolymers on gold clusters and further reduction of gold salt ions on the surfaces of these gold clusters for the growth of gold particles in steps, and finally its stabilization by block copolymers. But this method usually has a limited-yield (nanoparticle concentration), which does not increase with the increase in the gold salt concentration. Ray et al. improved this synthesis method by enhancing the nanoparticle yield by manyfold at ambient temperature.

Active site

From Wikipedia, the free encyclopedia

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

 

Organisation of enzyme structure and lysozyme example. Binding sites in blue, catalytic site in red and peptidoglycan substrate in black. (PDB: 9LYZ​)

In biology, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate (binding site) and residues that catalyse a reaction of that substrate (catalytic site). Although the active site occupies only ~10–20% of the volume of an enzyme, it is the most important part as it directly catalyzes the chemical reaction. It usually consists of three to four amino acids, while other amino acids within the protein are required to maintain the tertiary structure of the enzymes.

Each active site is evolved to be optimised to bind a particular substrate and catalyse a particular reaction, resulting in high specificity. This specificity is determined by the arrangement of amino acids within the active site and the structure of the substrates. Sometimes enzymes also need to bind with some cofactors to fulfil their function. The active site is usually a groove or pocket of the enzyme which can be located in a deep tunnel within the enzyme, or between the interfaces of multimeric enzymes. An active site can catalyse a reaction repeatedly as residues are not altered at the end of the reaction (they may change during the reaction, but are regenerated by the end). This process is achieved by lowering the activation energy of the reaction, so more substrates have enough energy to undergo reaction.

Binding site

Diagram of the lock and key hypothesis

 

Diagram of the induced fit hypothesis

Main article: Binding site

Usually, an enzyme molecule has only two active sites, and the active sites fit with one specific type of substrate. An active site contains a binding site that binds the substrate and orients it for catalysis. The orientation of the substrate and the close proximity between it and the active site is so important that in some cases the enzyme can still function properly even though all other parts are mutated and lose function.

Initially, the interaction between the active site and the substrate is non-covalent and transient. There are four important types of interaction that hold the substrate in a defined orientation and form an enzyme-substrate complex (ES complex): hydrogen bonds, van der Waals interactions, hydrophobic interactions and electrostatic force interactions. The charge distribution on the substrate and active site must be complementary, which means all positive and negative charges must be cancelled out. Otherwise, there will be a repulsive force pushing them apart. The active site usually contains non-polar amino acids, although sometimes polar amino acids may also occur. The binding of substrate to the binding site requires at least three contact points in order to achieve stereo-, regio-, and enantioselectivity. For example, alcohol dehydrogenase which catalyses the transfer of a hydride ion from ethanol to NAD⁺ interacts with the substrate methyl group, hydroxyl group and the pro-(R) hydrogen that will be abstracted during the reaction.

In order to exert their function, enzymes need to assume their correct protein fold (native fold) and tertiary structure. To maintain this defined three-dimensional structure, proteins rely on various types of interactions between their amino acid residues. If these interactions are interfered with, for example by extreme pH values, high temperature or high ion concentrations, this will cause the enzyme to denature and lose its catalytic activity.

A tighter fit between an active site and the substrate molecule is believed to increase the efficiency of a reaction. If the tightness between the active site of DNA polymerase and its substrate is increased, the fidelity, which means the correct rate of DNA replication will also increase. Most enzymes have deeply buried active sites, which can be accessed by a substrate via access channels.

There are three proposed models of how enzymes fit their specific substrate: the lock and key model, the induced fit model, and the conformational selection model. The latter two are not mutually exclusive: conformational selection can be followed by a change in the enzyme's shape. Additionally, a protein may not wholly follow either model. Amino acids at the binding site of ubiquitin generally follow the induced fit model, whereas the rest of the protein generally adheres to conformational selection. Factors such as temperature likely influences the pathway taken during binding, with higher temperatures predicted to increase the importance of conformational selection and decrease that of induced fit.

Lock and key hypothesis

This concept was suggested by the 19th-century chemist Emil Fischer. He proposed that the active site and substrate are two stable structures that fit perfectly without any further modification, just like a key fits into a lock. If one substrate perfectly binds to its active site, the interactions between them will be strongest, resulting in high catalytic efficiency.

As time went by, limitations of this model started to appear. For example, the competitive enzyme inhibitor methylglucoside can bind tightly to the active site of 4-alpha-glucanotransferase and perfectly fits into it. However, 4-alpha-glucanotransferase is not active on methylglucoside and no glycosyl transfer occurs. The Lock and Key hypothesis cannot explain this, as it would predict a high efficiency of methylglucoside glycosyl transfer due to its tight binding. Apart from competitive inhibition, this theory cannot explain the mechanism of action of non-competitive inhibitors either, as they do not bind to the active site but nevertheless influence catalytic activity.

Induced fit hypothesis

Daniel Koshland's theory of enzyme-substrate binding is that the active site and the binding portion of the substrate are not exactly complementary. The induced fit model is a development of the lock-and-key model and assumes that an active site is flexible and changes shape until the substrate is completely bound. This model is similar to a person wearing a glove: the glove changes shape to fit the hand. The enzyme initially has a conformation that attracts its substrate. Enzyme surface is flexible and only the correct catalyst can induce interaction leading to catalysis. Conformational changes may then occur as the substrate is bound. After the reaction products will move away from the enzyme and the active site returns to its initial shape. This hypothesis is supported by the observation that the entire protein domain could move several nanometers during catalysis. This movement of protein surface can create microenvironments that favour the catalysis.

Conformational selection hypothesis

This model suggests that enzymes exist in a variety of conformations, only some of which are capable of binding to a substrate. When a substrate is bound to the protein, the equilibrium in the conformational ensemble shifts towards those able to bind ligands (as enzymes with bound substrates are removed from the equilibrium between the free conformations).

Types of non-covalent interactions

Positively charged sodium ion and negatively charged fluoride ion attract each other to form sodium fluoride under electrostatic interaction.

 

Hydrogen bond between two water molecules.

 

Van der Waals force between two acetone molecules. The lower acetone molecule contains a partially negative oxygen atom that attracts partially positive carbon atom in the upper acetone.

 

Hydrophobic and hydrophilic groups tend to assemble with the same kind of molecules.

Electrostatic interaction: In an aqueous environment, the oppositely charged groups in amino acid side chains within the active site and substrates attract each other, which is termed electrostatic interaction. For example, when a carboxylic acid (R-COOH) dissociates into RCOO⁻ and H⁺ ions, COO⁻ will attract positively charged groups such as protonated guanidine side chain of arginine.

Hydrogen bond: A hydrogen bond is a specific type of dipole-dipole interaction between a partially positive hydrogen atom and a partially negative electron donor that contain a pair of electrons such as oxygen, fluorine and nitrogen. The strength of hydrogen bond depends on the chemical nature and geometric arrangement of each group.

Van der Waals force: Van der Waals force is formed between oppositely charged groups due to transient uneven electron distribution in each group. If all electrons are concentrated at one pole of the group this end will be negative, while the other end will be positive. Although the individual force is weak, as the total number of interactions between the active site and substrate is massive the sum of them will be significant.

Hydrophobic interaction: Non-polar hydrophobic groups tend to aggregate together in the aqueous environment and try to leave from polar solvent. These hydrophobic groups usually have long carbon chain and do not react with water molecules. When dissolving in water a protein molecule will curl up into a ball-like shape, leaving hydrophilic groups in outside while hydrophobic groups are deeply buried within the centre.

Catalytic site

Main article: Enzyme catalysis

See also: Catalytic triad

The enzyme TEV protease contains a catalytic triad of residues (red) in its catalytic site. The substrate (black) is bound by the binding site to orient it next to the triad. PDB: 1lvm​

Once the substrate is bound and oriented to the active site, catalysis can begin. The residues of the catalytic site are typically very close to the binding site, and some residues can have dual-roles in both binding and catalysis.

Catalytic residues of the site interact with the substrate to lower the activation energy of a reaction and thereby make it proceed faster. They do this by a number of different mechanisms including the approximation of the reactants, nucleophilic/electrophilic catalysis and acid/base catalysis. These mechanisms will be explained below.

Mechanisms involved in Catalytic process

Approximation of the reactant

During enzyme catalytic reaction, the substrate and active site are brought together in a close proximity. This approach has various purposes. Firstly, when substrates bind within the active site the effective concentration of it significantly increases than in solution. This means the number of substrate molecules involved in the reaction is also increased. This process also reduces the desolvation energy required for the reaction to occur. In solution substrate molecules are surrounded by solvent molecules and energy is required for enzyme molecules to replace them and contact with the substrate. Since bulk molecules can be excluded from the active site this energy output can be minimised. Next, the active site is designed to reorient the substrate to reduce the activation energy for the reaction to occur. The alignment of the substrate, after binding, is locked in a high energy state and can proceed to the next step. In addition, this binding is favoured by entropy as the energy cost associated with solution reaction is largely eliminated since solvent cannot enter active site. In the end, the active site may manipulate the Molecular orbital of the substrate into a suitable orientation to reduce activation energy.

The electrostatic states of substrate and active site must be complementary to each other. A polarized negatively charged amino acid side chain will repel uncharged substrate. But if the transition state involves the formation of an ion centre then the side chain will now produce a favourable interaction.

Covalent catalysis

Many enzymes including serine protease, cysteine protease, protein kinase and phosphatase evolved to form transient covalent bonds between them and their substrates to lower the activation energy and allow the reaction to occur. This process can be divided into 2 steps: formation and breakdown. The former step is rate-limit step while the later step is needed to regenerate intact enzyme.

Nucleophilic catalysis: This process involves the donation of electrons from the enzyme's nucleophile to a substrate to form a covalent bond between them during the transition state. The strength of this interaction depends on two aspects.: the ability of the nucleophilic group to donate electrons and the electrophile to accept them. The former one is mainly affected by the basicity(the ability to donate electron pairs) of the species while the later one is in regard to its pK_a. Both groups are also affected by their chemical properties such as polarizability, electronegativity and ionization potential. Amino acids that can form nucleophile including serine, cysteine, aspartate and glutamine.

Electrophilic catalysis: The mechanism behind this process is exactly same as nucleophilic catalysis except that now amino acids in active site act as electrophile while substrates are nucleophiles. This reaction usually requires cofactors as the amino acid side chains are not strong enough in attracting electrons.

Metal ions

Metal ions have multiple roles during the reaction. Firstly it can bind to negatively charged substrate groups so they will not repel electron pairs from active site's nucleophilic groups. It can attract negatively charged electrons to increase electrophilicity. It can also bridge between active site and substrate. At last, they may change the conformational structure of the substrate to favour reaction.

Acid/base catalysis

In some reactions, protons and hydroxide may directly act as acid and base in term of specific acid and specific base catalysis. But more often groups in substrate and active site act as Brønsted–Lowry acid and base. This is called general acid and general base theory. The easiest way to distinguish between them is to check whether the reaction rate is determined by the concentrations of the general acid and base. If the answer is yes then the reaction is the general type. Since most enzymes have an optimum pH of 6 to 7, the amino acids in the side chain usually have a pK_a of 4~10. Candidate include aspartate, glutamate, histidine, cysteine. These acids and bases can stabilise the nucleophile or electrophile formed during the catalysis by providing positive and negative charges.

Conformational distortion

Quantitative studies of enzymatic reactions often found that the acceleration of chemical reaction speed cannot be fully explained by existing theories like the approximation, acid/base catalysis and electrophile/nucleophile catalysis. And there is an obvious paradox: in reversible enzymatic reaction if the active site perfectly fits the substrates then the backward reaction will be slowed since products cannot fit perfectly into the active site. So conformational distortion was introduced and argues that both active site and substrate can undergo conformational changes to fit with each other all the time.

Preorganised active site complementarity to the transition state

This theory is a little similar to the Lock and Key Theory, but at this time the active site is preprogrammed to bind perfectly to substrate in transition state rather than in ground state. The formation of transition state within the solution requires a large amount of energy to relocate solvent molecules and the reaction is slowed. So the active site can substitute solvent molecules and surround the substrates to minimize the counterproductive effect imposed by the solution. The presence of charged groups with the active site will attract substrates and ensure electrostatic complementarity.

Examples of enzyme catalysis mechanisms

In reality, most enzyme mechanisms involve a combination of several different types of catalysis.

Glutathione reductase

the mechanism of glutathione reductase

The role of glutathione(GSH) is to remove accumulated reactive oxygen species which may damage cells. During this process, its thiol side chain is oxidised and two glutathione molecules are connected by a disulphide bond to form a dimer(GSSG). In order to regenerate glutathione the disulphide bond has to be broken, In human cells, this is done by glutathione reductase(GR).

Glutathione reductase is a dimer that contains two identical subunits. It requires one NADP and one FAD as the cofactors. The active site is located in the linkage between two subunits. The NADPH is involved in the generation of FADH-. In the active site, there are two cysteine residues besides the FAD cofactor and are used to break the disulphide bond during the catalytic reaction. NADPH is bound by three positively charged residues: Arg-218, His-219 and Arg-224.

The catalytic process starts when the FAD is reduced by NADPH to accept one electron and from FADH⁻. It then attacks the disulphide bond formed between 2 cysteine residues, forming one SH bond and a single S⁻ group. This S⁻ group will act as a nucleophile to attack the disulphide bond in the oxidised glutathione(GSSG), breaking it and forming a cysteine-SG complex. The first SG⁻ anion is released and then receives one proton from adjacent SH group and from the first glutathione monomer. Next the adjacent S⁻ group attack disulphide bond in cysteine-SG complex and release the second SG⁻ anion. It receives one proton in solution and forms the second glutathione monomer.

Chymotrypsin

Mechanism of peptide bond cleavage by chymotrypsin.

Chymotrypsin is a serine endopeptidase that is present in pancreatic juice and helps the hydrolysis of proteins and peptide. It catalyzes the hydrolysis of peptide bonds in L-isomers of tyrosine, phenylalanine, and tryptophan. In the active site of this enzyme, three amino acid residues work together to form a catalytic triad which makes up the catalytic site. In chymotrypsin, these residues are Ser-195, His-57 and Asp-102.

The mechanism of chymotrypsin can be divided into two phases. First, Ser-195 nucleophilically attacks the peptide bond carbon in the substrate to form a tetrahedral intermediate. The nucleophilicity of Ser-195 is enhanced by His-57, which abstracts a proton from Ser-195 and is in turn stabilised by the negatively charged carboxylate group (RCOO⁻) in Asp-102. Furthermore, the tetrahedral oxyanion intermediate generated in this step is stabilised by hydrogen bonds from Ser-195 and Gly-193.

In the second stage, the R'NH group is protonated by His-57 to form R'NH₂ and leaves the intermediate, leaving behind the acylated Ser-195. His-57 then acts as a base again to abstract one proton from a water molecule. The resulting hydroxide anion nucleophilically attacks the acyl-enzyme complex to form a second tetrahedral oxyanion intermediate, which is once again stabilised by H bonds. In the end, Ser-195 leaves the tetrahedral intermediate, breaking the CO bond that connected the enzyme to the peptide substrate. A proton is transferred to Ser-195 through His-57, so that all three amino acid return to their initial state.

Unbinding

Substrate unbinding is influenced by various factors. Larger ligands generally stay in the active site longer, as do those with more rotatable bonds (although this may be a side effect of size). When the solvent is excluded from the active site, less flexible proteins result in longer residence times. More hydrogen bonds shielded from the solvent also decrease unbinding.

Cofactors

Redox states of Flavin.

Main article: Cofactor (biochemistry)

Enzymes can use cofactors as ‘helper molecules’. Coenzymes are referred to those non-protein molecules that bind with enzymes to help them fulfill their jobs. Mostly they are connected to the active site by non-covalent bonds such as hydrogen bond or hydrophobic interaction. But sometimes a covalent bond can also form between them. For example, the heme in cytochrome C is bound to the protein through thioester bond. In some occasions, coenzymes can leave enzymes after the reaction is finished. Otherwise, they permanently bind to the enzyme. Coenzyme is a broad concept which includes metal ions, various vitamins and ATP. If an enzyme needs coenzyme to work itself, it is called an apoenzyme. In fact, it alone cannot catalyze reactions properly. Only when its cofactor comes in and binds to the active site to form holoenzyme does it work properly.

One example of the coenzyme is Flavin. It contains a distinct conjugated isoalloxazine ring system. Flavin has multiple redox states and can be used in processes that involve the transfer of one or two electrons. It can act as an electron acceptor in reaction, like the oxidation of NAD to NADH, to accept two electrons and form 1,5-dihydroflavin. On the other hand, it can form semiquinone(free radical) by accepting one electron, and then converts to fully reduced form by the addition of an extra electron. This property allows it to be used in one electron oxidation process.

Inhibitors

Main article: Enzyme inhibitor

Inhibitors disrupt the interaction between enzyme and substrate, slowing down the rate of a reaction. There are different types of inhibitor, including both reversible and irreversible forms.

Competitive inhibitors are inhibitors that only target free enzyme molecules. They compete with substrates for free enzyme acceptor and can be overcome by increasing the substrate concentration. They have two mechanisms. Competitive inhibitors usually have structural similarities to the substrates and or ES complex. As a result, they can fit into the active site and trigger favourable interactions to fill in the space and block substrates from entry. They can also induce transient conformational changes in the active site so substrates cannot fit perfectly with it. After a short period of time, competitive inhibitors will drop off and leave the enzyme intact.

Inhibitors are classified as non-competitive inhibitors when they bind both free enzyme and ES complex. Since they do not compete with substrates for the active site, they cannot be overcome by simply increasing the substrate concentration. They usually bind to a different site on the enzyme and alter the 3-dimensional structure of the active site to block substrates from entry or leaving the enzyme.

Irreversible inhibitors are similar to competitive inhibitors as they both bind to the active site. However, irreversible inhibitors form irreversible covalent bonds with the amino acid residues in the active site and never leave. Therefore, the active site is occupied and the substrate cannot enter. Occasionally the inhibitor will leave but the catalytic site is permanently altered in shape. These inhibitors usually contain electrophilic groups like halogen substitutes and epoxides. As time goes by more and more enzymes are bound by irreversible inhibitors and cannot function anymore.

	Example	Binds active site?	Reduces rate of reaction?
Competitive reversible inhibitor	HIV protease inhibitors	Yes	Yes
Non-competitive reversible inhibitor	Heavy metals such as lead and mercury	No	Yes
Irreversible inhibitor	Cyanide	Yes	Yes

Examples of competitive and irreversible enzyme inhibitors

Competitive inhibitor: HIV protease inhibitor

Indinavir, an HIV protease inhibitor.jpg

HIV protease inhibitors are used to treat patients having AIDS virus by preventing its DNA replication. HIV protease is used by the virus to cleave Gag-Pol polyprotein into 3 smaller proteins that are responsible for virion assembly, package and maturation. This enzyme targets the specific phenylalanine-proline cleave site within the target protein. If HIV protease is switched off the virion particle will lose function and cannot infect patients. Since it is essential in viral replication and is absent in healthy human, it is an ideal target for drug development.

HIV protease belongs to aspartic protease family and has a similar mechanism. Firstly the aspartate residue activates a water molecule and turns it into a nucleophile. Then it attacks the carbonyl group within the peptide bond (NH-CO) to form a tetrahedral intermediate. The nitrogen atom within the intermediate receives a proton, forming an amide group and subsequent rearrangement leads to the break down of the bond between it and the intermediate and forms two products.

Inhibitors usually contain a nonhydrolyzable hydroxyethylene or hydroxyethylamine groups that mimic the tetrahedral intermediate. Since they share a similar structure and electrostatic arrangement to the transition state of substrates they can still fit into the active site but cannot be broken down, so hydrolysis cannot occur.

Non-competitive inhibitor: Strychnine

Strychnine is a neurotoxin that causes death by affecting nerves that control muscular contraction and cause respiration difficulty. The impulse is transmitted between the synapse through a neurotransmitter called acetylcholine. It is released into the synapse between nerve cells and binds to receptors in the postsynaptic cell. Then an action potential is generated and transmitted through the postsynaptic cell to start a new cycle.

Glycine can inhibit the activity of neurotransmitter receptors, thus a larger amount of acetylcholinesterase is required to trigger an action potential. This makes sure that the generation of nerve impulses is tightly controlled. However, this control is broken down when strychnine is added. It inhibits glycine receptors(a chloride channel) and a much lower level of neurotransmitter concentration can trigger an action potential. Nerves now constantly transmit signals and cause excessive muscular contraction, leading to asphyxiation and death.

Irreversible inhibitor:Diisopropyl fluorophosphate

Irreversible inhibition of a serine protease by DIPF.

Diisopropyl fluorophosphate (DIFP) is an irreversible inhibitor that blocks the action of serine protease. When it binds to the enzyme a nucleophilic substitution reaction occurs and releases one hydrogen fluoride molecule. The OH group in the active site acts as a nucleophile to attack the phosphorus in DIFP and form a tetrahedral intermediate and release a proton. Then the P-F bond is broken, one electron is transferred to the F atom and it leaves the intermediate as F⁻ anion. It combines with a proton in solution to form one HF molecule. A covalent bond formed between the active site and DIFP, so the serine side chain is no longer available to the substrate.

In drug discovery

Identification of active sites is crucial in the process of drug discovery. The 3-D structure of the enzyme is analysed to identify active site residues and design drugs which can fit into them. Proteolytic enzymes are targets for some drugs, such as protease inhibitors, which include drugs against AIDS and hypertension. These protease inhibitors bind to an enzyme's active site and block interaction with natural substrates. An important factor in drug design is the strength of binding between the active site and an enzyme inhibitor. If the enzyme found in bacteria is significantly different from the human enzyme then an inhibitor can be designed against that particular bacterium without harming the human enzyme. If one kind of enzyme is only present in one kind of organism, its inhibitor can be used to specifically wipe them out.

Active sites can be mapped to aid the design of new drugs such as enzyme inhibitors. This involves the description of the size of an active site and the number and properties of sub-sites, such as details of the binding interaction. Modern database technology called CPASS (Comparison of Protein Active Site Structures) however allows the comparison of active sites in more detail and the finding of structural similarity using software.

Application of enzyme inhibitors

	Example	Mechanism of action
Anti-bacterial agent	Penicillin	The bacterial cell wall is composed of peptidoglycan. During bacterial growth the present crosslinking of peptidoglycan fibre is broken, so new cell wall monomer can be integrated into the cell wall. Penicillin works by inhibiting the transpeptidase which is essential for the formation of crosslinks, so the cell wall is weakened and will burst open due to turgor pressure.
Anti-fungi agent	Azole	Ergosterol is a sterol that forms the cell surface membrane of the fungi. Azole can inhibit its biosynthesis by inhibiting the Lanosterol 14 alpha-demethylase, so no new ergosterol is produced and harmful 14α-lanosterol is accumulated within the cell. Also, azole may generate reactive oxygen species.
Anti-viral agent	Saquinavir	HIV protease is needed to cleave Gag-Pol polyprotein into 3 individual proteins so they can function properly and start viral packaging process. HIV protease inhibitors like Saquinavir inhibit it so no new mature viral particle can be made.
Insecticides	Physostigmine	In the animal nervous system, Acetylcholinesterase is required to break down the neurotransmitter acetylcholine into acetate and choline. Physostigmine binds to its active site and inhibits it, so impulse signal cannot be transmitted through nerves. This results in the death of insects as they lose control of muscle and heart function.
Herbicides	Cyclohexanedione	Cyclohexanedione targets the Acetyl-CoA carboxylase which is involved in the first step of fat synthesis: ATP-dependent carboxylation of acetyl-CoA to malonyl-CoA. Lipids are important in making up the cell membrane.

Allosteric sites

Main article: Allosteric regulation

A – Active site B – Allosteric site C – Substrate D – Inhibitor E – Enzyme. This is a diagram of allosteric regulation of an enzyme. When inhibitor binds to the allosteric site the shape of active site is altered, so substrate cannot fit into it

An allosteric site is a site on an enzyme, unrelated to its active site, which can bind an effector molecule. This interaction is another mechanism of enzyme regulation. Allosteric modification usually happens in proteins with more than one subunit. Allosteric interactions are often present in metabolic pathways and are beneficial in that they allow one step of a reaction to regulate another step. They allow an enzyme to have a range of molecular interactions, other than the highly specific active site.