Learn Molecular Kinetics Of Protein Inhibition And Activation, To Understand MIT Explanation Of Homeopathy

MIT is trying to explain homeopathy in terms of removal of pathological molecular inhibitions using molecular imprints of drug molecules contained in potentizef drugs. As such, it is essential that homeopaths should learn the fundemental molecular kinetics of protein inhibition and activation, for understanding the scientific explanations regarding biological mechanism of SIMILIA SIMILIBUS CURENTUR.

A protein inhibitor is a molecule , which binds to proteinsand decreases their activity. Since blocking an essential protein’s activity can produce derangements in the whole down stream molecular processes in that particular biochemical pathway, it leads to a state of pathology. Bacterial and viral toxins, various endogenous or exogenous chemical molecules, drugs and toxic substances can act as protein inhibitors. Protein inhibitors are also used as anti-microbial drugs, herbicides and pesticides .

Not all molecules that bind to proteins are inhibitors; activators also bind to proteons and increase their enzymatic activity. Normal biological ligands of proteins bind to them as part of normal biochemocal interactions and conversions.

The binding of an inhibitor can stop a natural ligand from entering the protein’s active site and/or hinder the protein from performing its normal interactions with ligands.Inhibitor binding is either reversible or irreversible. Irreversible inhibitors usually react with the protein and change it chemically via covalent bond formation. These inhibitors modify key amino acid residues needed for the activity of that particular protein. In contrast, reversible inhibitors bind non-covalently and different types of inhibition are produced depending on whether these inhibitors bind to the protein, the protein-ligand complex, or both

Many drug molecules are protein inhibitors, so their discovery and improvement is an active area of research in biochemistry and pharmacology. A medicinal protein inhibitor is often judged by its lack of binding to other proteins, and its minimum concentration needed to inhibit the target proteins. A high specificity and minimum concentration ensure that a drug will have few side effects and thus low toxicity.

Protein inhibitors also occur naturally in the body, and are involved in the regulation of metabolism. For example, enzymes in a metabolic pathway can be inhibited by downstream products. This type of negative feedback slows the production line when products begin to build up and is an important way to maintain homeostasis in a living system.

Natural protein inhibitors can also be poisons and are used as defences against predators or as ways of killing prey.

Reversible inhibitors bind to proteins with non-covalent interactions such as hydrogen bonds, hydrophobic interactions and ionic bonds. Multiple weak bonds between the inhibitor and the active site combine to produce strong and specific binding. In contrast to natural ligands and irreversible inhibitors, reversible inhibitors generally do not undergo chemical reactions when bound to the proteins and can be easily removed by dilution or dialysis.

There are four kinds of reversible protein inhibitors.

In competitive inhibition, the natural ligand and the inhibitor cannot bind to the protein at the same time. This usually results from the inhibitor having an affinity for the active site of a protein where the natural ligand also binds; the natural ligand and inhibitor compete for access to the protein’s active site. This type of inhibition can be in certain occasions overcome by sufficiently high concentrations of natural ligand, by out-competing the inhibitor. Competitive inhibitors are often similar in structure to the natural ligand of the protein.

In uncompetitive inhibition , the inhibitor binds only to the protein-ligand complex, it should not be confused with non-competitive inhibitors. This type of inhibition causes a decrease in rate of normal biochemical processes and conversions.

In mixed inhibition , the inhibitor can bind to the protein at the same time as the natural ligand. However, the binding of the inhibitor affects the binding of the natural ligand, and vice versa. This type of inhibition can be reduced, but not overcome by increasing concentration of natural ligand. Although it is possible for mixed-type inhibitors to bind in the active site, this type of inhibition generally results from an allosteric effect where the inhibitor binds to a different site on a protein. Inhibitor binding to this allosteric site changes the three dimensional conformation of the protein so that the affinity of the natural ligand for the active site is reduced.

Non-competitive inhibition is a form of mixed inhibition where the binding of the inhibitor to the protein reduces its activity but does not affect the binding of natural ligand. As a result, the extent of inhibition depends only on the concentration of the inhibitor.

Natural ligands as well as products also can some time act as protein inhibitors. This happens where either the natural ligand or the product of an enzyme reaction inhibit the same enzyme’s activity. This inhibition may follow the competitive,uncompetitive or mixed patterns. In natural ligand inhibition there is a progressive decrease in activity at high ligand concentrations. This may indicate the existence of two substrate-binding sites in the enzyme. At low substrate, the high-affinity site is occupied and normal kinetics are followed. However, at higher concentrations, the second inhibitory site becomes occupied, inhibiting the enzyme.

Product inhibition is often a regulatory feature in metabolism and can be a form of negative feedback .

Irreversible inhibitors usually covalently modify a protein, and inhibition can therefore not be reversed. Irreversible inhibitor often contain reactive functional groups such as nitrogen mustards , aldehydes , haloalkanes, alkenes, Michael acceptors, phenyl sulfonates , or fluorophosphonates . These electrophilic groups react with amino acid side chains to form covalent adducts. The residues modified are those with side chains containing nucleophiles such as hydroxyl or sulfhydryl groups; these include the amino acids serine, cysteine, threonine or tyrosine. Irreversible inhibitors are generally specific for one class of proteins and do not inactivate all proteins; they do not function by destroying protein structure but by specifically altering the active site of their target.

Proten inhibitors are found in nature and are also designed and produced as part of pharmacology and biochemistry . Natural poisons are often protein inhibitors that have evolved to defend a plant or animal against predators . These natural toxins include some of the most poisonous compounds known. Artificial inhibitors are often used as drugs, but can also be insecticides such as malathion, herbicides such as glyphosate , or disinfectants uch as triclosan .

The most common uses for protein inhibitors are as drugs to treat disease in modern medicine. Many of these inhibitors target a human enzyme and aim to correct a pathological condition.

An example of a medicinal protein inhibitor is sildenafil (Viagra), a common treatment for male erectile dysfunction. This compound is a potent inhibitor of cGMP specific
phosphodiesterase type 5, the enzyme that degrades the signalling molecule cyclic guanosine monophosphate. This signalling molecule triggers smooth muscle relaxation
and allows blood flow into the corpus cavernosum , which causes an erection. Since the drug decreases the activity of the enzyme that halts the signal, it makes this signal last for a longer period of time.

Another example of the structural similarity of some inhibitors to the natural ligands of the proteins they target is seen in the the anti-cancer drug methotrexate and folic acid. Folic acid is a natural ligand of dihydrofolate reductase , an enzyme involved in making nucleotides that is potently inhibited by methotrexate. Methotrexate blocks the action of dihydrofolate reductase and thereby halts the productionnof nucleotides. This block of nucleotide biosynthesis is more toxic to rapidly growing cells than non-dividing cells, since a rapidly growing cell has to carry out DNA replication , therefore methotrexate is often used in cancer chemotherapy.

Drugs also are used to inhibit enzymes needed for the survival of pathogens. For example, bacteria are surrounded by a thick cell wall made of a net-like polymer called peptidoglycan. Many antibiotics such as penicillin and vancomycin inhibit the enzymes that produce and the cross-link the strands of this polymer together. This causes the cell wall to lose strength and the bacteria to burst.

Drug design is facilitated when an enzyme that is essential to the pathogen’s survival is absent or very different in humans. In the example above, humans do not make peptidoglycan, therefore inhibitors of this process are selectively toxic to bacteria. Selective toxicity is also produced in antibiotics by exploiting differences in the structure of the ribosomes in bacteria, or how they make fatty acids.

Protein inhibitors are also important in metabolic control. Many metabolic pathways in the cell are inhibited by metabolites that control protein activity through allosteric regulation or substrate inhibition. However,nmetabolic pathways are not just regulated through inhibition since proteinbactivation is equally important.

Many herbicides and pesticides are protein inhibitors. Aetylcholinesterase is an enzyme found in animals from insects to humans. It is essential to nerve cell function through its mechanism of breaking down the neurotransmitter acetylcholine into its constituents, acetate and choline. This is somewhat unique among neurotransmitters as most, including serotonin, dopamine , and norepinephrine, are absorbed from the synaptic cleft rather than cleaved. A large number of acetylcholineesterase inhibitors are used in both medicine and agriculture. Reversible competitive inhibitors, such as edrophonium , physostigmine , and neostigmine , are used in the treatment of myasthenia gravis and in anaesthesia. The carbamatenpesticides are also examples of reversible AChE inhibitors. The organophosphate insecticides such as malathion, parathion , and chlorpyrifos irreversibly inhibit acetylcholinesterase. The herbicide glyphosate is an inhibitor of 3-phosphoshikimate 1-carboxyvinyltransferase, other herbicides, such as the sulfonylureas inhibit the enzyme acetolactate synthase. Both these enzymes are needed for plants to make branched-chain amino acids . Many other enzymess are inhibited by herbicides, including enzymes needed for the biosynthesis of lipids and carotenoids andnthe processes of photosynthesis and oxidative phosphorylation. NTo discourage seed predators , pulses contain trypsin inhibitors that interfere with digestion.

Animals and plants have evolved to synthesise a vast array of poisonous products including secondary metabolites , peptides and proteins that can act as inhibitors. Natural toxins are usually small organic molecules and are so diverse that there are probably natural inhibitors for most metabolic processes.

The metabolic processes targeted by natural poisons encompass more than enzymes in metabolic pathways and can also include the inhibition of receptor, channel and structural protein functions in a cell. For example, paclitaxel (taxol), an organic molecule found in the Pacific yew tree , binds tightly to tubulin dimers and inhibits their assembly into microtubules in the cytoskeleton .

Many natural poisons act as neurotoxins that can cause paralysis leading to death and have functions for defence against predators or in hunting and capturing prey. Some of these natural inhibitors, despite their toxic attributes, are valuable for therapeutic uses at lower doses. An example of a neurotoxin are the glycoalkaloids, from the plant species in the Solanaceae family (includes potato , tomato and eggplant), that are acetylcholinesterase inhibitors. Inhibition of this enzyme causes an uncontrolled increase in the acetylcholine neurotransmitter, muscular paralysis and then death.

Neurotoxicity can also result from the inhibition of receptors; for example, atropine from deadly nightshade ( Atropa belladonna ) that functions as a competitive antagonist of the muscarinic acetylcholine receptors . Although many natural toxins are secondary metabolites, these poisons also include peptides and proteins. An example of a toxic peptide is alpha-amanitin , which is found in relatives of the death cap mushroom. This is a potent enzyme inhibitor, in this case preventing the RNA polymerase II enzyme from transcribing DNA. The algaltoxin microcystin is also a peptide and is an inhibitor of protein phosphatases. This toxin can contaminate water supplies after algal blooms and is a known carcinogen that can also cause acute liver hemorrhage and death at higher doses.

Proteins can also be natural poisons or antinutrients , such as the trypsin inhibitors that are found in some legumes , as shown in the figure above. A less common class of toxins are toxic enzymes: these act as irreversible inhibitors of their target enzymes and work by chemically modifying their substrate enzymes. An example is ricin , an extremely potent protein toxin found in castor oil beans . This enzyme is a glycosidase that inactivates ribosomes. Since ricin is a catalytic irreversible inhibitor, this allows just a single molecule of ricin to kill a cell.


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