1.
PubChem
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PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information, a component of the National Library of Medicine, PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be downloaded via FTP. PubChem contains substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds, more than 80 database vendors contribute to the growing PubChem database. PubChem consists of three dynamically growing primary databases, as of 28 January 2016, Compounds,82.6 million entries, contains pure and characterized chemical compounds. Substances,198 million entries, contains also mixtures, extracts, complexes, bioAssay, bioactivity results from 1.1 million high-throughput screening programs with several million values. PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments. In the text search form the database fields can be searched by adding the name in square brackets to the search term. A numeric range is represented by two separated by a colon. The search terms and field names are case-insensitive, parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used, example,0,5000,50,10 -5,5 PubChem was released in 2004. The American Chemical Society has raised concerns about the publicly supported PubChem database and they have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the societys revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress, soon after PubChems creation, the American Chemical Society lobbied U. S. Congress to restrict the operation of PubChem, which they asserted competes with their Chemical Abstracts Service
2.
ChemSpider
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ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry, the database contains information on more than 50 million molecules from over 500 data sources including, Each chemical is given a unique identifier, which forms part of a corresponding URL. This is an approach to develop an online chemistry database. The search can be used to widen or restrict already found results, structure searching on mobile devices can be done using free apps for iOS and for the Android. The ChemSpider database has been used in combination with text mining as the basis of document markup. The result is a system between chemistry documents and information look-up via ChemSpider into over 150 data sources. ChemSpider was acquired by the Royal Society of Chemistry in May,2009, prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a release form. ChemSpider has expanded the generic support of a database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation. A number of services are available online. SyntheticPages is an interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry. Users submit synthetic procedures which they have conducted themselves for publication on the site and these procedures may be original works, but they are more often based on literature reactions. Citations to the published procedure are made where appropriate. They are checked by an editor before posting. The pages do not undergo formal peer-review like a journal article. The comments are moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab, while experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Comments by submitters are included as well, other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses
3.
European Chemicals Agency
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ECHA is the driving force among regulatory authorities in implementing the EUs chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and it is located in Helsinki, Finland. The Agency, headed by Executive Director Geert Dancet, started working on 1 June 2007, the REACH Regulation requires companies to provide information on the hazards, risks and safe use of chemical substances that they manufacture or import. Companies register this information with ECHA and it is freely available on their website. So far, thousands of the most hazardous and the most commonly used substances have been registered, the information is technical but gives detail on the impact of each chemical on people and the environment. This also gives European consumers the right to ask whether the goods they buy contain dangerous substances. The Classification, Labelling and Packaging Regulation introduces a globally harmonised system for classifying and labelling chemicals into the EU. This worldwide system makes it easier for workers and consumers to know the effects of chemicals, companies need to notify ECHA of the classification and labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100000 substances, the information is freely available on their website. Consumers can check chemicals in the products they use, Biocidal products include, for example, insect repellents and disinfectants used in hospitals. The Biocidal Products Regulation ensures that there is information about these products so that consumers can use them safely. ECHA is responsible for implementing the regulation, the law on Prior Informed Consent sets guidelines for the export and import of hazardous chemicals. Through this mechanism, countries due to hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have effects on human health and the environment are identified as Substances of Very High Concern 1. These are mainly substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment, other substances considered as SVHCs include, for example, endocrine disrupting chemicals. Companies manufacturing or importing articles containing these substances in a concentration above 0 and they are required to inform users about the presence of the substance and therefore how to use it safely. Consumers have the right to ask the retailer whether these substances are present in the products they buy, once a substance has been officially identified in the EU as being of very high concern, it will be added to a list. This list is available on ECHA’s website and shows consumers and industry which chemicals are identified as SVHCs, Substances placed on the Candidate List can then move to another list
4.
Chemical formula
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
5.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
6.
Simplified molecular-input line-entry system
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The simplified molecular-input line-entry system is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules, the original SMILES specification was initiated in the 1980s. It has since modified and extended. In 2007, a standard called OpenSMILES was developed in the open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. The Environmental Protection Agency funded the project to develop SMILES. It has since modified and extended by others, most notably by Daylight Chemical Information Systems. In 2007, a standard called OpenSMILES was developed by the Blue Obelisk open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, in July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI, the term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also used to refer to both a single SMILES string and a number of SMILES strings, the exact meaning is usually apparent from the context. The terms canonical and isomeric can lead to confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive, typically, a number of equally valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol, algorithms have been developed to generate the same SMILES string for a given molecule, of the many possible strings, these algorithms choose only one of them. This SMILES is unique for each structure, although dependent on the algorithm used to generate it. These algorithms first convert the SMILES to a representation of the molecular structure. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database, there is currently no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, and these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES
7.
International Chemical Identifier
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Initially developed by IUPAC and NIST from 2000 to 2005, the format and algorithms are non-proprietary. The continuing development of the standard has supported since 2010 by the not-for-profit InChI Trust. The current version is 1.04 and was released in September 2011, prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Not all layers have to be provided, for instance, the layer can be omitted if that type of information is not relevant to the particular application. InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names and they can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI, the InChI algorithm converts input structural information into a unique InChI identifier in a three-step process, normalization, canonicalization, and serialization. The InChIKey, sometimes referred to as a hashed InChI, is a fixed length condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds and it should be noted that, unlike the InChI, the InChIKey is not unique, though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released and this provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string, the standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Every InChI starts with the string InChI= followed by the version number and this is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, the layers and sub-layers are separated by the delimiter / and start with a characteristic prefix letter. The six layers with important sublayers are, Main layer Chemical formula and this is the only sublayer that must occur in every InChI. The atoms in the formula are numbered in sequence, this sublayer describes which atoms are connected by bonds to which other ones. Describes how many hydrogen atoms are connected to each of the other atoms, the condensed,27 character standard InChIKey is a hashed version of the full standard InChI, designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, the full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. With all databases currently having below 50 million structures, such duplication appears unlikely at present, a recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. Example, Morphine has the structure shown on the right, as the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure
8.
Camylofin
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Camylofin is a smooth muscle relaxant with both anticholinergic action as well as direct smooth muscle action. Anticholinergic action is produced by inhibiting the binding of acetylcholine to muscarinic receptors, direct smooth muscle relaxation is achieved by inhibiting phosphodiesterase type IV, which leads to increased cyclic AMP and eventually reduced cytosolic calcium. Thus camylofin has an action to relieve smooth muscle spasm. It is used to treat stomach ache in infants and children, usually it is given in combination with paracetamol to treat stomach ache, as well as pyrexia
9.
Mebeverine
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Mebeverine is a drug whose major therapeutic role is in the treatment of irritable bowel syndrome and the associated abdominal cramping. It works by relaxing the muscles in and around the gut and it is a musculotropic antispasmodic drug without anticholinergic side effects. The drug is indicated for treatment of gastrointestinal spasm secondary to organic disorder. It is also an inhibitor of calcium-depot replenishment, musculotropic compounds act directly on the gut muscles at the cellular level to relax them. This relieves painful muscle spasms of the gut, without affecting its normal motility, mebeverine is used to relieve symptoms of irritable bowel syndrome and related intestinal disorders that are the result of spasms in the intestinal muscles. These include colicky abdominal pain and cramps, diarrhoea alternating with constipation, most reactions consisted of urticaria or maculopapular rash, sometimes accompanied by fever, polyarthritis, thrombocytopenia or angioedema. Very rarely, people taking this medicine may develop allergic reactions, mebeverine passes into breast milk, but the amount is considered too small to be harmful to a nursing infant. Mebeverine is unlikely to affect the ability to operate machinery or to drive and it was first registered in 1965. Mebeverine is a drug and is available internationally under many brand names
10.
Trimebutine
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Trimebutine is a drug with antimuscarinic and weak mu opioid agonist effects. The maleic acid salt of trimebutine is marketed under the trademark of Debridat, Recutin, Polybutin, or Modulon for treatment of irritable bowel syndrome and other gastrointestinal disorders. The major product from drug metabolism of trimebutine in human beings is nortrimebutine, Trimebutine exerts its effects in part due to causing a premature activation of phase III of the migrating motor complex in the digestive tract. Both Trimebutine and its metabolite are commercially available
11.
Quaternary ammonium
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Quaternary ammonium cations, also known as quats, are positively charged polyatomic ions of the structure NR+4, R being an alkyl group or an aryl group. Unlike the ammonium ion and the primary, secondary, or tertiary ammonium cations, Quaternary ammonium salts or quaternary ammonium compounds are salts of quaternary ammonium cations. Quaternary ammonium compounds are prepared by the alkylation of amines with a halocarbon. In older literature this is called a Menshutkin reaction, however modern chemists usually refer to it simply as quaternization. The reaction can be used to produce a compound with unequal alkyl chain lengths and they also are stable toward most nucleophiles. The latter is indicated by the stability of the hydroxide salts such as tetramethylammonium hydroxide, because of their resilience, many unusual anions have been isolated as the quaternary ammonium salts. Examples include tetramethylammonium pentafluoroxenate, containing the highly reactive pentafluoroxenate ion, permanganate can be solubilized in organic solvents, when deployed as its NBu+4 salt. With exceptionally strong bases, quat cations degrade and they undergo Sommelet–Hauser rearrangement and Stevens rearrangement, as well as dealkylation under harsh conditions. Quaternary ammonium cations containing N–C–C–H units can also undergo the Hofmann elimination, Quaternary ammonium salts are used as disinfectants, surfactants, fabric softeners, and as antistatic agents. In liquid fabric softeners, the salts are often used. In dryer anticling strips, the salts are often used. Spermicidal jellies also contain quaternary ammonium salts, Quaternary ammonium compounds have also been shown to have antimicrobial activity. Certain quaternary ammonium compounds, especially those containing long alkyl chains, are used as antimicrobials, also good against fungi, amoebas, and enveloped viruses, quaternary ammonium compounds are believed to act by disrupting the cell membrane. Quaternary ammonium compounds are lethal to a variety of organisms except endospores, Mycobacterium tuberculosis. Quaternary ammonium compounds are cationic detergents, as well as disinfectants and they are very effective in combination with phenols. Quaternary ammonium compounds are deactivated by anionic detergents, also, they work best in soft waters. Effective levels are at 200 ppm and they are effective at temperatures up to 100 °C. Quaternary ammonium salts are used in the foodservice industry as sanitizing agents
12.
Glycopyrronium bromide
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Glycopyrronium bromide is a medication of the muscarinic anticholinergic group. It does not cross the barrier and consequently has no to few central effects. A synthetic quaternary amine, it is available in oral and intravenous forms and it was developed by Sosei and licensed to Novartis in 2005. The cation, which is the moiety, is called glycopyrronium or glycopyrrolate. It is also used in conjunction with neostigmine, a neuromuscular blocking reversal agent and it is also used to reduce excessive saliva, and Ménières disease. It decreases acid secretion in the stomach and so may be used for treating stomach ulcers and it has been used topically and orally to treat hyperhidrosis, in particular, gustatory hyperhidrosis. In inhalable form it is used to treat chronic obstructive pulmonary disease, doses for inhalation are much lower than oral ones, so that swallowing a dose will not have an effect. Since glycopyrronium reduces the bodys sweating ability, it can even cause hyperthermia, dry mouth, difficulty urinating, headaches, diarrhea and constipation are also observed side effects of the medication. The medication also induces drowsiness or blurred vision, an effect exacerbated by the consumption of alcohol, glycopyrronium blocks muscarinic receptors, thus inhibiting cholinergic transmission. Glycopyrronium bromide affects the gastrointestinal tracts, liver and kidney but has a limited effect on the brain. Excretion was mainly in urine and in the form of an unchanged drug, glycopyrronium has a relatively slow diffusion rate, and in a standard comparison to atropine, is more resistant to penetration through the blood-brain barrier and placenta. It has been studied in asthma
13.
Phosphodiesterase inhibitor
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The potential for selective phosphodiesterase inhibitors as therapeutic agents was predicted as early as 1977 by Weiss and Hait. This prediction meanwhile has proved to be true in a variety of fields, vinpocetine EHNA BAY 60-7550 Oxindole PDP Inamrinone, milrinone and Enoximone are used clinically for short-term treatment of cardiac failure. These drugs mimic sympathetic stimulation and increase cardiac output, anagrelide Cilostazol is used in the treatment of intermittent claudication. Pimobendan is FDA approved for use in the treatment of heart failure in animals. PDE3 is sometimes referred to as cGMP-inhibited phosphodiesterase, piclamilast, a more potent inhibitor than rolipram. Luteolin, supplement extracted from peanuts that also possesses IGF-1 properties, crisaborole, used to treat atopic dermatitis. PDE4 is the major cAMP-metabolizing enzyme found in inflammatory and immune cells, PDE4 inhibitors have proven potential as anti-inflammatory drugs, especially in inflammatory pulmonary diseases such as asthma, COPD, and rhinitis. They suppress the release of cytokines and other signals. PDE4 inhibitors may have effects and have also recently been proposed for use as antipsychotics. On October 26,2009, The University of Pennsylvania reported that researchers at their institution had discovered a link between elevated levels of PDE4 in sleep deprived mice, treatment with a PDE4 inhibitor raised the deficient cAMP levels and restored some functionality to Hippocampus-based memory functions. Sildenafil, tadalafil, vardenafil, and the newer udenafil and avanafil selectively inhibit PDE5 and these phosphodiesterase inhibitors are used primarily as remedies for erectile dysfunction, as well as having some other medical applications such as treatment of pulmonary hypertension. This results in added benefit when given together with NO or statins, recent studies have shown Quinazoline type PDE7 inhibitor to be potent anti-inflammatory and neuroprotective agents. Papaverine, an alkaloid, has been reported to act as a PDE10 inhibitor. PDE10A is almost exclusively expressed in the striatum and subsequent increase in cAMP and cGMP after PDE10A inhibition is a novel therapeutic avenue in the discovery of antipsychotics
14.
Drotaverine
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Drotaverine is an antispasmodic drug, used to enhance cervical dilation during childbirth. It is structurally related to papaverine, is an inhibitor of phosphodiesterase 4. It is available in Asian and Eastern European countries under several brand names, an article from 2013 described the effects from overdose as including vomiting, seizures and fatal cardiac toxicity. In 2016, the young Russian chess player Ivan Bukavshin died of an overdose of the drug
15.
5-HT receptor
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They mediate both excitatory and inhibitory neurotransmission. The serotonin receptors are activated by the serotonin, which acts as their natural ligand. The serotonin receptors influence various biological and neurological processes such as aggression, anxiety, appetite, cognition, learning, memory, mood, nausea, sleep, and thermoregulation. Serotonin receptors are found in almost all animals and humans and are known to regulate longevity and behavioral aging in the primitive nematode. In 2014 a novel 5-HT receptor was described that was isolated from the white butterfly, Pieris rapae. It shares relatively low similarity to the known 5-HT receptor classes and does not occur in mammals, the 7 general serotonin receptor classes include a total of 14 known serotonin receptors. Very nonselective agonists of 5-HT receptor subtypes include ergotamine, which activates 5-HT1A, 5-HT1D, 5-HT1B, D2, LSD is a 5-HT1A, 5-HT2A, 5-HT2C, 5-HT5A, 5-HT5, 5-HT6 agonist. Serotonin Receptors at the US National Library of Medicine Medical Subject Headings 5-Hydroxytryptamine Receptors, IUPHAR Database of Receptors and Ion Channels. International Union of Basic and Clinical Pharmacology, activation of G protein-coupled receptors entails cysteine modulation of agonist binding. Paterson LM, Kornum BR, Nutt DJ, Pike VW, 5-HT radioligands for human brain imaging with PET and SPECT
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