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Chapter 9: Making new antibiotics. Model organisms are used to speed drug discovery.

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Chapter 9:

Making new antibiotics

Model organisms are used to speed drug discovery

A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms.

Model organisms are in vivo models and are widely used to research human disease when human experimentation would be unfeasible or unethical.This strategy is made possible by the common descent of all living organisms, and the conservation of metabolic and developmental pathways and genetic material over the course of evolution.

In addition, model organisms can be used to study other systems when the model circumvents a wide variety of bottlenecks. Of particular importance to us is that a closely related (less dangerous) bacterium can be studied in lieu of having to expose scientists to particularly virulent bugs.

Model organisms are used to speed drug discovery

Fruit fly

E. coli


C. elegans



Model organisms are used to speed drug discovery

Studying model organisms can be informative, but care must be taken when extrapolating from one organism to another.

M. bovis BCG

M. tuberculosis

Also grows slowly. Does not require BS3 protocols, but can also enter a dormant state after infection.

Grows very slowly. Due to its virulence, M. tuberculosis requires BS3 protocols.

M. smegmatis: Grows faster and easier to handle than M. bovis.

Model organisms are used to speed drug discovery

Studying model organisms can be informative, but care must be taken when extrapolating from one organism to another.

M. tuberculosis

E. coli

Works for fluoroquinolones because they inhibit replication in a similar way, but not for b-lactams due to differences in the cell wall structure.

Natural products

Salicylic acid

From the bark of the willow tree. The Greek physician Hippocrates wrote in the 5th century BC about a bitter powder extracted from willow bark that could ease aches and pains and reduce fevers. This remedy was also mentioned in texts from ancient Sumer, Lebanon, and Assyria. The Cherokee and other Native Americans used an infusion of the bark for fever and other medicinal purposes for centuries.

Acetylsalicylic acid

Aspirin, the most popular drug in the world, is a nonsteroidal anti-inflammatory drug (NSAID) used to treat a wide variety of conditions. Aspirin is a prodrug that metabolizes into the active form (salicylic acid).

High-throughput screening

High-throughput screening (HTS) is a method for scientific experimentation especially used in drug discovery and relevant to the fields of biology and chemistry.

Using robotics, data processing and control software, liquid handling devices, and sensitive detectors, HTS allows a researcher to quickly conduct millions of chemical, genetic, or pharmacological tests.

Through this process one can rapidly identify active compounds, antibodies, or genes that modulate a particular biomolecular pathway.

The results of these experiments provide starting points for drug design and for understanding the interaction or role of a particular biochemical process in biology.

Drug discovery from in silicohigh-throughput screening

Drug discovery library

  • Druglikeness is a qualitative concept used in drug design for how "druglike" a substance is with respect to factors like bioavailability. It is estimated from the molecular structure before the substance is even synthesized and tested. A druglike molecule has properties such as:

  • Solubility in both water and fat, as an orally administered drug needs to pass through the intestinal lining after it is consumed, carried in aqueous blood and penetrate the lipid cellular membrane to reach the inside of a cell. A model compound for the lipophilic cellular membrane is 1-octanol (a lipophilic hydrocarbon), so the logarithm of the octanol/water partition coefficient, known as LogP, is used to predict the solubility of a potential oral drug. This coefficient can be experimentally measured or predicted computationally.

  • Potency at the target of interest. High potency (high value of IC50) is a desirable attribute in drug candidates, as it reduces the risk of non-specific, off-target pharmacology at a given concentration. When associated with low clearance, high potency also allows for low total dose, which lowers the risk of idiosyncratic drug reactions.

  • Several scoring methods can be used to express druglikeness as a function of potency and physicochemical properties, for example ligand efficiency and lipophilic efficiency.

Drug discovery library, cont.

  • Since the drug is transported in aqueous media like blood and intracellular fluid, it has to be sufficiently water-soluble in the absolute sense. Solubility in water can be estimated from the number of hydrogen bond donors vs. alkyl sidechains in the molecule. Low water solubility translates to slow absorption and action. Too many hydrogen bond donors, on the other hand, lead to low fat solubility, so that the drug cannot penetrate the cell membrane to reach the inside of the cell.

  • Molecular weight: The smaller the better, because diffusion is directly affected. Eighty percent of traded drugs have molecular weights under 450 daltons; they belong to the group of small molecules.

  • Substructures that have known chemical or pharmacological properties. For example, alkylnitro compounds tend to be irritants, and Michael acceptors, such as enones, are alkylating agents and thus potentially mutagenic and carcinogenic.

  • A traditional method to evaluate druglikeness is to check compliance of Lipinski's Rule of Five, which covers the numbers of hydrophilic groups, molecular weight and hydrophobicity.

Lipinski’s rule of 5

  • A traditional method to evaluate druglikeness is to check compliance of Lipinski's Rule of Five, which covers the numbers of hydrophilic groups, molecular weight and hydrophobicity.

  • Lipinski's rule states that, in general, an orally active drug has no more than one violation of the following criteria:

  • No more than 5 hydrogen bond donors (nitrogen or oxygen atoms with one or more hydrogen atoms)

  • Not more than 10 hydrogen bond acceptors (nitrogen or oxygen atoms)

  • A molecular mass less than 500 daltons

  • An octanol-water partition coefficient[5] log P not greater than 5

  • Note that all numbers are multiples of five, which is the origin of the rule's name. As with many other rules of thumb, there are many exceptions to Lipinski's Rule.

Pharmacological assays

An assay is an experimental procedure for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity, which can be a drug or biochemical substance or a cell in an organism or organic sample.

Rational drug design

aka, Computer Aided Drug Design (CADD) or Computer Aided Molecular Design (CAMD)

HIV Protease

Rational drug design

HIV Protease