CHAPTER 3

Calculation of molecular properties, Lipinski

“Rule of Five”, prediction of bioactivity score

3.Molecular properties, Lipinski “Rule of Five” and Bioactivity score:

This chapter highlights the importance of Lipinski “Rule of Five”,

Calculation of important molecular properties such as logP, polar surface area,

number of hydrogen bond donors, number of hydrogen bond acceptors and

molecular weight, as well as prediction of bioactivity score for the most important

drug targets like GPCR ligands, kinase inhibitors, ion channel modulators and

nuclear receptors.

Experimental and computational approaches to estimate solubility and

permeability in discovery and development settings are described. In the discovery

setting `the rule of 5' predicts that poor absorption or permeation is more likely

when there are more than 5 H-bond donors, 10 H-bond acceptors, the molecular

weight (MWT) is greater than 500 and the calculated Log P (CLogP) is greater

than 5 (or MlogP>4.15). Computational methodology for the rule-based Moriguchi

Log P (MLogP) calculation is described. Turbidimetric solubility measurement is

described and applied to known drugs. High throughput screening (HTS) leads

tend to have higher MWT and Log P and lower turbidimetric solubility than leads

in the pre-HTS era. In the development setting, solubility calculations focus on

exact value prediction and are difficult because of polymorphism. Recent work on

linear free energy relationships and Log P approaches are critically reviewed.

Useful predictions are possible in closely related analog series when coupled with

experimental thermodynamic solubility measurements.

3.1 Lipinski's rule of five:

Lipinski's rule of five (RO5) is a rule of thumb to evaluate druglikeness

or determine if a chemical compound with a certain pharmacological or biological

activity has properties that would make it a likely orally active drug in humans.

The rule was formulated by Christopher A. Lipinski in 1997, based on the

observation that most medication drugs are relatively small and lipophilic

molecules.The rule describes molecular properties important for a drug's

pharmacokinetics in the human body, including their absorption, distribution,

metabolism, and excretion ("ADME"). However, the rule does not predict if a

compound is pharmacologically active.

The rule is important to keep in mind during drug discovery when a

pharmacologically active lead structure is optimized step-wise to increase the

activity and selectivity of the compound as well as to insure drug-like

physicochemical properties are maintained as described by Lipinski's rule.

Candidate drugs that conform to the RO5 tend to have lower attrition rates during

clinical trials and hence have an increased chance of reaching the market.

3.1.1 Components of the rule

Lipinski's rule states that, in general, an orally active drug has no more

than one violation of the following criteria:

• Not 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 log P not greater than 5

Note that all numbers are multiples of five, which is the origin of the rule's name.

3.1.2 Variants

In an attempt to improve the predictions of druglikeness, the rules have spawned

many extensions, for example the following:

• Partition coefficient log P in −0.4 to +5.6 range

• Molar refractivity from 40 to 130

• Molecular weight from 180 to 500

• Number of atoms from 20 to 70 (includes H-bond donors [e.g.;OH's and

NH's] and H-bond acceptors [e.g.; N's and O's])

• Polar surface area no greater than 140 Ǻ2

Also the 500 molecular weight cutoff has been questioned. Polar surface area and

the number of rotatable bonds has been found to better discriminate between

compounds that are orally active and those that are not for a large data set of

compounds. In particular, compounds which meet only the two criteria of:

• 10 or fewer rotatable bonds and

• polar surface area equal to or less than 140 Å2

are predicted to have good oral bioavailability.

3.1.3 Lead-like

During drug discovery, lipophilicity and molecular weight are often

increased in order to improve the affinity and selectivity of the drug candidate.

Hence it is often difficult to maintain drug-likeness (i.e., RO5 compliance) during

hit and lead optimization. Hence it has been proposed that members of screening

libraries from which hits are discovered should be biased toward lower molecular

weight and lipophility so that medicinal chemists will have an easier time in

delivering optimized drug development candidates that are also drug-like. Hence

the rule of five has been extended to the rule of three (RO3) for defining lead-like

compounds.

A rule of three compliant compound is defined as one that has:

• octanol-water partition coefficient log P not greater than 3

• molecular mass less than 300 daltons

• not more than 3 hydrogen bond donors

• not more than 3 hydrogen bond acceptors

• not more than 3 rotatable bonds

This is best explained using the below graphical representation (Fig 3.1)

of chemical space introduced by Lipinski and Hopkins where compounds are

mapped onto coordinates of chemical descriptors of physicochemical or

topological properties. For example, it is known that active site inhibitors for

protease families cluster together in a discrete region of chemical space. The

intersection of this cluster with the descriptor space for drug-like compounds

would contain in this example the protease inhibitors that have the potential to be

developed as oral drugs. Such an overlap would allow the conclusion that the

protease family is druggable. The most challenging part of a protease inhibitor

optimization is changing a peptidic lead compound into an orally bioavailable

peptidomimetic. This step has proven to be relatively straightforward for some

proteases (e.g. thrombin), whereas for others it may be an almost impossible job

due to the amino acid content of the lead and the shallowness of the binding

pocket. The latter case would probably constitute an exception in the generally

druggable protease family (Fig 3.2). Such subtleties create uncertainties about the

reliability of druggability arguments for strategic decision making, especially in

cases of well validated targets with borderline druggability.

A first step towards a more reliable way to assess the druggability of

individual proteins is the identification of binding sites for drug-like molecules.

Kellenberger and co-workers have created an annotated database of ligand binding

sites extracted from several experimental structure databases. Such data can be

used to derive rules or training sets for the computational identification of binding

pockets. Many algorithms are available for this purpose and in general they have

been successfully applied in identifying true ligand binding pockets on the surface

of proteins.

(Fig 3.1) Representation of the relationship between the continuum of chemical space

A graphical representation of the relationship between the continuum of

chemical space (light blue) and the discrete areas occupied by compounds with

specific affinity for certain protein classes. The independent intersection of

compounds with drug-like properties is shown in green. The second step of

quantitatively assessing the druggability of the identified pockets is more

challenging. An obvious approach is to screen a large library of drug-like

compounds (pharmaceutical compound collection or a chemical genetics library

and assess the resulting hits. Unfortunately, this approach has three significant

drawbacks: it is very expensive, applied rather late in the drug discovery process

and it produces a large number of false positives and promiscuous hits which

complicate the analysis.

Fig 3.2 the chemical space occupied by active site serine protease inhibitors.

A close-up of the Fig 3.1 that shows the chemical space occupied by

active site serine protease inhibitors. Since this bubble intersects with the oral

drug-like space, we would come to the conclusion that the serine protease family is

druggable. The situation is, however, more complex. Some serine proteases will be

druggable whereas others are not.

Another method has recently been developed by researchers from

Abbott. Using 2-D heteronuclear-NMR they studied the interactions of 10 000

lead-like or fragment-like compounds with protein surfaces. This approach has the

advantage that it samples a large fraction of chemical space (even though the size

of the library is small) and yields more reliable data than conventional high-

throughput screening. Furthermore, such an NMR based analysis of druggability

could be performed with limited resources and relatively early in the drug

discovery process. Most importantly, an analysis of the NMR data has led to the

development of ‘druggability-indices’ that can be used for the computational

assessment of proteins with known structure. Such quantitative assessments of

druggability would find wide application if it were not for the limited availability

of experimental 3-D structures. Despite the progress that has been made in

structural biology, especially with the structural genomics approaches, only a small

fraction of all proteins have been experimentally characterized. As a consequence,

most structure-based assessments of target druggability still need to be performed

with homology models. Unfortunately the predictive quality of homology models

and therefore their usefulness is rather uncertain since often no closely related

protein with known 3-D structure is available.

3.1.4 Exception to the rule of five:

In the period 1970-2006, a total of 24 unique natural products were

discovered that led to an approved drug. We analyze these successful leads in

terms of drug-like properties, and show that they can be divided into two equal

subsets. The first falls in the 'Lipinski universe' and complies with the Rule of Five.

The second is a 'parallel universe' that violates the rules. Nevertheless, the latter

compounds remain largely compliant in terms of logP and H-bond donors,

highlighting the importance of these two metrics in predicting bioavailability.

Natural products are often cited as an exception to Lipinski's rules. We believe this

is because nature has learned to maintain low hydrophobicity and intermolecular

H-bond donating potential when it needs to make biologically active compounds

with high molecular weight and large numbers of rotatable bonds. In addition,

natural products are more likely than purely synthetic compounds to resemble

biosynthetic intermediates or endogenous metabolites, and hence take advantage of

active transport mechanisms. Interestingly, the natural product leads in the Lipinski

and parallel universe had an identical success rate (50%) in delivering an oral drug.

Compound classes that are substrates for biological transporters:

• Antibiotics

• Fungicides-Protozoacides -antiseptics

• Vitamins

• Cardiac glycosides.

3.1.5 Conclusion on RO5:

The RO5 and its extensions have been useful tools to generate awareness

about the importance of PK parameters for development. In addition, this concept

has led to the realization that there may be whole families of proteins for which it

is either extremely challenging or impossible to design compounds with good oral

bioavailability.

The available evidence suggests that qualitative druggability arguments

are useful strategic tools; however, more accurate, quantitative assessments are

needed, especially for proteins with borderline druggability. Recent developments

suggest that NMR-based screening could deliver such information. In our view,

this is a very attractive approach that can be used in the early stages of drug

discovery and provides a solid basis for computational druggability estimations. It

has been suggested that the inability of the pharmaceutical industry to solve

druggability problems is due to limitations in current medicinal chemistry

approaches. As outlined above, druggability is defined by molecular properties and

therefore it is unlikely that advances in synthesis, profiling or innovative design

will solve these problems. The much-quoted advances in this area (e.g., finding

rinhibitors for protein–protein interactions) rarely address the real problems: PK

and especially oral bioavailability. It is often possible to find inhibitors of proteins

with questionable druggability, but this is only the first step.

The real druggability challenge arrives when these ‘leads’ have to be

turned into orally bio available, pharmaceutically useful drug candidates. It has

never been challenging to make inhibitors of proteins with questionable

druggability, but rather the challenge has been to make orally bio available,

pharmaceutically useful inhibitors that successfully advance through clinical

evelopment. It is likely that oral drugs for the modulation of such proteins will

continue to come from the natural-product pool. In addition, future advances in

drug delivery may offer solutions to address problems of druggability.

3.2 Biological activity

In pharmacology, biological activity or pharmacological activity

describes the beneficial or adverse effects of a drug on living matter. When a drug

is a complex chemical mixture, this activity is exerted by the substance's active

ingredient or pharmacophore but can be modified by the other constituents.

Activity is generally dosage-dependent. Further, it is common to have effects

ranging from beneficial to adverse for one substance when going from low to high

doses. Activity depends critically on fulfillment of the ADME criteria. Whereas a

material is considered bioactive if it has interaction with or effect on any cell tissue

in the human body, pharmacological activity is usually taken to describe beneficial

effects, i.e. the effects of drug candidates as well as a substance's toxicity.

3.2.1 Biological target

A biological target is a biopolymer such as a protein or nucleic acid

whose activity can be modified by an external stimulus. The definition is context-

dependent and can refer to the biological target of a pharmacologically active drug

compound, or the receptor target of a hormone (like insulin). The implication is

that a molecule is "hit" by a signal and its behavior is thereby changed. Biological

targets are most commonly proteins such as enzymes, ion channels, and receptors.

3.2.2 Mechanism

The external stimulus (i.e., chemical substance) physically binds to the

biological target. The interaction between the substance and the target may be:

• Noncovalent

• Reversible covalent - A chemical reaction occurs between the stimulus and

target in which the stimulus becomes chemically bonded to the target, but

the reverse reaction also readily occurs in which the bond can be broken.

• Irreversible covalent - The stimulus is permanently bound to the target

through irreversible chemical bond formation.

Depending on the nature of the stimulus, the following can occur:

• There is no direct change in the biological target, except that the binding of

the substance prevents other endogenous substances such as activating

hormone to bind to the target. Depending on the nature of the target, this

effect is referred as receptor antagonism, enzyme inhibition, or ion channel

blockade.

• A conformational change in the target is induced by the stimulus which

results in a change in target function. This change in function can mimic the

effect of the endogenous substance in which case the effect is referred to as

receptor agonism (or channel or enzyme activation) or be the opposite of the

endogenous substance which in the case of receptors is referred to as inverse

agonism.

3.2.3 Drug targets

The term biological target is frequently used in pharmaceutical research to

describe the native protein in the body whose activity is modified by a drug

resulting in a desirable therapeutic effect. In this context, the biological target is

often referred to as a drug target. The most common drug targets of currently

marketed drugs include:

• Proteins

o G protein-coupled receptors (GPCR) (target of 50% of drugs)

o Enzymes (especially protein kinases, proteases, esterases, and

phosphatases)

o Ion channels

� ligand-gated ion channels

� voltage-gated ion channels

o Nuclear hormone receptors

o Structural proteins such as tubulin

o Membrane transport proteins

• Nucleic acids.

3.2.4 G protein-coupled receptor

G protein coupled receptors (GPCRs) are also known as seven-

transmembrane domain receptors, heptahelical receptors, serpentine receptor, and

G protein-linked receptors (GPLR), constitute a large protein family of receptors

that sense molecules outside the cell and activate inside signal transduction

pathways and, ultimately, cellular responses. They are called transmembrane

receptors because they pass through the cell membrane, and they are called seven-

transmembrane receptors because they pass through the cell membrane seven

times. G protein-coupled receptors are found only in eukaryotes, including yeast,

choanoflagellates and animals. The ligands that bind and activate these receptors

include light-sensitive compounds, odors, pheromones, hormones, and

neurotransmitters, and vary in size from small molecules to peptides to large

proteins.

G protein-coupled receptors are involved in many diseases, and are also

the target of approximately 40% of all modern medicinal drugs. The 2012 Nobel

prize in chemistry was awarded to Brian Kobilka and Robert Lefkowitz for their

work that was "crucial for understanding how G-protein–coupled receptors

function." There are two principal signal transduction pathways involving the G

protein-coupled receptors: the cAMP signal pathway and the phosphatidylinositol

signal pathway. When a ligand binds to the GPCR it causes a conformational

change in the GPCR, which allows it to act as a guanine nucleotide exchange

factor (GEF). The GPCR can then activate an associated G-protein by exchanging

its bound GDP for a GTP. The G-protein's α subunit, together with the bound GTP,

can then dissociate from the β and γ subunits to further affect intracellular

signaling proteins or target functional proteins directly depending on the α subunit

type (Gαsr, Gαi/o, Gαq/11, Gα12/13).

3.2.5 Protein kinase

A protein kinase is a kinase enzyme that modifies other proteins by

chemically adding phosphate groups to them (phosphorylation). Phosphorylation

usually results in a functional change of the target protein (substrate) by changing

enzyme activity, cellular location, or association with other proteins. The human

genome contains about 500 protein kinase genes and they constitute about 2% of

all human genes. Protein kinases are also found in bacteria and plants. Up to 30%

of all human proteins may be modified by kinase activity, and kinases are known

to regulate the majority of cellular pathways, especially those involved in signal

transduction.The chemical activity of a kinase involves transferring a phosphate

group from a nucleoside triphosphate (usually ATP) and covalently attaching it to

specific amino acids with a free hydrorxyl group. Most kinases act on both serine

and threonine (serine/threonine kinases), others act on tyrosine (tyrosine kinases),

and a number act on all three (dual-specificity kinases). There are also protein

kinases that phosphorylate other amino acids, including histidine kinases that

phosphorylate histidine residues.

The human protein kinase family is divided into the following groups and

shown in table 3.1:

Tab 3.1:

Protein kinase groups

AGC kinases Containing PKA, PKC and PKG.

CaM kinases The calcium/calmodulin-dependent protein kinases.

CK1 Containing the casein kinase 1 group.

CMGC Containing CDK, MAPK, GSK3 and CLK kinases.

STE Containing the homologs of yeast Sterile 7, Sterile 11, and Sterile 20 kinases.

TK Containing the tyrosine kinases.

TKL Containing the tyrosine-kinase like

group of kinases.

3.2.6 Inhibitors

Deregulated kinase activity is a frequent cause of disease, in particular

cancer, wherein kinases regulate many aspects that control cell growth, movement

and death. Drugs that inhibit specific kinases are being developed to treat several

diseases, and some are currently in clinical use, including Gleevec (imatinib) and

Iressa (gefitinib).

A protein kinase inhibitor is a type of enzyme inhibitor that specifically

blocks the action of one or more protein kinases. Protein kinases are enzymes that

add a phrosphate (PO4) group to a protein or other organic molecule, usually on the

serine, threonine, or tyrosine amino acid. Hence, protein kinase inhibitors can be

subdivided or characterised by the amino acids whose phosphorylation is inhibited:

most kinases act on both serine and threonine, the tyrosine kinases act on tyrosine,

and a number (dual-specificity kinases) act on all three. There are also protein

kinases that phosphorylate other amino acids, including histidine kinases that

phosphorylate histidine residues. Phosphorylation is a necessary step in some

cancers and inflammatory diseases. Inhibiting the protein kinases, and therefore the

phosphorylation, can treat these diseases. Therefore, protein kinase inhibitors are

used as drugs.

Kinase inhibitors such as dasatinib are often used in the treatment of

cancer and inflammation. The novel kinase inhibitor PLX5568 is currently in

clinical trials for treatment of polycystic kidney disease as well as pain. Some of

the kinase inhibitors used in treating cancer are inhibitors of tyrosine kinases. The

effectiveness of kinase inhibitors on various cancers can vary from patient to

patient.

Table 3.2

Drugs, launched or in development that target protein kinases and the receptors that activate them.

Name Target Company Class FDA

approval

Afatinib EGFR/ErbB2 Boehringer

Ingelheim

Small

molecule

Not yet

Axitinib VEGFR1/VEGFR2

/VEGFR3/PDGFR

B/c-KIT

Pfizer Small

molecule

2012 Renal

cell

carcinoma

Bevacizu

mab

VEGF Genentech Monoclona

l antibody

2004

Colorectal

Bosutinib BcrAbl /SRC Pfizer Small

molecule

2012

Chronic

myelogenou

s leukemia

Cetuxima

b

ErbB1 Imclone/BMS Monoclona

l antibody

2006 Mar

(SCCHN)

Crizotinib ALK/Met Pfizer Small

molecule

2011 Aug

(NSCLC

with Alk

mutation)

Dasatinib multiple targets BMS Small

molecule

2006

Erlotinib ErbB1 Genentech/Ro

che

Small

molecule

2005 Nov?

Fostamati

nib

Syk Rigel

Pharmaceutic

als/AstraZene

ca

Small

molecule

Not yet [1]

Gefitinib EGFR AstraZeneca Small

molecule

2003

Imatinib Bcr-Abl Novartis Small

molecule

2001

(CML),

2002 (GIST)

[4]

Lapatinib ErbB1/ErbB2 GSK Small

molecule

2007

(HER2+

Breast)

Lenvatini

b

VEGFR2/VEGFR2 Eisai Co. Small

molecule

Not yet

Mubritini

b

? Takeda Small

molecule

Not yet,

possibly

abandoned

Nilotinib Bcr-Abl Novartis Small

molecule

2007

Panitumu

mab

EGFR Amgen Monoclona

l antibody

2006

Pazopanib VEGFR2/PDGFR/

c-kit

GlaxoSmithK

line

Small

molecule

2009 (RCC)

Pegaptani

b

VEGF OSI/Pfizer RNA

Aptamer

2004

(AMD)

Ranibizu

mab

VEGF Genentech Monoclona

l antibody

2006

(AMD)

Ruxolitini

b

JAK Incyte Small

molecule

2011

(Myelofibro

sis)

Sorafenib multiple targets Onyx/Bayer Small

molecule

2005 Dec

(kidney)

Sunitinib multiple targets SUGEN/Pfize

r

Small

molecule

2006 Jan

(RCC &

GIST)

Trastuzu

mab

Erb2 Genentech/Ro

che

Monoclona

l antibody

1998

(HER2+

breast

cancer)

Vandetani

b

RET/VEGFR/EGF

R

AstraZeneca Small

molecule

No,

submission

withdrawn

Oct09 [2]

Vemurafe

nib

BRAF Roche Small

molecule

2011 Aug

Melanoma

3.2.7 Ion channel modulators

Ion channels allow the movement of charged particles, known as ions,

across cell membranes. Ion channels function in a variety of biological pathways

including the firing of neurons and muscle cells and the activation of immune cells.

Ion channels are used to restore the balance of ions across a membrane.

When open, ion channels allow charged molecules to move from an area of high

concentration to low concentration without using energy. Ion channels serve as a

counterbalance to active transport, a process whereby a cell uses energy to actively

pump ions and other charged molecules across a membrane in order to establish

ion gradients or alter the pH of an organelle to activate enzymes. There are two

major types of ion channels:

• Voltage-gated ion channels

• Ligand-gated ion channels

When ions are present in a higher concentration on one side of a

membrane than the other, a difference in voltage occurs across that membrane,

creating a membrane potential. Voltage-gated ion channels open in response to a

change in membrane potential, allowing the ions to move from the side of the

membrane with the higher ion concentration to the side with the lower ion

concentration.

Ligand-gated ion channels rely on the binding of a small molecule to

the channel. The small molecule binding causes a change in the channel protein,

opening the pore for the ions to travel through. As with voltage-gated ion channels,

when ligand-gated ion channels open ions move from the side of the membrane

with the higher ion concentration to the side with the lower ion concentration.

When targeted by therapeutics, ion channels are either inhibited,

preventing the flow of ions, or held constitutively open by the action of agonists,

preventing the accumulation of ions on one side of the membrane. The desired

activity of the ion channel modulator depends on the disease being targeted.

Table 3.3:

There are several ion channel modulators currently in use. Examples are included in the table below.

Channel

Type Target Name Development Status

Voltage-

gated

Ca2+ channel Multiple FDA approved anti-hypertensives

Na+ channel

Multiple FDA approved products including

local anaesthetics and anticonvulsants

K+ channel Multiple sulfonylureas approved for diabetes

Ligand-

gated

Glutamate-

gated chloride

channel

Ivermectin, FDA approved for onchocerciasis

and in use for the treatment of lymphatic

filariasis

Acetylcholine-

gated chloride

Levamisole, pyrantal, and tribendamadine

(China only), for treatment of helminth

channels infections

Multiple FDA approved products for the

treatment of tobacco dependence

Ion Channel Modulators as Non-Neglected Tropical Disease

3.2.8 Therapeutics

Ion channel inhibitors are used to treat a wide range of conditions including:

• Hypertension

• Pain

• Convulsions

• Diabetes

• Tobacco dependence

The most well-known and widely-used ion channel inhibitors are the

calcium channel inhibitors used to treat high blood pressure. The movement of

calcium across cell membranes causes muscle contractions. While this is a normal

biological process, contraction of the muscles of the circulatory system can

exacerbate the condition of patients with high blood pressure or hypertension.

Calcium channel blockers are used in patients with hypertension to reduce

contraction of the smooth muscles of the arteries, allowing the arteries to dilate to

reduce blood pressure.

Ion Channel Modulators as Neglected Tropical Disease Therapeutics

Ion channel inhibitors are used to treat parasitic worm infections including:

• Onchocerciasis

• Lymphatic filariasis

• Ascariasis

• Hookworm

• Schistosomiasis

Ivermectin is a glutamate-gated chloride channel inhibitor that is widely used in

mass drug administration programs in the developing world to treat infections with

parasitic worms that cause onchocerciasis and lymphatic filariasis. Ivermectin is

also used widely in veterinary medicine for the treatment of worm infections. The

drug is believed to work in these organism by inhibiting glutamate-gated chloride

channels, which are only found in invertebrates, allowing these drugs to selectively

target parasitic worms over their human hosts. Disruption of the flow of chloride

causes paralysis and starvation of the worm leading to death.

Levamisole and pyrantal pamoate can be used to treat the soil transmitted

helminths ascariasis and hookworm, but are not widely used. Tribendamadine is

used to treat ascariasis in China but has not been extensively evaluated or used

outside of China. All three of these products are agonists of acetylcholine-gated

chloride channels. These drugs force the chloride channels to remain open rather

inhibiting them; the resulting imbalance of chloride ions results in death of the

worms.

Praziquantel is the only on market drug for the treatment of

schistosomiasis. Although the mechanism of action of praziquantel is not entirely

clear, it is believed that the drug inhibits calcium channels on the parasite. More

research is needed to understand if inhibition of calcium channels is the primary

mechanism of action of praziquantel or part of a multi-target mechanism.

Modulation of ion channel function has been a successful area for drug

development, with ion channel modulating drugs being used in the therapeutic

treatment of epilepsy, hypertension, diabetes and chronic pain. Most of the ion

channel-modulating drugs that are currently on the market were developed without

extensive knowledge of the molecular structure of ion channels, or an

understanding of the full complexity of ion channel subtypes or knowledge of how

ion channel expression is regulated during pathology. As new information on the

roles that different ion channel subtypes play in pathophysiological processes

becomes available, drugs will be designed to target specific ion channel subtypes

via mechanisms that involve either direct channel block or modulation of ion

channel functional expression.

3.2.9 Nuclear receptor

In the field of molecular biology, nuclear receptors are a class of proteins

found within cells that are responsible for sensing steroid and thyroid hormones

and certain other molecules. In response, these receptors work with other proteins

to regulate the expression of specific genes, thereby controlling the development,

homeostasis, and metabolism of the organism.

Nuclear receptors have the ability to directly bind to DNA and regulate

the expression of adjacent genes, hence these receptors are classified as

transcription factors. The regulation of gene expression by nuclear receptors

generally only happens when a ligand — a molecule that affects the receptor's

behavior — is present. More specifically, ligand binding to a nuclear receptor

results in a conformational change in the receptor, which, in turn, activates the

receptor, resulting in up-regulation or down-regulation of gene expression.

A unique property of nuclear receptors that differentiates them from other

classes of receptors is their ability to directly interact with and control the

expression of genomic DNA. As a consequence, nuclear receptors play key roles in

both embryonic development and adult homeostasis