Structural Relationships for Receptors and Ligands

Created on Thu, 02/08/2018 - 22:14
Last updated on Mon, 02/12/2018 - 02:02

This chapter is related to the aims of Section C(iv) from the 2017 CICM Primary Syllabus, which expects the exam candidate to "explain receptor activity with regard to... structural relationships for receptors and ligands". What precisely they mean is difficult to guess, in the context of assessment-driven learning (given that it has never come up in the exams before and we don't even have a rude examiner comment about how much the answers sucked). Given the wording and intentions of the curriculum, one can make best guess estimates of what might be important. This chapter represents a series of such guesses.

Using one's imagination, it would seem from from the way the learning objective is worded that the college wanted trainees to know something about the ways in which receptor structure and ligand structure influences their interaction. This is something fairly fundamental to biology in general. "Highly specific molecular recognition is one of the fundamental principles of functioning of living systems",  starts a biomedical engineering article by Guryanov et al (2016). Clearly, the discussion of something like that is probably outside of the scope of an Intensive Care pharmacodynamics syllabus. Instead, the 

As far as finding peer-reviewed published literature on the subject, the pickings are slim. Indeed, if one googles the phrase "structural relationships for receptors and ligands", the only search result is the CICM 2017 syllabus document (i.e. in all human written communication this combination of words has never been used before). That makes it difficult to track down anything useful as a point of reference, even to begin writing a structure for this topic. Fortunately, there is a whole textbook on the general topic. Phillip Michael Dean's Molecular Foundations of Drug-Receptor Interaction is probably the definitive text, albeit somewhat dated (1987). Some recently updated and scaled-down versions of the same material can be found in reviews such as the one by Pierre Bongrand (1999). Because Dean's book is out of print, one might instead need to use something like Steed and Atwood's Supramolecular Chemistry (mine is the 2nd edition from 2009). 

Given the vagueness of the learning objectives and the absence of historical SAQ examples, this is an unlikely question topic. Having said that, weirder things have been asked about (endothelial glycocalyx, seriously). Ergo, a short summary is left here for the primary exam candidates who should only want to develop a very superficial grasp of this topic.

  • Ligands are usually small molecules; but they range from ions and small peptides to dissolved proteins.
  • Receptors are usually large proteins with complex 3D structure
  • Receptors and ligands have molecular complimentarity: i.e. the shape and chemical properties of their binding sites are matching to permit high-affinity selective binding.
  • The chemical bonds which mediate their interaction are:
    • Van der Waals forces (most important for highly complimentary molecules, for example monoclonal antibodies and their targets)
    • Hydrophobic attraction (eg. sugammadex and rocuronium)
    • Hydrogen bonding (binding of a local anaesthtic to a voltage-gated sodium channel).
    • Electrostatic attraction, eg. acetylcholine and its receptor
    • π–π "stacking" interactions between aromatic rings or π– cation interactions, eg. neurotransmitters such as dopamine
    • Rarely, a receptor and a ligand will bond covalently (a "suicide" bond - eg. phenoxybenzamine)
  • The specificity of receptor and ligand binding forms one of the elements of a drug's pharmacophore - the "ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target"

Pharmacophore

Paul Ehrlich's  first definition of the pharmacophore, from his 1909 "Über den jetzigen Stand der Chemotherapie", was as follows:

"A molecular framework that carries (phoros) the essential features responsible for a drug’s (pharmacon) biological activity".

The more recent 1998 IUPAC definition contains slightly scienced-up language, but remains essentially unchanged in spirit:

"An ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target and to trigger (or block) its biological response"

As such, a pharmacophore is not a real molecular structure like an OH side group or a disulfide bond; it is an abstract concept which describes all the properties which account for the ability of one molecule to specifically recognise another molecule, and with a high affinity bind it. Of these properties, the molecular structure and shape of the binding regions is probably the most important factor. 

The concept of molecular complimentarity

The term "molecular complimentarity" describes the matching of surface shape and chemical properties between receptors and ligand molecules. It is essential for high-affinity bonds to form. Both the surface structure and the chemical properties of the ligand-binding site must fit the ligand like a lock fits a key. 

The keyhole is small. The contact surface which is complimentary to the ligand molecule may be in the order of several hundred to several thousand square Angstrom (Å2). Bongrand (1999) offers some examples from biology. For instance, the contact surface between a T-cell HLA A2 receptor and its viral oligopeptide ligand was 1,011 Å2

molecular complimentarity

The lock and key imagery actually dates back to the early 20th century; the concept has now evolved into the "induced fit" theory (Koshland, 1994) which describes a more complex process, one with several possible stages. The ligand and receptor first interact weakly at a distance, then both change shape, interact more strongly, and finally bind.

Not all ligand molecules are specific for unique receptors. There exists a number of "privileged scaffolds", molecular structures which seem to act as ligands for a whole array of receptors (Welsh et al, 2010). These include such examples as the quinoline rings (the reason for why hydroxychloroquine is both an antimalarial agent and an immunosuppressant).

Molecular characteristics of ligands and receptors

Ligands can be any damn thing. They could be an ion (eg. sodium or calcium), a small molecule (ethanol), a small peptide (vasopressin) or a large peptide (insulin) or a protein (infliximab). 

Receptors are generally alarge protein with a complex structure. A receptor is defined by Goodman And Gilman as 

"the cellular macromolecule or macromolecular complex with which the drug interacts to elicit a cellular or systemic response"

This is in contrast to a drug acceptor such as albumin, to which the drug binds with no discernable physiological effect. Only the pharmacokinetics of the drug are altered by this acceptor binding. 

Receptor-ligand chemical interactions

Receptors and ligands connect via a variety of bonds, ranginng from fairly weak (like Van Der Waal and hydrophobic bonding) to very strong (covalent, "suicide" bonds). Apart from the latter, these are not firm and irreversible associations. Rather, it can be said that at any given time there are some ligand molecules bound and some unbound, and that the higher the affinity of the receptor for the ligand the greater the bound proportion. 

The bonds in a bit of detail:

Van der Waals forces are attractive forces resulting from the polarisation of an electron cloud by the proximity of an adjacent positively charged nucleus, resulting in a weak electrostatic attraction. The amount of force is vaguely proportional to the available area for contact, i.e. the more electron clouds and nuclei there are to interact the greater the total force. It also diminishes rapidly with distance.

Van Der Waals forces

These forces are probably the weakest of all the forces responsible for drug-receptor interactions. However, they are probable also the most important for high specificity. Because of their dependence on short distances, these forces can only really take effect when the surfaces are in close apposition, i.e. when the molecules are highly complimentary. Examples of such highly complimentary pairings would have to include such agents as monoclonal antibodies.

Hydrophobic forces produce bonding because of the exclusion of poorly solvated complexes from pools of polar solvent. In general water molecules bind each other with high affinity and in a body of water they will all tend to be strongly attracted to one another. Non-polar molecules will end up being pushed out of the way of strongly attracted water molecules as they crowd together. Non-polar neighbours will end up being pushed together by this effect; it is demonstrated by the immiscibility of oil in water (the oil molecules end up being pushed together into blebs).  

hydrophobic forces

 This effect can give the impression of attraction, but in fact the receptor and ligand have no chemical affinity for one another. This effect has several examples, for instance the binding of organic guests such as rocuronium by cyclodextrin hosts such as sugammadex. The inside of the cyclodextrin cavity is highly non-polar, and the hydrophobic muscle relaxant molecules huddle in there, seeking refuge from the watery environment outside.

Hydrogen bond

Hydrogen bonds  are a kind of dipole–dipole interaction where a hydrogen atom  is attracted to a dipole on an adjacent molecule.  A hydrogen bond is stronger than hydrophobic or Van Der Waals forces. This is illustrated by the fact that highly hydrogen-bonded H2O has a boiling point of 100° C, and the non-hydrogen-bonded H2S has a boiling point of -60° C. This is one of the bonds which facilitates the binding of a local anaesthetic to a voltage-gated sodium channel.

Electrostatic interactions are simple interactions between opposing charges as described by Coulomb's law. This is how the quaternary amine (N+) of acetylcholine and suxamethonium binds in this manner to the anionic active site of the acetylcholine receptor (Harel et al, 1993).

π-π  interactions describe "stacking" of aromatic rings, which occurs often in situations where one is relatively electron rich and one is electron poor. Examples of this effect taking place include the spontaneous helical curling of the DNA double helix and the binding of dopamine to its target site (Nishihira et al, 1997). In fact many neurotransmitters bind to their receptor sites by π-π or π-cation interactions.

pi-pi stacking

Covalent bonding  is mentioned here because it is one of the more interesting ways receptors and ligands can interact in clinical chemistry, of interest to the intensivist particularly because it is often something very dramatic. Particular examples include phenozybenzamine, a potent α-1 antagonist which binds covalently to the α-1 receptor. It is used in the management of phaemochromocytoma. 

 

References

Guryanov, Ivan, Stefano Fiorucci, and Tatiana Tennikova. "Receptor-ligand interactions: Advanced biomedical applications." Materials Science and Engineering: C 68 (2016): 890-903.

Suvarna, B. S. "Drug-Receptor Interactions." Kathmandu University Medical Journal 9.3 (2012): 203-207.

Yang, Sheng-Yong. "Pharmacophore modeling and applications in drug discovery: challenges and recent advances." Drug discovery today 15.11-12 (2010): 444-450.

Ehrlich, Paul. "Über den jetzigen Stand der Chemotherapie." European Journal of Inorganic Chemistry 42.1 (1909): 17-47.

Wermuth, Camille-Georges, et al. "Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998).Annual reports in medicinal chemistry 33 (1998): 385-395.

Root-Bernstein, Robert S., and Patrick F. Dillon. "Molecular complementarity I: the complementarity theory of the origin and evolution of life." Journal of Theoretical Biology 188.4 (1997): 447-479.

Lengauer, Thomas, and Matthias Rarey. "Computational methods for biomolecular docking." Current opinion in structural biology 6.3 (1996): 402-406.

Mannhold, Raimund, Hugo Kubinyi, and Gerd Folkers. Protein-ligand interactions: from molecular recognition to drug design. Vol. 19. John Wiley & Sons, 2006.

Welsch, Matthew E., Scott A. Snyder, and Brent R. Stockwell. "Privileged scaffolds for library design and drug discovery." Current opinion in chemical biology 14.3 (2010): 347-361.

Helm, Christiane A., Wolfgang Knoll, and Jacob N. Israelachvili. "Measurement of ligand-receptor interactions." Proceedings of the National Academy of Sciences 88.18 (1991): 8169-8173.

Frei, Andreas P., et al. "Direct identification of ligand-receptor interactions on living cells and tissues." Nature biotechnology30.10 (2012): 997.

Zhang, Yanling, et al. "Ligand-Receptor Interactions and Drug Design." (2015): BCI-S37978.

Tallarida, Ronald J., Robert B. Raffa, and Paul McGonigle. "Drugs and Receptors: Chemical Bonding." Principles in General Pharmacology. Springer, New York, NY, 1988. 115-136.

Andrews, P. R., D. J. Craik, and J. L. Martin. "Functional group contributions to drug-receptor interactions." Journal of medicinal chemistry 27.12 (1984): 1648-1657.

Koshland, Daniel E. "The key–lock theory and the induced fit theory." Angewandte Chemie International Edition 33.23‐24 (1995): 2375-2378.

Gijsenbergh, Francois, et al. "First human exposure of Org 25969, a novel agent to reverse the action of rocuronium bromide." Anesthesiology: The Journal of the American Society of Anesthesiologists 103.4 (2005): 695-703.

Roth, Charles M., Brian L. Neal, and Abraham M. Lenhoff. "Van der Waals interactions involving proteins." Biophysical journal 70.2 (1996): 977-987.

Lipkind, Gregory M., and Harry A. Fozzard. "Molecular modeling of local anesthetic drug binding by voltage-gated sodium channels." Molecular pharmacology 68.6 (2005): 1611-1622.

Harel, M., et al. "Quaternary ligand binding to aromatic residues in the active-site gorge of acetylcholinesterase." Proceedings of the National Academy of Sciences 90.19 (1993): 9031-9035.

Zacharias, Niki, and Dennis A. Dougherty. "Cation–π interactions in ligand recognition and catalysis." Trends in pharmacological sciences 23.6 (2002): 281-287.

Nishihira, Jun, and Hiroto Tachikawa. "Theoretical Study on the Interaction Between Dopamine and its Receptor byab initioMolecular Orbital Calculation." Journal of theoretical biology 185.2 (1997): 157-163.