Supramolecular Pharmacy 5. The supramolecular chemistry of life Ondřej Jurček 1 Supramolecular chemistry is inspired by Nature 2 • Nature has evolved highly specific, hierarchical, selective, and cooperative chemistry • Supramolecular hosts are the receptor sites of enzymes, genes, antibodies of the immune system, and ionophores or ion channels • Guests are substrates, inhibitors, co-factors, drugs, antigens • These components exhibit supramolecular behavior such as molecular recognition, self-assembly, self-organization, self-replication and kinetic and thermodynamic complementarity • The vast majority is mediated via coordination (ion-dipole) bonds, hydrogen bonds, π-π stacking • The greatest supramolecular chemist is Nature • Insight has been gained into biochemistry by the study of supramolecular compounds • Synthetic and model systems mimic these biological processes Alkali metal cations in biochemistry 3 • Energy is vital to life: plants use light (photosynthesis), humans eat food – energy from food is transformed and stored as the chemical bond energy of ATP (adenosine triphosphate) • ATP anion is 4- balanced by alkaline and alkaline earth metal cations • Energy is released by enzymes ATPases, mainly the transmembrane enzyme Na+/K+-ATPase (1 mole ATP = 35 kJ of energy) • Muscle contraction – consumes ATP, transport of Na+ from the inside out and K+ from the outside in against gradient Alkali metal cations in biochemistry 4 • In the intracellular fluid there is a high concentration of K+, outside there is a high concentration of Na+ • Uneven distribution of alkali metal cations across the cell membrane is a highly important and results in a transmembrane electrical potential • Very important feature in many processes, e.g., transfer of neural signal Membrane transport • Chemistry of cell membrane • Cation does not penetrate itself, needs lipophilic coat or hydrophilic channel • Ionophores, e.g., valinomycin POPC 5 Valinomycin • Isolated from Streptomyces fulvissimus in 1955 • Exchange of K+ and H+ across the membrane of mitochondria via carrier mechanism • N–H···O=C to both ester and amide carbonyl groups plays an important role in the conformation of valinomycin, where it helps the peptide chain wrap around the metal cation • Selectivity to K+ because of octahedral array of hard carbonyl oxygens • Potential antibiotic because of the potential to disturb the balance of ions in bacteria 6 Log K in MeOH at 25 °C Ion channels 7 • Sequential desolvation–complexation–transport–decomplexation mechanism of ionophore-mediated cation transport is far too slow for effective use in the generation of nerve impulses • Passage of ions through ion channels results in transport close to the diffusion limits (about 108 ions per channel per second) • K+ channel from Streptomyces lividans possesses ion throughput rate and the vital 105-fold selectivity of the channel for K+ over Na+ Alkali metal cations in biochemistry 8 • In the intracellular fluid there is a high concentration of K+ outside there is a high concentration of Na+ • Uneven distribution of alkali metal cations across the cell membrane is a highly important and results in a transmembrane electrical potential • Very important feature in many processes, e.g., transfer of neural signal • multiple sclerosis • dalfampridine (4-aminopyridine) (FDA, 2010) Na+ K+ Action potential Impulse Stimulus Chemical transmission (acetylcholine) Anion channels 9 • Chloride maintains regulation of pH, volume homeostasis, organic solute transport, cell migration, cell proliferation and differentiation • CIC chloride channel - Salmonella typhimurium, the 2003 Nobel prize in chemistry for Roderick MacKinnon • Cystic fibrosis transmembrane conductance regulator (CFTR) – coding gene mutations cause cystic fibrosis (CZ 1:4000 live births, over 54 000 cases across Europe) • movement of Na+ ions in the same direction to balance the charge (Na+/Cl- symport) https://www.mayoclinic.org/diseases-conditions/cystic-fibrosis/symptoms-causes/syc-20353700 Rhodopsin 10 • alkali metal cation transport is also of importance in the stimulation by visible light of rod and cone cells in the retina of the eye Rhodopsin 11https://www.youtube.com/watch?v=dhd2fja0LZ4 Porphyrins and tetrapyrrole macrocycles 12 • Macrocyclic compounds able to bind metals via chelate and macrocyclic effect • Tetrapyrrols have extensive redox chemistry because of conjugated ring net • Chlorophylls (Mg2+) energy harvesting system of photosynthesis • Cobalamins – active form of vitamin B12 (corrin system) pyrrole porphyrin Chlorophyll a Porphyrins and tetrapyrrole macrocycles 13 • Hem complexes having iron center – binding site for O2 in hemoglobin pyrrole porphyrin Chlorophyll a Properties of tetrapyrrole macrocycles 14 • The near planar ring system is very stable • The tetrapyrrole ring can bind even highly labile metal cations • Highly selective because of the cycle rigidity - preorganization • Most contain conjugated π-system (colored) • Macrocycle contains four coordinating atoms in a planar arrangement, leaving two available sites on an octahedral metal centre available to bind the substrate and a regulating ligand Photosynthesis 15 • Green plants = about 1 g of glucose per hour per 1 m2 of leaf surface area • Chlorophylls contain a fully conjugated tetrapyrrole π-system (18 π electrons) with a low-energy π−π* transition • The complementary colours blue (after short-wavelength absorption) and yellow (after long-wavelength absorption) combine to give the characteristic green colour of fresh leaves (λmax 455 and 630 nm) Why Mg? 16 • High natural abundance • Lack of redox activity • Strong tendency for penta- or hexacoordination • Suitable ionic radius • Contributes to the arrangement of the pigments in photosynthetic membrane by binding to polypeptide • Electron is promoted to an excited state and used to effect a chemical reaction (production of O2 from H2O) „Dark“ reaction (Calvin cycle) Hemoglobin 18 • Oxygen is used to metabolically oxidize sugars (glucose, sucrose) to release energy, which is used in ATP synthesis • Hemoglobin is tetrameric protein containing four myoglobins, each has iron-porphyrin complex protein by a coordination interaction between an axial site of the octahedral Fe(II) centre and a nitrogen atom from the proximal protein histidine residue • Iron binds the oxygen (water) Hemoglobin 19 • O2 is binding reversibly, its complexation and release occur rapidly and at the correct controlled concentrations • O2 binding must occur selectively amongst other atmospheric components such as water, N2, CO2 and even excellent ligands for Fe(II) such as CO • Haemoglobin is an excellent example of a functional and selective supramolecular receptor Hemoglobin 20 • Single electron transfer from O2 to Fe(II) leads to Fe(III) formation • Smaller ionic radius for Fe(III), better fit in porphyrin, no doming • CO or readily adsorbed salts such as CN- are extremely toxic as they are binding irreversibly to the Fe in haemoglobin preventing oxygen transport and resulting in rapid suffocation 200 Enzymes and coenzymes 21 • Enzymes catalyze all biological processes – great inspiration for supramolecular chemists • Polypeptide chains > 10000 Da • Polypeptide chains are folded into a unique conformation giving a globular structure incorporating surface clefts and crevices • Active sites lie in these clefts and often contain a metal ion • Binding involves hydrophobic effects, hydrogen bonding, salt bridges (ion–ion) and other forms of intermolecular interaction • Extremely fast chemical conversion of substrates • Enzyme structure may be divided into primary, secondary, tertiary and quaternary features 22 • Enzyme tertiary and quaternary structure is responsible for the organisation of the binding site(s) • Enzymes are generally named according to the reaction they carry out with the suffix -ase being added to the name of the substrate • Na+/K+-ATPase, DNA polymerase, lactace, esterase… Enzymes and coenzymes Mechanism of enzymatic catalysis 23 • Linus Pauling stated in 1948 that ‘enzymes are molecules that are complementary in structure to the transition states of the reactions they catalyze’ • Non-covalent forces involved in substrate binding should be sufficient to distort the substrate such that it becomes more like a transition state, lowering activation energy required to form [ES] • Effective concentration, desolvation of the bound state • Both, enzyme and substrate, undergo conformational change Coenzymes 24 • Coenzyme is a non-enzyme ‘helper molecule’ that forms one constituent of a biological catalytic system (e.g., ATP, or vitamins) • Full system requires the coenzyme, an apoenzyme and a substrate • The nature of the coenzyme determines the type of the reaction, while the nature of the apoenzyme determines the selectivity of the reaction in terms of the substrate and the regiospecificity Coenzyme B12, cobalamin, vitamin B12 25 • Can be used with various apoenzymes • Alkylation • Required for amino acid metabolism in the liver and its absence, as a result of genetic defects, is lethal (pernicious anemia) • The X-ray crystal structure earned the 1964 Nobel Prize in Chemistry for Dorothy Crowfoot-Hodgkin Neurotransmitters and hormones • messengers and activating agents • E.g., sex hormones (testosteron, estrogen, progesteron), or neurotransmitters such as dopamine, acetylcholine Acetylcholine • Nerve pulses are passed among neurons across synapses (gaps between nerve cells, 30–40 nm thick) by transfer of acetylcholine (highly selective binding involves cation-π interactions) – ligand-gated ion channel • This opens Na+ channels, part of the nicotinic acetylcholine receptor protein (nAChR), Na+ flows into the cell in concentration gradient, current flow • Then acetylcholine esterase hydrolyses the ester functionality preventing the molecule from further binding to nAChR, closing the Na+ channel • Nicotine × acetylcholine testosterone × lower selectivity Acetylcholine and nAChR https://www.youtube.com/watch?v=P7pEUF3-IXI Rocuronium, acetylcholin, sugammadex 28 • In general, many drugs used utilize the low selectivity of various receptors • Sugammadex – used as reversal of neuromuscular blockade induced by rocuronium and vecuronium in general anaesthesia (by competing for the cholinoceptors at the motor end plate, thereby exerting its muscle-relaxing properties, which are used adjunctively to general anesthesia) Drugs 2009, 69, 919–942 acetylcholin sugammadex rocuronium HG-complex acetylcholin receptor Na+ Insect juvenile hormones and analogues (insecticides) 29 • Juvenile hormones (JH) regulate development, reproduction, diapause, and polyphenisms in insect • Juvenile hormone receptors are less selective • JH analogues can have insecticidal properties – block development and metamorphosis of insect (mosquitoes, termites) • Juvabion – paper factor • Juvenoids, juvenogens • Very low general toxicity 0 1 2 3 4 5 methoprene – JH analogue used juvenile hormone III Jurček et al. Steroids 2009, 74, 779 / J. Agric. Food Chem. 2009, 57, 10852 / J. Agric. Food Chem. 2007, 55, 7387. juvenoid Biochemical self-assembly 30 • Viruses are built of numerous protein sub-units, encoded by viral RNA, which self-assemble reversibly to form protective hollow coatings termed capsids sacbrood honeybee virus Plevka et al. NATURE COMMUNICATIONS | (2019) 10:1138 enterovirus Plevka et al. PNAS 2018, 115 (30) 7759-7764. DNA 31https://en.wikipedia.org/wiki/Base_pair#/media/File:DNA_base-pair_diagram.jpg DNA 32 • Molecule that bears all of the genetic information necessary to construct and operate a living organism • Held together in double helix through hydrogen bonding and π–π stacking interactions (each cell has about 3 cm long and 2·10-9 m thin) • Nucleotides, molecules that contain a nucleobase (either adenine (A), thymine (T), cytosine (C) or guanine (G)) attached to a sugar and a phosphate tail • Genetic information on DNA is stored as a large number of three letter codons = triplets of nucleobases (e.g., GCC, CAG, ATC etc.). Each codon is translated biochemically into one of the 20 amino acids building proteins Watson–Crick base pairing Binding to DNA 33 • Pairing enables DNA to replicate itself as well as passing on its encoded genetic information to messenger RNA guanosine binding phenanthriplatinnetropsin Ribosomes as supramolecular molecular machines 34https://www.youtube.com/watch?v=TfYf_rPWUdY&t=2s In the next class… Gels and metallogels Thank you for your attention! With thanks to Jonathan W. Steed, Jerry L. Atwood for Supramolecular Chemistry, ISBN: 978-1-119-58251-9 and Wikipedia for several lovely images.