Molecular Interactions

Transcription

1 Molecular Interactions (non-covalent) كيمياء دوائية -1 lمحمد نورالدين محمود القطان 1 st edtition 2017

2 Introduction to molecular dynamics Molecular dynamics deals with the reversible molecular interaction. The reversible molecular interaction could be: 1. Between similar molecules (E.g. water) Can be used to estimate dissociation constant physicochemical properties like b.p., m.p., surface tension,..etc 2. Different molecules (E.g. drug-receptor as Glutathione-GST ) Can be used to estimate dissociation constant pharmacological activity

3 Reversible (non-covalent) interactions are present in almost all biological processes. Enzyme catalysis Flagellum motor Vesicles transport DNA-transcription

4 Reversible non-covalent interactions may be used to design molecular machines

5 Intermolecular interactions Most of the drugs interact with the receptors through reversible intermolecular interactions. Very few drugs interact with the receptors through irreversible intermolecular interactions. Those which interact irreversibly are usually poisonous drugs. There are several types of non-covalent interactions that take place between molecules: 1. Electrostatic 2. Hydrogen bond 3. Ion-dipole 4. Dipole-dipole 5. Dipole-induced dipole 6. Induced dipole-induced dipole (Van der Waals) 7. Hydrophobic The non-covalent interactions differs in their: 1. Physicochemical principle 2. Effective distance 3. Strength

6 Types of molecular interactions The non-covalent interactions can occur between: 1. Intramolecular interaction: like drug with itself This can affects drug physicochemical properties like solubility, volatility, freezing and boiling point 2. Intermolecular interaction : - Drug-Drug :affects physicochemical properties like solubility, volatility, freezing and boiling point - Drug-receptor: affects potency of pharmacological activity receptor

7 1. Electrostatic Electrostatic or ionic interactions is the strongest (20-40 KJ/mol) Takes place between groups which have opposite charges such as carboxylate and ammonium ions It usually drags the drug to inter the binding site, before other interactions takeplace E ij = q iq j 4πεr ij The strength of interaction is 1. Inversely proportional to the distance between the two charged atoms 2. Depends on the dielectric constant of the medium (stronger in hydrophobic than in polar environments, thus drug interaction with deep binding site usually is stronger than with superficial binding site) 3. Is the most important interaction to drag drug to enter the binding site. 4. The range is the longest (>3 Å) and depends on medium

8 2. Hydrogen bonds (HB) Is most important after electrostatic interactions It takes place between electron-rich heteroatom and electron-deficient hydrogen. - The electron-rich heteroatom has to have a lone pair of electrons and is usually oxygen or nitrogen (H-bond acceptor). - The electron-deficient hydrogen is usually lined by a covalent bond to an electronegative atom such as oxygen or nitrogen (H-bond donner). - Therefore, some electronegative atoms can act as H-bond donner and acceptor at the same time. Although H-bond can be considered as subtype of electrostatic interaction, it is the electron orbital sharing is involved between the two electronegative atoms Acceptor High electron density at O atom H Low electron density at H atom Donner H-bond range is 2-3 Å with energy of KJ/mol High electron density at N atom

9 2. Hydrogen bonds (HB) (Cont.)

10 2. Hydrogen bonds (HB) (Cont.) The orbital containing the lone pair of electrons on heteroatom (Y) interacts with the atomic orbitals normally involved in the covalent bond between X and H. This result in weak form of sigma (σ) bonding and has an important directional consequence that is not evident in electrostatic bonds The directionality of lone pair orbital of Y affects the strength of HB. - The optimum orientation is where the X H bond points directly to the lone pair on Y such that the angle formed between X, H, and Y is 180 (Strong:180, moderate: , weak ). - For example N in pyridine ring is sp2 hybridized and the lone pairs are points radially from the ring, which is different than piperidine The distance between Y and H affects the strength of HB. - The shorter the distance the stronger the bond. Typical distance is Å (compared to covalent Å) piperidine Pyridine

11 2. Hydrogen bonds (HB) (Cont.) The common types of electronegative atoms involved in drug-target interactions include: O, N and S. Oxygen has two lone pairs and can accepts two hydrogen bonds Nitrogen has one lone pair and can accepts one hydrogen bond. Sulfur is weak hydrogen bond acceptor because the lone pairs are in 3 rd -shell orbital which is large and diffuse. This means that the orbitals concerned interact less efficiently with the small 1s orbitals of hydrogen atoms. Fluorine is so electronegative, that it not shares e orbitals with other atoms (BAD HB acceptor) O N S

12 2. Hydrogen bonds (HB) (Cont.) Electronegative atoms are usually bound to other atoms within the drug molecule. Therefore, the electronegativity (or the electron density) is affected by other atoms. ē density of HBA strong HB Oxygen for COO - is stronger HBA than oxygen for COOH Most HBA in drugs and targets binding sites are neutral functional groups such as ethers, alcohols, phenols, amides, amines and ketones. These groups forms moderately strong HB Electron density of pi (π) systems (alkynes and aromatic rings) are diffuse and difficult to be shared by third party atoms (Hs), therefore behave as poor HBA. The localized electron density is more available for HB than the delocalized (i.e. resonance).

13 2. Hydrogen bonds (HB) (Cont.) Examples of strong hydrogen bond acceptors - carboxylate ion, phosphate ion, tertiary amine Examples of moderate hydrogen bond acceptors - carboxylic acid, amide oxygen, ketone, ester, ether, alcohol Examples of poor hydrogen bond acceptors - sulphur, fluorine, chlorine, aromatic ring, amide nitrogen, aromatic amine Example of good hydrogen bond donors - Quaternary ammonium ion

14 Examples DNA The stability of H-bonds falls roughly in the following order, OH---O > OH----N > NH----N Crystal structure of a short peptide l -Lys-d-Ala-d-Ala (bacterial cell wall precursor in green) bound to the antibiotic vancomycin (in blue) through 5 hydrogen bonds.

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16 3. Ion-dipole interactions Occur where the charge on one molecule interacts with the dipole moment of another Stronger than a dipole-dipole interaction Strength of interaction falls off less rapidly with distance than for a dipole-dipole interaction R O C d+ d- R O C O R O d- C d+ R H 3 N Binding site Binding site

17 4. Dipole-dipole interactions Can occur if the drug and the binding site have dipole moments Dipoles align with each other as the drug enters the binding site Dipole alignment orientates the molecule in the binding site Orientation is beneficial if other binding groups are positioned correctly with respect to the corresponding binding regions Orientation is detrimental if the binding groups are not positioned correctly with respect to corresponding binding regions The strength of the interaction decreases with distance more quickly than with electrostatic interactions, but less quickly than with van der Waals interactions d- d+ R O C R Dipole moment Localised d ipole moment R C O R Binding site Binding site

18 5. Ion-induced dipole interactions Occur where the charge on one molecule induces a dipole on another Occurs between a quaternary ammonium ion and an aromatic ring + R N R 3 d+ d- Binding site The pi electrons are shared among orbitals of the 6 carbon atoms. Thus can form two electron clouds above and below the plane of the benzene ring

19 Example of Dipole-induced dipole interaction

20 6. Induce dipole-induced dipole (Van der Waals) Very weak interactions (2-4 KJ/Mol) with a ragne of 3-4 Angstroms Occur between hydrophobic regions of the drug and the target Due to transient areas of high and low electron densities leading to temporary dipoles Interactions drop off rapidly with distance Drug must be close to the binding region for interactions to occur The overall contribution of van der Waals interactions can be crucial to binding d+ d- Hydrophobic regions Transient dipole on drug van der Waals interaction DRUG d+ d- d- d+ Binding site

21 Examples of special induced-dipole induced-dipole interaction (π- π stacking) Heterocyclic π stacking between dump and the anticancer drug 1843U89 bound at the active site of thymidylate synthase (PDB code: 1TSD).

22 7. Hydrophobic interactions Hydrophobic regions of a drug and its target are not solvated Water molecules interact with each other and form an ordered layer next to hydrophobic regions - negative entropy Interactions between the hydrophobic interactions of a drug and its target free up the ordered water molecules Results in an increase in entropy Beneficial to binding energy التحول من الترتيب للعشوائية هو عملية تلقائية الوصول الى العشوائية اليستهلك طاقة بخالف الوصول الى الترتيب DRUG Drug Binding Binding site DRUG Drug Binding site Hydrophobic regions Water

23 7. Hydrophobic interactions (Cont.)

24 7. Hydrophobic interactions (Cont.)

25 Factors affecting the reversible interactions Several factors should be considered when studying the formation of reversible intermolecular interactions. Those factors affects the strength of the interactions and the final energy ( G) A) Factors related to the environment (affects enthalpy H) 1. The distance between interacting groups 2. The energy required to dry (desolvate) the surfaces before interaction takes place 3. The solvent conductivity or dielectric constant B) Factors related to the ligand and receptor molecule (affects entropy S) * Restriction of ligand and receptor conformational freedom

26 1. Distance All intermolecular interactions are distance dependent The strength of interaction is reduced by increasing the distance. Electrostatic E 1 r 2 H bond E 1 r 8 Van der Waals E 1 r 12 Best distance Therefore, the longer ranged interactions are electrostatic, followed by H-bond, then Van der Waals. For a given distance, the reduction in van der Waals potential is 10,000 times the reduction in H-bonding. Lowest energy

27 2. Desolvation penalty Desolvation is removal of solvent. The solvent is mainly water in biology. Although removing water from oil is spontaneous, it is very difficult to remove water from ethanol. WHY? Answer: no attraction between water and oil strong attraction between water and ethanol The increase in entropy can not compensate the energy required to الوصول الى العشوائية detach water from polar surfaces اليستهلك طاقة ولكن نزع الماء من السطح يستهلك طاقة Wet polar surface + DRUG Drug Binding Wet waxy surface - Binding site - + DRUG Drug Binding site Hydrophilic regions Water

28 2. Desolvation penalty (Cont.) Polar regions of a drug and its target are solvated prior to interaction Desolvation is necessary and requires energy The energy gained by drug-target interactions must be greater than the energy required for desolvation H O H O H O H H O O R C R H O H H O R C R H O O H O H R C R Binding site Binding site Desolvation - Energy penalty Binding site Binding - Energy gain

29 2. Desolvation penalty (Cont.) Solvation/desolvation ذوبان ملح الطعام يمثل عملية االذابة بالماء وترسب ملح الطعام يمثل عملية نزع الماء بما ان الملح هو مركب ايوني )قطبي( فان نزع الماء منه وتجفيفه تحتاج الى حرارة باالضافة الى ان عملية الترسب الى بلورات هي عكس العشوائية فتكون غير سهلة Dissolution of NaCl is a solvation process Precipitation of NaCl is a desolvation process Since NaCl is an ionic (polar) compound, the desolvation process to remove water molecules from its surface requires energy Inaddition, the process of NaCl crystallization lead to loss in entropy so it is not favourable

30 3. Dielectric constant The medium composition affects the interaction between charged groups electrostatic interactions The strength of ionic interactions is crucially depends on the dielectric constant of the medium. In biological systems, charges are separated by water molecules with different other molecules. The dielectric constant is - higher in bulk-phase of water (~80), - almost 28 at polar surface of proteins and - almost 4 in interior hydrophobic region of the proteins. The strength of interaction is increased as the dielectric constant is decreased. 1 strengt of interaction dielectric constant The dielectric constant is reduced as the binding pocket becomes more hydrophobic, more deep (away from the protein surface) and ligand best fit the binding pocket The interaction is stronger in vacuum than in water filled medium Low ligand fitness, water filled space < < Surface binding site, the ligand highly interacted with water during binding Deep binding site, the ligand slightly interacted with water during binding

31 4. Conformational changes The intramolecular interactions of the molecule determine the lowest energy conformation of the unbound drug. If the unbound drug can bind the receptor with its current conformation, no energy need to be paid to change the conformation. So the only loss will be in entropy. If the unbound drug can not bind the receptor with it s current conformation, the conformation need to be changed to fit the binding site, and this usually costs unfavorable energy. So the loss will be in enthalpy (take suitable conformation) and entropy (reduce the conformation randomness) Acetylcholine Acetylcholoine exist in solution in 1000s of conformations (only the most important are shown). Acetylcholine binds the nicotininc receptor with only one conformation Acetylcholine binds the muscarininc receptor with only one conformation

32 Molecular structural properties 2. Rigidity Nicotine showed selectivity for cholinergic receptors present on skeletal muscle or at the synapses between different neurons. Whereas muscarine showed selectivity for cholinergic receptors present on smooth muscle and cardiac muscle. Both of nicotine and muscarine are more rigid, thus more selective to particular subtype of cholinergic receptors More flexible Muscarine Acetylcholine Nicotine Less flexible Can fit only muscarinic receptors More flexible Can fit both receptors Less flexible Can fit only nicotininc receptors Muscarinic receptor Nicotinic receptor

33 Factors affecting the ligands-receptor interactions Energy (binding energy (طاقة االتحاد Enthalpy (heat of interaction (التغير بالحرارة Gibbs fee energy formula G = H T S Temperature (Abs Temp of medium (درجة حرارة الوسط Entropy (measure of randomness (التغير بالعشوائية Factors which affect the affinity (energy G) of ligand binding to receptor includes: 1. Enthalpy ( H): Number, types and strength of non-covalent interactions 2. Entropy ( S): Change in randomness of drug conformations, receptor side-chains conformations,. Spontaneous (favorable interactions) have G < 0 1. When H < 0 2. When S > 0

34 Factors affecting the ligands-receptor interactions (Cont.) Factors which affect the affinity (energy G) of ligand binding to receptor includes: التغير بالحرارة ( H): 1. Enthalpy - Gain ( H < 0): Formation of non-covalent interactions (Number, types and strength) - Loss ( H > 0): Destruction of water-ligand or water-receptor interactions (Desolvation of water) التغير بالعشوائية ( S): 2. Entropy - Gain ( S > 0): Removing the layer or arranged water around hydrophobic sites (hydrophobic interaction) - Loss ( S < 0): Reduction in randomness in drug conformations, receptor side-chains conformations.

35 Brief discussion about the relationship between entropy and binding affinity Consider the formation of a specific noncovalent bond (e.g. A B for the transformation A B A B ). An increase in its strength (which corresponds to an increasing negative contribution to Δ H, and a more favorable binding process) will be accompanied by an increasing restriction in the relative motion of A and B in A B (which corresponds to a negative contribution to Δ S, and so unfavorable to binding). This opposing interplay between enthalpy and entropy is known as enthalpy/entropy compensation, and is a fundamental property of noncovalent interactions. It can be interpreted that an enhancement of intermolecular binding is accompanied by a loss in degrees of freedom of mobility and vice versa. The two effects can be traded off against each other because the strength of noncovalent bonds is, at room temperature, comparable to the thermal energies that oppose them. The enthalpy/entropy compensation is of particular importance for the prediction of receptor ligand interactions: whereas the individual enthalpic and entropic contributions can vary over large ranges, the total change in free enthalpy is frequently close to zero. As a consequence, small relative errors in the prediction of Δ H and Δ S can have significant influence on Δ G. This concept is less important in the study of covalent bonds, which are typically too strong to be effectively opposed by thermal motions at room temperature.

36 You can view energy in different ways This is how we can correlate interaction energy with Kd The change in energy مقدار التغير في الطاقة + K on K off Using Gibbs free energy equation we can view energy as heat and randomness Using Arrhenius equation we can view energy as dissociation H T S = G = RT lnk d The change in heat مقدار التغير في الحرارة Temp * The change in randomness درجة الحرارة * التغير بالعشوائية Gas constant ثابت الغاز Temp درجة الحرارة Dissociation constant ثابت التفكك

37 You can view energy in different ways This is how we can correlate interaction energy with Kd The change in energy مقدار التغير في الطاقة + K on K off -ve for spontaneous rxn +ve for nonspontaneous rxn Zero at equilibrium (i.e. at Kd=1) Path independent (depend on starting and end states) Give information on rxn spontaneousity Give no information on rxnrate H T S = G = RT lnk d

38 Applications of non-covalent interactions 1. Receptor sof drugs Non-covalent interactions help the newly formed proteins to get their proper quaternary structure Proteins are synthesized as threads The folding of theses threads give the final protein structure (quaternary structure) The process of protein folding is driven usually by interactions between functional groups of the neiboring amino acids (intramolecular interaction) Folding of a polypeptide chain illustrating the hierarchy of protein structure from primary structure through secondary structure and tertiary structure. Source: From Copeland (2000).

39 Applications of non-covalent interactions 2. Biochemical behavior of drugs Binding interactions between pyruvic acid and lactate dehydrogenase. Binding interactions between enalaprilate and angiotensin-converting enzyme.

40 Applications of non-covalent interactions 3. Physicochemical properties of drugs o-hydroxybenzoic acid (Salicylic acid) p-hydroxybenzoic acid Forms intramolecular hydrogen bonding Forms intermolecular hydrogen bonding pka 3.0 pka 4.5 Less soluble in water More soluble in water Low melting point High melting point Low boiling point High boiling point Good anti-inflammatory effect Low anti-inflammatory effect