Protein- Ligand Interactions

Protein- Ligand Interactions

Outline Introduction Interm olecular bonding forces Electrostatic or ionic bonds Hydrogen bonds Van der Waals interactions Dipole- dipole and ion- dipole interactions Repulsive interactions The role of water and hydrophobic interactions

Outline Ligplot Conclusion VMD

Introduction Ligand: a molecule that binds to a specific site on a protein or/... The molecule which binds to a protein m olecule (eg, receptor). A ligand binds through the interaction of m any weak, noncovalent bonds which form s with the binding site of a protein. The tight binding of a ligand depends upon a precise fit to the surface- ex posed am ino acid residues on the protein.

Introduction Substrates, drugs, ligands interacts with m acrom olecular m olecules by a process called binding. The specific areas are called binding sites Binding sites: Typically a hallow or canyon on macrom olecule surface Allowing sm all m olecules to sink into them Most ligand interact through interactions known as intermolecular bonds

Introduction University of Surrey

Introduction Interm olecular interactions not as strong as covalent bonds found in the target Can be formed and broken again There is an equilibrium between ligands bound and unbound The tim e a ligand will bind to a target depends on the strength of these interactions Ligands having a larger num ber of interactions tend to bind stronger

Introduction Functional groups of a ligand is important in form ing interm olecular bonds. These groups are referred to as binding groups The carbon skeleton of ligands play an im portant role in binding i.e. The targets binding site contains carbon skeleton groups which interacts with the ligands carbon skeleton The specific regions in the target which interacts is known as binding regions

Introduction Adapted from: An Introduction to Medicinal Chemistry by Patrick

Intermolecular bonding forces There are several types of intermolecular bonding interactions which differs in their bond strengths Protein ligand interactions depends: The struct ure of the ligand The functional groups present

Intermolecular bonding forces Electrostatic or ionic bonds Is the strongest of intermolecular bonds Takes place between two groups with opposite charges i.e. Carbox ylate ion and an am m onium ion

Intermolecular bonding forces Strength of bond inversely proport ional to the distance between the t wo groups Bond strength dependent on environm ent Stronger in hydrophobic environm ent The drop- off effect in ionic bonding strength with separation is less than other interm olecular interactions Usually the m ost im portant interaction during initial binding of ligands

Intermolecular bonding forces Hydrogen bonds Takes place between an electron- rich heteroatom and a electron- deficient hydrogen Heteroatom : not a carbon or hydrogen

Intermolecular bonding forces The eletron- rich heteroatom has to have a lonepair of electrons and is usually an ox ygen or nitrogen The electron- deficient hydrogen is linked by a covalent bond to an electron negative atom such as nitrogen or ox ygen The electron negative atom has a greater attraction for electrons The electron distribution in the covalent bond is weighted towards the electron negative charge giving the hydrogen a slight positive charge.

Interm olecular bonding forces These functional groups are known as hydrogen bond donors (HBD), since they provide a hydrogen for a hydrogen bond

Intermolecular bonding forces The functional group that provide the electron- rich atom to receive the hydrogen bond is known as the hydrogen bond acceptor (HBA)

Interm olecular bonding forces Hydrogen bonds has been viewed as a weak form of electrostatic bonds Due to the slight positive HBD and negative HDA Unlike other intermolecular interactions an interaction of orbitals is involved

Intermolecular bonding forces The orbital containing the lone pair of electrons on heteroatom (Y) interacts with the orbitals involved in the bond between X and H Resulting in a weak form of sigm a bond which have an im portant directional consequence The optim um orientation is where the angle between X- H and Y equals 180 180 is the strongest bond Varies between 130 and 180 for strong Hbonds Can be as low as 90 for weak HBonds

Intermolecular bonding forces Important to note is the directionality of the lone pair of the HBA i.e. The nitrogen of a pyridine ring is sp2 hybridized and points directly away and out of plane from the m olecule

Intermolecular bonding forces HBonds have m oderate strengths and varies between 16 and 60 kjm ol - 1 The HBonds is 10 times weaker than covalent bonds and is reflected in the bond lengths Covalent bonds 1-1.5Å HBonds 1.5-2.2Å The strength of HBonds depends on the strength of the HBA and HBD Most com mon HBA in biology nitrogen and ox ygen Nitrogen 1 HBond Ox ygen 2 HBond

Interm olecular bonding forces

Intermolecular bonding forces Good HBD's contains Elect ron deficient proton linked to a ox ygen or nitrogen The m ore electron deficient the proton the better it will react as a HBD i.e. A proton attached to a posit ively charged quaternary nitrogen is a stronger HBond donor than those attached to a prim ary or secondary am ine

Intermolecular bonding forces Van der Waals interactions Weak interactions 2-4kJm ol - 1 Involve the interact ions between hydrophobic regions Many interactions which m ake strong interact ion overall The electronic distribution of neutral, nonpolar regions is never totally even or sym metrical Transient areas of high and low elect ron densities These leads to tem porary dipoles Dipoles on one m olecule can lead to a dipole on

Interm olecular bonding forces Hydrophobic regions of ligand and target Transient dipole in ligand Induced dipole on target and van der Waals interactions

Intermolecular bonding forces Dipole- dipole and ion- dipole interactions Many m olecules have perm anent dipoles Results from different electronegativities of different atom s and functional groups Both ligands and active sites (binding sites) have dipoles It is thought that dipole m om ents of the ligand interact with t hat of the binding site. Aligning the ligand so that the dipole m om ents are parallel and in opposite directions Stronger than van der Waals but weaker HBond

Intermolecular bonding forces An high electron density region on one m olecule can have an attraction on a low electron density of another molecule

Intermolecular bonding forces Ion- dipole interactions Where a charge or ionic group of one m olecule interacts with the dipole of another m olecule Stronger than dipole- dipole interact ion

Intermolecular bonding forces Repulsive interactions Repulsive force also important If molecules com e to close toe each other their molecular orbitals start to overlap Also identical charges

Interm olecular bonding forces The role of water and hydrophobic interactions Important interactions is that of water with m olecules Macrom olecular targets ex ist is aqueous environm ent Water needs to be stripped before binding Resulting in tighter binding of ligand

Conclusion There is various different ways in which a ligand and its target can interact Im portance of these interactions Better understanding of protein- ligand interactions Better understanding of catalytic m echanism of action Guide site- directed m utagenesis Guide to m odify ligand for better binding

Ligplot Ligplot is a program used to determ ine m olecular interactions Ligplot determ ines: Hydrogen bonds Polar interactions Hydrophobic residues

Ligplot

VMD