Drug design and discovery New and old drugs

Secondary stage rash in syphylis on the palms of the hands. Bacteria Treponema pallidum Old drugs: treated with arsenic and mercury Adverse side effects: inflammation of the gums, destruction of the teeth and jaws, and organ damage New drugs: penicillin 1928 Alexander Fleming Beta-lactam antibiotics 1941 WWII Large scale production of penicillin

Beta-lactam antibiotics Beta-lactamase Bacteria develop drug resistance Clavulanic acid Beta-lactamase inhibitor Until 2003, more than half of all commercially available antibiotics in use were β-lactam antibiotics

The peptidoglycan (or murein) layer in the bacterial cell wall is a crystal lattice structure formed from linear chains of two alternating amino sugars, namely N-acetylglucosamine ( NAG) and N- acetylmuramic acid (NAM). Attached to the NAM is an oligopeptide chain of three to five amino acids. The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D mesh-like layer.

PBP – Penicillin binding proteins (DA-DA-transpeptidase) cleave the terminal D-Ala to perform the crosslinking.

Penicillin binds to transpeptidase The cell wall growth is stoped

Lab2-peptides Penicillin mimics the D-alanyl-D-alanine (DA-DA) residues that normally bind to the active site in the transpeptidase enzyme: -similar structure -similar functional groups -better binding than DA-DA, irreversible binding

Penicillin biosynthesis Company Pfizer engineered production of gluconic acid and vitamin C using deep-tank fermentation and extended it to penicillin. The first penicillin plant was built in 1944 with several 7,500 gallon tanks. In 1942, there was enough drug for ten doses, by 1945 there was enough to treat 646 billion.

Beta-lactamase secreted by bacteria destroys the antibiotic active site structure

Ampicillin Amoxicillin Ampicillin isn't well absorbed with a bioavailability of 40%. Amoxicillin, was designed this time by changing the benzene to a phenol. The addition of the hydroxyl group (-OH) now increases the bioavailability of Amoxicillin to 95% and allow it to be taken orally. Structural differences between penicillin (1) and cephalosporins (2) Cephalosporins are more stable (due to a double bond) to the action of beta-lactamase that destroy the antibiotic activity.

D-alanyl-D-alanine carboxypeptidase/ transpeptidase Penicillin 

Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls M Yusupov et al 2012 New J. Phys peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein interaction with O3, O2 and O atoms

One phospholipid unit interacting with an OH radical at the glycerol group (left), and zoomed pictures of the reaction evolution leading to breaking of a C-C bond (hydrolysis)

Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall Wang et all. PNAS 2012

80% of chronic infections are related to biofilms

Docking search method

Until 1905 cocaine was used as local anesthetic in dentistry Side effects – addiction Novocaine (Procaine) Side effects – allergy due to its metabolites From 1950 Lidocaine with epinephrine

cocaine epinephrine

I – isoleucine, F –phenylalanine, Y - tyrosine