LECTURE 10. Contents. In silico drug design. Basic terminology

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1 LECTURE 10 Contents In silico drug design Basic terminology Pharmacon (Gr.φάρµακον = drug ): a compound affecting living organisms Pharmacy: is a transitional field between health sciences and chemical sciences Pharmacology: (Gr. λόγος = science): is the study of how substances interact with living organisms to produce a change in function. Main points in history 16 th century Iatrochemistry (Paracelsus) only the dose permits something not to be poisonous. 18th century allopathy: treating symptoms, this is the traditional medicine, where a disease is treated by producing a second condition that is incompatible with or antagonistic to the first 19th century homeopathy (Hahnemann): treating the sick with extremely diluted agents that, in undiluted doses, produce similar symptoms in the healthy 1850 Pharmacodynamics, homeostasis (Claude Bernard) "To have a free life, independent of the external environment, requires a constant internal environment" Which parameters should be optimized during drug development? Pharmacodynamics: is the study of the biochemical and physiological effects of drugs and the mechanisms of drug action and the relationship between drug concentration and effect. Pharmacokinetics: the study of the time course of substances and their relationship with an organism or system (ADME) Possibilities of drug discovery - Accidentally (e.g. penicillin, antibacterial by Fleming) - Using biochemical knowledge (e.g. allopurinol against gout) - Screening (experimental or virtual)

2 Costs of drug discovery million $, 75 % of which goes for useless drug 28 % lack of efficiency, 5 % bad marketing strategy, 20 % toxicity, 37 % bad pharmacokinetics - Chemicals and biohazards (environmental problems) - Killed animals (ethical problems) In silico (computational) methods helps to reduce the - monetary costs - amount of experiments and waste chemicals - amount of killed animals Drug design strategies Trends in drug design Merck Pfizer-Groton (HTS)

3 Hierarchy of in silico methods Merck Pharmacodynamics Pfizer-Groton (HTS) Pharmacokinetics Absorption Distribution Excretion 1D/2D 1D/2D

4 Ghose et al. (Comprehensive Medicinal Chemistry Database) 80 % The 1D/2D filters are implemented in program packages AlogP 5.6 (average: 2.52) 160 MW 480 (average: 357) 20 number of atoms 70 (average: 48) BBB (Blood Brain Barrier) penetration of drugs Complex cell system formed by the endothel cells of brain capillaries. Maintains the homeostasis of central nervous system. BBB should allow drugs acting on central nervous system but not the periferial drugs. Metabolism of xenobiotics The structure of cytochrome (CYP) 3A4 complexed with progesteron NADPH + H + + O 2 + Drug = NADP + + H 2 O + Oxidized Drug logbb=-0.148psa+0.152clogp n=55 r 2 =0.79 logbb= psa+1.33 n=45 r 2 =0.84 logbb= tpsa mw n=55 r 2 =0.703 O 2 CYP Fe +2 Drug 2H + H 2 O CYP Fe +3 Drug OH

5 Toxicity Nitrils -logld 50 =-1.69α/ E+0.47 N=13 r=0.87 (α:polarizability E:HOMO-LUMO diff. Substituted benzenes log(1/lc 50 )= logP+13.7SDELOC N=114 r 2 =0.81 ADMETox Painful lessons Nature Structural & Molecular Biology 12, 205 (2005) The risk of heart attacks and strokes associated with Vioxx and Celebrex reminds us that all drugs have side effects. The serious side effects of pain relievers have been in the news lately. The increased risk of heart attacks and strokes associated with rofecoxib (Vioxx, Merck) and celecoxib (Celebrex, Pfizer) has led to the withdrawal of rofecoxib in late 2004 (the largest withdrawal in history) and reduced the sales of celecoxib by 50%. Because rofecoxib and celecoxib are top-selling prescription medicines, the issue has drawn widespread response. At a US congressional hearing, we heard testimony that the FDA failed to protect the public from unsafe drugs. Similar to the development of imatinib (Gleevec, Novartis), the success of rofecoxib and celecoxib validated the concept that drugs targeted to specific molecules have fewer side effects, at least until recently. The problem facing rofecoxib and celecoxib that they avoided gastric bleeding only to incur the severe side effects of heart attacks and strokes seems to contradict this particular strategy. Nevertheless, the case is a clear reminder that all drugs have side effects; the question is whether their benefits outweigh their risks. Side-effects of drugs (some statistics) Selectivity and inverse docking A clinical patient consumes an average of 15 drugs. Doctors order some kind of drugs for 75 % of their patients. Antibiotics consumed in hospitals are unnecessary in 64 % of the cases. A 15 % of clinical patients suffer from side-effects and a 5 % becomes a clinical case because of side-effects.

6 Summary Structure Optimized Structure + Energy ( G) Theories are only verified hypotheses, verified by more or less numerous facts. Those verified by the most facts are the best, but even then they are never final, never to be absolutely believed. (C. Bernard) Other Properties Drug-likeness ADMETox Side-effects etc.