Molecular Pharmacology PDF

MOLECULAR AND EXPERIMENTAL PHARMACOLOGY Pharmacotherapy vs Molecular Pharmacology  Pharmacogenetics/Pharmacogenomics Therapeutic problem  core drugs (different mol target/common end point)  it starts from the disease Molecular Target (e.g. GPCRs, Transporters)  drugs for different pathological...

MOLECULAR AND EXPERIMENTAL PHARMACOLOGY Pharmacotherapy vs Molecular Pharmacology  Pharmacogenetics/Pharmacogenomics Therapeutic problem  core drugs (different mol target/common end point)  it starts from the disease Molecular Target (e.g. GPCRs, Transporters)  drugs for different pathological conditions/therapeutic problems  classes of receptors (there are different subtype of these kind of receptors)  it starts from the molecular target proteins.  The goal of molecular pharmacology is to describes why certain drugs are used for certain disease and their effects Pharmacodynamics  describes what drugs do to the body, mechanism of the drug effects, explain how the drugs produce their pharmacological effects. It starts from: ✓ Drug targets (target structural features, localization) ✓ Different mode of action (antagonist, inhibitor…) ✓ Signaling pathways  Understanding for the rational use of drugs (risk to benefit)  Identification of new drug targets/new drugs (related to the same signal pathways) Drug discovery process  It has changed a lot of times during these years Characterizing new biological activities  functional studies (whole body  cellular and molecular assay)  drugs were used for their role, defining the molecular target discovered lot of years later, basically this approach was used to test the biological affect of the drugs that they were used for their efficacy and the side effects were unknown. Functional studies is still use to test a specific biological response of compound libraries (e.g. 106) (e.g. cellular and molecular assays)  phenotypic screening  based on the analysis their different capacity  the next step is the target deconvolution, means that the target is identified  this approach overall is a compound stand approach. At the present the drugs discovery take the opposite direction  defining the molecular target (e.g. genomic studies) having a critical role of the disease, often the definition of the target is the first step of these studies, this target oriented approach is called  reverse pharmacology, this approach takes advantages from molecular genetics/genomics, overtime candidates are studied and the genomics factors helps to identify the target even for new drugs. ✓ High throughput screening of high affinity ligands (also in silico analysis) ✓ From hits to leads: > affinity and > specificity  Functional studies After the target identification and the screening of several compound, the functional studies came later, and so the functional studies based on function-to-target starts to be more like  TARGET- to-function. Pharmacokinetics  “what the body does to a drug” Dose of drug administered  [drug concentration]  drug action site (target)  drug action response. Pharmacokinetics is important because it involves several steps after a drug is injected into the body: ✓ Absorption ✓ Distribution ✓ Metabolism ✓ Excretion  ADME Pharmacodynamics & Molecular Pharmacology  “what the drug does to the body” Instead for this topic is more something about the interaction with a “drug target”  activation of a cellular response Why pharmacokinetics is important? ✓ How well will the compound be absorbed if given orally? ✓ How well does it distribute to the targeted organs and tissues? ✓ How rapidly and by what mechanisms is it eliminated? ✓ Is it metabolized to an active metabolite? ✓ Speed of onset ✓ Duration of action (T1/2) ✓ Drug safety ✓ Drug development  Pharmacokinetics affects the concentration of a drug at its sites of action: therapeutic and unwanted  Pharmacokinetics is relevant in drug development process, it starts from target selection to clinical trials  40% of the compounds in development were discontinued due to inappropriate PK properties The relationship between pharmacokinetics and pharmacodynamics of a drug: ✓ Pharmacokinetics: dose  concentration vs time ✓ Pharmacodynamics: concentration  effect ✓ PK/PD: dose  effect vs time NB. Pharmacodynamics = molecular pharmacology Mechanism of drug action on the body  levels of action ✓ Molecular: interaction with the drug’s molecular target  the drug target (e.g. receptor, ion channel, enzyme, carrier molecule) ✓ Cellular: transduction x the biochemicals linked to the drug target (e. g. ion channel, enzyme, G protein) ✓ Tissue: an effect on tissue function  electrogenesis, contraction, secretion, metabolic activity, proliferation ✓ System: an effect on system function x integrated systems including linked systems (e. g. nervous system, cardiovascular system) E.g. atenolol, beta-adrenergic receptor antagonists Mechanisms of drug action ✓ Drugs often interfere with cellular responses to endogenous molecules (modified by diseases)  ✓ Drugs should act selectively in some cells or tissue:  Discrete target distribution (on-target side effects)  High degree of binding site specificity (complementary specificity of ligands and binding sites) Drugs and targets with low specificity  several rugs hit multiple targets by accident: undesidered off-target effects  unspecific interaction of a selected target with several drugs: antipsicotics, TCA, ecc… Drugs specificity and psychiatric disorders BROAD specificity is a feature of drugs for psychiatric diseases, highly specific drugs have failed in the clinics for the limited knowledge of pathophysiology and disease mechanisms. Mechanisms of drug action Biological systems often contain redundant elements and can adapt to the drug. Explanation of redundancy: multiple receptors leading to a common response multiple signaling downstream a specific receptor. Early and late effects of drugs ✓ antidepressant drugs: therapeutic effects require weeks to appear ✓ antypsycotics: dyskineasia (prolonged drug exposure) ✓ opioids: analgesia (early), drug tolerance and addiction (late) Drug: molecular Targets Most drugs act by specifically combining with proteins (receptors”) which are an integral part of the cell, so as to alter its biochemical and biophysical properties ✓ conventional/Physiological receptors  mediate the effects of soluble endogenous molecules such as neurotransmitters, hormones, … (membrane and nuclear receptor) ✓ other receptors (integrins, PD-1) respond to proteins attached to cell surfaces or matrix  proteins; Toll-like receptors for LPS there are many molecular targets of drugs with different properties and functions: ✓ receptors  transporters, ion channels, enzymes (all of them are proteins) and other biomolecules (RNA or DNA). These are not true receptors, although these are referred to as receptors since translate the binding of a drug into a cellular effect ✓ molecular targets of drugs used as therapeutics  some drugs act through multiple targets by design: multiple kinase inhibitors, bispecific antibodies, bitopic agonists Target identification ✓ Knowledge of disease mechanisms ✓ Receptor biology/signaling pathways ✓ Genomics What are suitable targets for future drug development? ✓ Protein with key role in the pathogenesis of a disease (oncogene-derived proteins, proteins involved in insulin release, cholesterol synthesis) ✓ Allows formation of specific hypothesis about how modulating its function would be effective against a disease ✓ The process of confirming such hypotheses is termed ‘target validation’ Failure in target validation: lesson from leptin ✓ The hormone leptin suppresses appetite, it affects body weights ✓ LOF mutations in the leptin/leptin receptor gene results in obesity in mice and humans, this mutations has affects on obesity. OBB mice are well know for the obesity. ✓ The scientist tried to make an agonist for the leptin, but it failed  the hypothesis was not validated maybe for redundancy leptin pathways and explained but leptin insensitivity for neutralizing-antibody. High leptin in the blood maybe become leptin-tolerance.  Leptin-receptor agonist? ✓ Some obese individuals appear insensitive to leptin action ✓ The hormone leptin suppress appetite  ✓ Imbalance in leptin or LEPR signaling (hyperleptinemia that results in leptin resistance or hypoleptinemia) causes obesity  Mab passed phase 1, LEPR “agonist” (mibavademab). Mab “agonist” succeed in rebalancing leptin signaling in patients with low leptin level ✓ Semaglutide and Liraglutide  peptide analogs of endogenous hormone for the incretin that showed efficient anti-obesity effects ✓ The MC4R agonist Setmelanotide for deficines affecting the leptin-MC4 pathway  it targets a protein downstream the leptin receptor, it is use for a specific genetic defects ✓ Targets validation is just for clinical trails Drugable targets Are there small molecules that bind the target electively and with high affinity? A general issue for the discovery of target is about the druggability  is the target drugable? ✓ Receptors for small endogenous ligands (e.g. βR and noradrenaline) or enzymes (protein kinase and ATP), prefer small molecules can bind in a selection target with high affinity (small endogenous molecules are more drugable targets)  good ✓ Receptors for peptides/proteins, often have large contact points with the ligands, this peptide are less druggable at least by the small molecules. (e.g. GLP1R and incretins)  not so good, but ok ✓ Disrupt protein-protein interaction in a signaling cascade, this is even more difficult to target, but they are not impossible, intracellular proteins usually are considered un-druggable but the scientist are trying to find a target (e.g. Ras and Sotorasib)  terrible Genome project and Genome-wide association studies: the identification of novel targets After the identification of several genomics mutations/variations, the idea was that proteins derived from disease associated gene variants could be nice to be a drug target. Several genome association studies has been performed to came out to identified common mutations associated with a disease that may serve like a drug target. Rarely a single mutation has a casual/driving role in the disease process  GWAs failed to find casual mutations relevant for novel target. Most disease are polygenic and can become a several different kind of disease  Genetic support to drug discovery, experiments of nature, rather than GWAs studies may support the discovery of novel drug targets  “impact of genetically supported target selection on R&D productivity”  various remedies have been proposed to tackle the long-standing problem of high attrition in drug development due to safety, efficacy and other causes. We are recently estimated that drug mechanisms with genetic support could succeed twice as often in the clinic as those without such support. This analysis high field the importance of the selection of the target  and the indication in subsequent phases of the pharmaceutical pipeline, at the influence must be quantified in order to appropriately inform decisions on overall R&D strategy and resource allocation”  genetics are useful to find successful compounds  the current idea is that experiments of nature can help to the discovery of novel targets  basically it means: “individuals that brings a rarely genetic mutations and they are at low for disease”. Genetic support to drug discovery “Experiments of nature” Loss of function mutations (LOF) protective against a human disease provide in vivo validation of therapeutic targets  Rare variants associated with a favorable phenotype: low LDLc (e.g. PCSK9, NCP1L1, ANGPT3) these individuals with low LDLc is support by these mutations, the scientist tried to mimic what happens in these lucky individuals by starting with these mutations, lucky individuals that are at low risk disease because they carry a loss of function mutations that protect that of the development of a specific disease  rare phenotypes support the identification for human validated drug targets. The absence of the targets did not affect in a dangerous way the individual, the safety was already demonstrated by the nature. Another area was about LOF in Mendelian diseases  new target therapies, there are personalized therapy with drugs on the market that affect for a specific gene mutations  the purpose is to restore the normal functionality Human genome sequencing/tumor signature: the identification of new drug targets ✓ Studying gene variants associated with a specific disease (germline mutations/in born mutations) may assist in identifying new drug targets  es PCSK9 LOF/low LDL levels  Evinacumab. CFTR/cystic fibrosis  lumacaftor/ivacaftor Phe508Del ✓ The analysis of tumor specific gene variants (somatic mutations) originated targeted therapies  there are some kind of somatic mutations that was founded in tumor cells, high rate of proliferation, by the way, drugs developed starting from the analysis of these tumor cells are called target therapies (like trastuzumab, a target example for specific proteins that are overexpressed in breast cancer cells) Novel molecular targets: to sum up Genetic studies may support target identification: ✓ “experiments of nature”  validated drug targets ✓ Oncogene-derived proteins in tumors, that have a driving role in the cancer development  oncongene proteins are basically targets for anticancer therapy ✓ Genes causative of a disease caused by somatic mutations  valid drug targets (e.g. CFTR in CF) ✓ Targets identified without the genetic support (ACEi/ACE; NSAID/COXs)  these targets are related to proteins involved in disease development or progression There are several way to find a novel targets, once identified a targets It need to be validated and it can be defined as an effector of a drug which, when modulated in vivo, in man, gives rise to a therapeutic effect  the only validated is in human. NB  ultimately, the only relevant ‘target validation’ is showing that a new drug for your new target is efficacious in human disease Personalized medicine  treating the single individual Further the idea to look at the therapeutic effects in humans, not just considered just a group of people but as like a single individual, patients are different each one have a different genetic background that maybe defined a different respond by the drugs. Patients and disease are heterogeneous  it is important to use therapy for single individual for maximum the efficiency and minimize the side effects. Targets therapy against cancer are an example of personalized therapy  basically designed for a specific patients, those who have a specific genetic mutations  like in a tumor caused by the genetic mutations of HER2. Companies are vary interested in personalized of personalized medicine Example of personalized treatments  targeted therapies against cancer mutated proteins/monogenic disease specific mutation NB. Patients are different, diseases are heterogenous  however, most medicines are not differentiated Target-oriented approach to pharmacology  novel approach in the drug discovery process  It fits well to the modern approach from target to drug discovery: ✓ Target-therapies for cancer-specific “protein” (e.g. RAS/melanoma) ✓ Personalized treatments for previously uncontrolled diseases (e.g. target therapies for Cystic fibrosis) Drug approvals The graph show the FDA drug approvals that shows that at least 15 drugs was develop in the last years (the blue one is small molecules and the red one is the biological molecules) Biopharmaceuticals/biologics as opposed to conventional small molecule ✓ Biopharmaceuticals are large molecules like proteins, antibodies, nucleic acid-based compounds produced mainly by biological sources ✓ First-generation biopharmaceuticals are mainly copies of endogenous proteins or antibodies/Ab fragment produced by recombinant DNA technology ✓ Over time second/third generation have been develop “engineered” proteins, antibody- drug conjugates, antisense agents,...  improved pharmacokinetics or efficiency or also better safety profile instead of the first generation compounds Biopharmaceuticals ✓ Canonical monoclonal antibodies (e.g. Trastuzumab), antibody-drug conjugates (e.g. trastuzumab emtansine), bispecifc antibodies that are more effective than naked antibodies (e.g. antiCD3 to recruit T cells+antiEGFR), nanobodies ✓ Engineered peptides/proteins to obtain more efficient pharmaco (e.g. insulin detemir longer acting, modified forms of GLP1) ✓ Rna-based drugs to control gene expression (ASO, anti-sens oligonucleotide they are produced by synthesis, siRNA) (e.g. Inclisiran, Etiplersen (for the distrofy of Duchen), Mipomersen, Casimersen) Differences in “size” Biopharmaceuticals are more wights than other, a further distinguish are for therapeutic peptides  they are intermediate molecules. These small peptides up to 40aa are include in the class of small molecules  Small molecules: ✓ Aspirin 180.16 Da (Mol Weight