Pharm 200 Study Guide.pdf

Pharm 200: The Science of Medicine ___ Lecture 1: Science of Medicines Dr. Pai Drug discovery and Development Medical need is driven by: ○ Lack of medications in that space ○ Total market share for that drug development process W...

Pharm 200: The Science of Medicine ___ Lecture 1: Science of Medicines Dr. Pai Drug discovery and Development Medical need is driven by: ○ Lack of medications in that space ○ Total market share for that drug development process What we are trying to do is develop assays to try to figure out what the disease is, how it is present, and how it progresses. Translational biomarkers ○ Can I actually measure this? What would I measure? How would I measure it? What’s the frequency of measurement? This whole process is iterative because you can’t just do one thing at a time (sequential). Lead Identification: ○ Find a molecule or biologic that might hit the target Lead optimization: ○ Once you have thousands of molecules, you screen them so that you only have a handful to work with. ○ Modifications to optimize molecule Development (very expensive) ○ Valley of Death- burning money trying to develop a drug with very limited grants or funds. The time scale from discovery to development of a drug is about 10-20 years. Once discovered → patent it. Once granted a patent, you have 17 years of exclusivity including drug approval and marketing. Primary Drivers of Drug Discoveries Academia - personal interest and funding ○ Ex: someone has a family member with the disease, has some experience  ○ In academic, most people are looking for grants (private foundation, government funding) Pharmaceutical Industry- very deliberate corporate strategy ○ If we develop this drug, is it even going to sell Ex: new drug for hypertension → must be better than every other drug existing (recognize market competitors) Most research is carried out on diseases which afflict “first world” countries (basically taking advantage— driven by market) ○ Ex: cancer, diabetes, depression Stakeholder input- you need participation from multiple patient advocacy groups to support your development. Due to emphasis on money, the only way to get traction on supporting development of drugs in less common diseases was The Orphan Drug Act. The Orphan Drug Act of 1983 was passed to encourage pharmaceutical companies to develop drugs to treat diseases which affect fewer than 200,000 people in the US. Unmet medical needs means there is no satisfactory method of diagnosis, prevention or treatment that’s available for that specific disease. Ex: Osteoporosis → developed by researchers (the disease didn’t exist in a sense) → people recognized fractures in older people → come up with diagnosis tools to measure bone density and classification system to classify osteoporosis → come up with therapeutics Stages of Drug Development 1) Target Discovery: Where do you start? Look at the literature, go through patents, talk to scientists involved in the field of study. What do drugs interact with? What is the target that you are going to hit? ○ Mostly proteins: receptors (GPCR), enzymes, ions channels, transporters, adhesion molecules ○ DNA & RNA ○ Sometimes may not want mammalian target: antimicrobials (bacterias) What are the pros and cons of selecting one or multiple targets for a disease? Reduce risks (backup plan) for multiple targets. The process… Conventional: use existing experience and data with effective drugs to explore mechanisms that could be exploited by new drugs. Modern Molecular (the typical pathway used) ○ Advances in molecular biology (human genome project) ○ Typically ends with “-omics” (ex: proteomics, metabolomics, genomics) Genome Wide Association Studies (GWAS) Taking individuals that have a certain disease (or carriers) and comparing their genes with non-diseased individuals to see if there are any outliers that might suggest that that is the gene we need to target. 2) Molecular Target Screening Patients vs. healthy If you think the gene is responsible for the disease, you need further tests Genomics: genetic differences, expression profiling, test in mouse models, identify new pathways Proteomics: tissue extraction, separation, sequencing 3) Target Validation Where a lot of failures happen because pharmaceutical companies or academia don’t have enough money and resources to validate that that disease is caused by that target. ○ What ends up happening is the drug development pathway starts based on that specific target, and when we get to the clinical studies, the drug fails because it didn’t target that disease. True validation only when effect is seen in patients (sometimes drug may work in animals but not humans— more than one pathway for disease to develop) Are the genes expressed in the appropriate tissue? Are the proteins expressed in the right place and have appropriate function? 4) Target Exploitation Figuring out how to measure this activity and then to screen. How do we create this enzyme, how do we test the activity of the enzyme in an assay, and can we modulate that with the molecule. Assay- measuring biological activity (receptor activation, enzyme activity, functional activity) Screen- ability of compare compound ability to modulate function, inhibition or induction of activity Selectivity is important! Hard to hit just one target, therefore try to increase selectivity of the molecule as much as possible. Consequences of hitting other targets: side-effects Is the target “druggable”? Does the target have a binding pocket? What is the affinity of this target? What is the Kd and IC50, potency (nM or uM)? Stability, solubility, synthetic feasibility Lipinski’s Rule of Five is used to measure whether a drug can be absorbed. Lipinski’s Rule of Five A small molecule: molecular weight < 500 daltons ○ Shows that the molecule is probably going to be absorbed super easily and get into tissues easily Partition coefficient: logP < 5 ○ Very likely going to be absorbed; means this molecule is very likely to be made into an oral drug. ○ Oral drug >> injectable drugs (cheaper to manufacture and easier to take) ○ < 5 H-bond donors (sum of NH and OH) → better ability to go through membranes ○ < 10 H-bond acceptors (sum of N and O) → better ability to go through membranes 5) Identification of Actives Chemome = 1062 drug-sized molecules (complex due to this) Where do you start? Natural substance and make it drug like (ex: snake venom kills prey by reducing blood pressure → Captopril → transformation of snake venom) Start with someone else’s compound (“patent bust”) → modifies someone’s molecule From scratch (need to know protein structure) High throughput screening: robotics systems that physically screens thousands of molecules per day to find lead molecules 6) Choose the Bioassay In vitro: in an artificial environment, as in a test tube or culture media (ex: antibiotics → on plate) Has advantages in terms of speed and requires relatively small amounts of compound Speed may be increased to the point where it is possible to analyze several hundred compounds in a single day (high throughput screening) Results may not translate in living animals In vivo: in the living body, referring to tests conducted in living organisms More expensive May cause suffering to animals Results may be clouded by interference with other biological systems Ex vivo: usually refers to doing the test on a tissue taken from a living organism. 7) Finding your Hits Hit: consistent activity of a molecule in a biochemical or cell based assay 8) Finding a lead compound Lead compound: structure that has some activity against the chosen target, but not yet good enough to be the drug itself If not known, determine the structure of the “lead compound” Any prior PK property profile (Absorption, Distribution, Metabolism, Excretion) → ADME Known toxicologic characteristics Synthetic feasibility (some drugs are tedious to make → nature make it way better) Occupational health associated with starting materials Solubility, permeability QT prolongation, mutagenicity 9) Determine pharmacodynamics and pharmacokinetics of the drug Figure out the dose → where is the molecule going? how much of it should be given? where is it safe to give and where is it toxic? Pharmacophore is the precise section of the molecule that is responsible for biological activity. You don’t want to change this section Change other pieces, not the active site (58:40) Metabolism of drugs The body regards drugs as foreign substances, not produced naturally, which are sometimes referred to as “xenobiotics” Body has “goal” of removing such xenobiotics from system by excretion in the urine For a drug to get absorbed (metabolize) → have enough lipophilicity to get through the cell membrane but also polar enough to be soluble The kidney is set up to allow polar substances to escape in the urine so the body tries to chemically transform the drugs into more polar substances Oral administration frequently brings the drugs (via the portal system) to the liver. Phase I: Metabolism involves the conversion of nonpolar bonds (ex: C-H bonds) to more polar bonds (ex: C-OH bonds) ○ Oxidation: oxidize substance ○ Key enzyme is the cytochrome P450 system, which catalyzes this reaction: RH + O2 + 2H + 2e- → ROH + H2O ○ Sometimes result in a substance more toxic than the originally ingested substance ○ Ex: acetonitrile Phase II: metabolism links the drug to still more polar molecules to render them even more easy to excrete ○ Glucuronidation: adding a sugar molecule to the oxidized substance Toxicity Toxicity standards are continually becoming tougher Must use in vivo (ie. animal) testing to screen for toxicity  ○ Each animal is slightly different, with different metabolic systems, thus a drug may be toxic to one species and not to another. Ex: Cardiotoxicity 10) Clinical Trials Phase 0: first clinical trials done among people. They aim to learn how a drug is processed in the body and how it affects the body. In these trials, a very small dose of a drug is given to about 10 to 15 people (microdosing) to find out where the drug metabolizes. Phase I: drug is tested on healthy volunteers to determine toxicity relative to dose and to screen for unexpected side effects. Phase II: Drug is tested on a small group of patients to see if drug has any beneficial effect to determine the dose level needed for this effect. These studies are sometimes divided into Phase 2A (designed to assess dosing) and Phase 2B (designed to determine efficacy) trials. Phase III: drug is tested on a much larger group of patients and compared with existing treatments or against a placebo (does my drug actually work?) → then is submitted to FDA Phase IV: post-marketing surveillance, new indications (ex: if drug may harm fetus, monitor fetus that are exposed) Phase V: is therapeutic effect realized in dat to day clinical practice (where we get the value proposition of the drug) Beach → Bedside → Community ___ Lecture 2: Therapies of Tomorrow Cancer Normal cells → becomes abnormal → divides rapidly (doesn’t go into apoptosis) → cells contribute to divide and blood vessels develop forming a cancer. Due to genetic or environmental Metastasis: abnormal cancer cells spread to other parts of the body through blood or lymphatic vessels (blood vessels become highways for cancer to travel) Cancer Trends People are living longer but not necessarily healthier Declines in smoking (vaping is not associated with cancer as of now), early detection, greatly improved treatments. Treating Cancer Approx 2 mil cases per year Women: predominantly breast cancer Men: predominantly prostate cancer Colorectal cancer is going up (age of 45+) ○ Detect by: colonoscopy or stool sample (polyps are cut off) Pancreatic cancer is hard to detect and once it’s detected, it’s fatal due to it being a deep organ cancer. ○ However there’s been a movement in the last 5 years to detect these types of cancer earlier. Treatment Options: ○ Hormone therapy: can be used to treat breast and prostate cancer (hormone sensitive)  ○ Surgery: remove tumor visualized by CT or PET scan (downside: how do surgeons know they cut all the cancer out?) → now there are technologies where the cells at the edges of that cancer to a pathologist that can visualize directly or use AI tools to look at the cells. LC-MS (probes) can be used to measure chemicals directly in the OR to look for cancer-type proteins ○ Bone marrow transplantation ○ Chemotherapy ○ Targeted therapy ○ Radiation therapy ○ Immunotherapy: kill cancers by using our own immune system or targeting specific antibodies; treating with vaccines (area we are working on a lot) Timeline in the Innovations of Blood Cancers Not just one person coming up with strategies. 1993- First generation of CAR-T cells Curing Cancer (Immunotherapy) Car-T Cell Therapy CAR = Chimeric Antigen Receptors T-cells are a type of white blood cells that patrol our bodies for diseases ○ T-cells have antigens that are uniquely designed to latch onto antigens of cancer cells.  ○ Kill harmful cells by injecting them with toxins T-cells are taken to the lab and turned into CAR-T cells by modifying the cell receptors to recognize your specific cancer. Before T-cells are placed back into the body, Lymphodepleting Chemotherapy which makes room for new cells. Pro: attacks cancer right away; Con: side effects can be severe, sickness Allogeneic CAR-T Personalized Cancer Vaccines Therapy Using AI and ML for Cancer Detection Artificial learning (AI): is a computer performing tasks commonly associated with human intelligence. Humans are coding or programming in a computer to act, reason, and learn. ○ An algorithm or model is the code that tells the computer how to act, reason, learn.  Machine learning (ML): is a type of AI that is not explicitly programmed to perform a specific task but rather can learn iteratively to make predictions or decisions. The more data an ML model is exposed to, the better it performs over time. Deep learning (DL): is a subset of ML that uses artificial neural networks modeled after how the human brain processes information to learn from huge amounts of data. A well-designed and well trained DL model is able to perform classification tasks and make predictions with high accuracy, sometimes exceeding human expert-level performance. Cervical cancer screening methods→ visual appearance, pap smear, and Automated visual evaluation AI based approach was more accurate than other methods Curing Cancer (Targeted Radiation Therapy) Proton Therapy (for brain cancer) Challenges of curing brain cancer: cannot take samples, has blood-brain barrier (unique capillary structure that keeps compound out of the brain) Detection of cancer → Imaging based (MRI) Traditional treatment approach: X-ray (photon) therapy → cannot get regional specificity → damage surrounding/healthy areas Proton therapy allows adjustment of degree of radiation delivery to different spaces (reduces normal cell damage) Alzhimer’s Disease Neurodegenerative brain disease where individuals develop memory loss. Cause: accumulation of beta-amyloid proteins that form tangles. Alzhimer’s tangles: neurofibrillary tangles that form when dying neurons bunch together and infect other cells with a distorted protein called tau. Current treatments: Challenges of treating neurodegenerative diseases: How do you know it is working and how do you design clinical trials? Cannot improve functionality, only prevent decline What is the cost-effectiveness of the therapy Key to drug development: safety, efficacy (measure of does this thing work), effectiveness (does it benefit the individual; measurable benefit) Future treatment: Photobiomodulation Robotic Surgery Precision surgery DaVinci device: to perform minimally invasive procedures using console, camera, and robotic arm Great precision, less tissue damage, but complex and expensive. Sickle Cell Disease Genetic disease; caused by cells in a certain oxygenated state where its hemoglobin proteins are organized differently, causing them to sickle, which then clog the capillary system. Curing sickle cell disease (gene therapy) CRISPR-Cas9 gene-editing therapy ○ 2021- first clinical trial Two new CRISPR-based gene therapies just approved in Dec 2023. Misconceptions & Concerns related to gene therapy It is not a cure. Not a magic solution to all diseases and may not result in complete cure; it is designed to target specific gene conditions. There are unpredictable long-term effects → still being researched Artificial Organ Replacement Bioartificial kidney Xenotransplantation (using animal organs → ethical?) Anti-Aging Expected to be a $420 billion dollar industry by 2030 Yamanaka factors: Sox2, Oct4, Klf4, and c-Myc  ○ Causes aging People are working to slow aging down We may go down a pathway that induces cancer (cancer cells are immortal) ___ Lecture 3: Pediatric Drug Development and Clinical Trials FDA Drug Development and Approval Processes Takes 11-20 years from discovery to FDA Approval. What is a drug defined by the FDA? ○ A drug is any product that is intended for use in the diagnosis, cure mitigation, treatment or prevention of disease, and that is intended to affect the structure or any function of the body. Pre-Clinical 1) Drug developed → animals tested (for toxicity, safely, and efficacy) 2) IND (Investigational New Drug) application Sponsor submits an IND application to FDA based on results from initial testing that include the drug’s composition and manufacturing, and develops a plan for testing the drug on humans. IND Review: FDA reviews the IND to assure that the clinical trials do not place human subjects at unreasonable risk of harm; also verifies adequate informed consent and human subject protection Clinical 3) Phase 1: 20-80 healthy volunteers are used. Emphasizes safety Goal: determine what the drug’s most frequent side effects are and, often, how the drug is metabolized and excreted 4) Phase 2: 100+ patients are used Emphasizes effectiveness Goal: obtain preliminary data on whether the drug works in people who have a certain disease or condition. Safety is evaluated and short-term effects are studied. Controlled (receive different drug or placebo) and Treatment groups At the end of phase 2, FDA and sponsors discuss how large-scale studies in Phase 3 will be done. 5) Phase 3: 1000+ patients are used Gather more information about safety and effectiveness, study different populations and different dosages, and use the drug in combination with other drugs. NDA (New Drug Application) Review Who reviews NDA? A team of CDER physicians, chemists, pharmacologists, and other scientists review the drug sponsor’s data and proposed labeling of drugs. 6) Review Meeting: FDA meets with drug sponsors prior to submission of a New Drug Application 7) NDA Application: Includes all animal and human data, analysis of the data, and information about how well the drug behaves in the body in terms of pharmacokinetics, and how it’s going to be manufactured. 8) Application Reviewed: FDA has 60 days to decide whether to file the NDA so it can be reviewed. If filed, the FDA Review team is assigned to evaluate the sponsor’s research on the drug’s safety and effectiveness. 9) Drug labeling: FDA reviews the drug’s professional labeling and assures appropriate information is communicated to health care professionals and consumers (dosing, what’s indicated for, how it’s processed in the body) 10) Facility Inspection: FDA inspects the facilities where the drug will be manufactured (safety, cleanness) 11) FDA Drug Approval: Approve application or issue a response letter Post-Marketing Phase 4: Because it’s not possible to predict all of a drug’s effects during clinical trials, monitoring safety issues after drugs get on the market is critical. Once FDA approves a drug, the post-marketing monitoring stage begins. The sponsor (manufacturer) is required to submit periodic safety updates to FDA. FDA’s MedWatch voluntary system makes it easier for physicians and consumers to report adverse events. When important new risks are uncovered, the risks are added to the drug’s labeling and the public is informed through letters, public health advisories, and other education. In some cases, use of drug is substantially limited, and in rare cases, drug needs to be withdrawn. Prescription Drug User Fee Act (PDUFA) Enabled FDA to bring access to new drugs as fast or faster than anywhere in the world, all while maintaining the same thorough review process. Under PDUFA, drug companies agree to pay fees that boost FDA resources, and FDA agrees to time frames for its review of new drug application Passed in 1992 Pediatric What is pediatric? In clinical practice: variation in definition for care by institution ○ Less than 17 years ○ Up to 21 years FDA Drug regulation: age less than 17 years ○ Neonate- birth to less than 1 month (28 days) ○ Infant- 1 month (28 days) to less than 2 years ○ Children- 2 years to less than 12 years ○ Adolescent- 12 years to less than 17 years Why do we need pediatric drug development and clinical trials? Disease states Dosing (by age, weight, etc.) Ways drugs (and other ingredients) are processed in the body (pharmacokinetics) ○ Whether organs are fully developed How drugs (and other ingredients) work in the body (pharmacodynamics) Ways to deliver/take medications The Path to Pediatric Drug Development in the US Pure Food and Drug Act - prohibited the sale of misbranded or adulterated food and drugs. Federal Food, Drug, and Cosmetic Act- mandate drug manufacturers to submit evidence of new drugs’ safety and effectiveness before marketing and distribution. Kefauver-Harris Amendments- required companies to prove their products to be safe and effective with adequate and well-controlled studies (implemented informed consent) Use of medications in pediatrics patients was not really well-regulated for safety or efficacy for decades.. Pediatric patients were considered therapeutic or pharmaceutical orphans because they were left out. History of Pediatric Drug Development Legislation BPCA vs PREA Best Pharmaceuticals for Children Act (BPCA): ○ Drugs and biologics ○ Voluntary Studies ○ Studies relate to entire moiety and may expand indications ○ Studies may be requested for orphan indications Pediatric Research Equity Act (PREA): ○ Drugs and biologics ○ Mandatory studies ○ Requires studies on indications under review ○ Orphan indications exempt from studies ○ Triggered by an application for: New indications New dosage form New dosing regimen New route of administration New active ingredient Ongoing Challenges to Pediatric Drug Development Ethical Issues All subjects in a research study undertakes risk Infants, children, adolescents are VULNERABLE ○ Increased risk of adverse events and side effects ○ Risk of permanent damage to developing bodies ○ Dependent on adults for care Thus the need for multiple safeguards to help ensure research is conducted ethically. Ethical Regulation Universal safeguards for research participants ○ 1962 Kefauver-Harris Amendments + 1979 Belmont Report (basic ethical principles and guidelines that address ethical issues arising from the conduct of research with human subjects.) ○ Informed consent  Informed consent → Parental consent + Child assent (can be pictures + verbal explanation) ○ Infants, children, adolescents do not have legal capacity to provided informed consent ○ The combination of parental consent and child assent is standard for ethical research in children when child is capable of assenting (eg. age 6-7 years) Small Population Makes recruitment into clinical trials difficult ○ Modest sample size weakens data Possible strategies ○ Patient enrichment: Decrease variability Choosing those who are more likely to respond to treatment (those without treatment/option) or those with greater likelihood of having disease related endpoints. ○ Master protocols: “One overarching protocol designed to answer multiple questions” Ex: shared control arm to decrease number of patients needed ○ Efficiently use adult data Extrapolate adult efficacy data (theorizing) Modeling studies (Bayesian technique) Finding the Optimal Dose Linear scaling of dose by weight, age, or body surface area are not safe nor effective Traditional dose finding studies ○ Common but slow and inefficient Dose selection methods, application of ○ PK-PD modeling and studies ○ Exposure-response analyses Trial Design and Failure Rate Selection of a study endpoint is crucial to trial success Greater trial success when: ○ Using endpoints that were the same between pediatric and adult populations ○ Combining adult and pediatric vs separating populations ○ Using objective vs subjective (weaker unless have validated scale) endpoints ○ Use of surrogate endpoints (ex: biomarkers) vs clinical endpoints Takeaway Message Medication use in pediatric-aged patients is complex— pediatric patients are not small adult patients The start of considerations of medication safety and efficacy specific to pediatric age populations was not THAT long ago  There are tough challenges to pediatric drug development— development and application strategies to address them are ongoing. ___ Lecture 4: Data Safety Monitoring in Clinical Trials Clinical Trial Participation - Benefit vs Risks Possible Benefits Possible Risks If well designed and performed, may Side effects from treatment, sometimes benefit directly while allowing requiring medical attention (rare case: participants to help others by serious or life-threatening complications) contributing to knowledge about new treatments. Time required for treatment or study visits. Gain access to new research treatments before they are widely available. Additional testing (ex: blood draws) Receive frequent and careful medical Unknown of long-term risks of treatment attention from research team, experts in that area Oversight of Clinical Trials Principal Investigator- person that reports to the IRB and main person/ people that runs the study (physician, pharmacist) Study Sponsor- usually a company that’s sponsoring the study Institutional Review Board (IRB)- review research involving human subjects to ensure safety and ethics of the research (whether trial should be terminated or continued) Office for Human Research Protections (OHRP)- work in partnership with IRB Data Safety Monitoring Board/Committee (DSMB/DMC)- consultant for the study to evaluate data and provide recommendations (not dictate) Other federal entities, if applicable, such as: ○ National Institute of Health (NIH) ○ Food and Drug Administration (FDA) The “What” of DSMB/DMC? DMC is a term used for a specific study vs DSMB is the larger body that has several active DMCs going This is an INDEPENDENT group of individuals who review accumulating clinical trial data, by treatment group, in order to: ○ Monitor patient safety and efficacy  ○ Ensure the validity and integrity of the trial, and ○ Make a benefit/risk assessment of trial continuation Assess or evaluate: ○ Safety ○ Efficacy to a certain extent ○ Futility Make recommendations to sponsors/investigators (cannot change budget or overrule IRB) The “Why” of DSMB/DMC? 1) Study participant safety. 2) Multiple stakeholders in a clinical trial Potential for influence, bias, etc Ex: money, name 3) Need for an independent body to evaluate interim data during a clinical trial to monitor for any concerning “safety signals” 4) To advocate for study participants Ensuring that there are not unduly or unfairly at risk for harm from active interventions or because of the denial of effective interventions The “Who” of DSMB/DMC? Medical and biostatistical experts with experience in clinical trials in the field of study Members should reflect the diversity of the patient population being recruited and for whom the intervention under study is targeted Each DMC has 3-5 people ___ Lecture 7: How Precise is Your Medicine Dan Hertz Standard/ Empiric Drug Selection Drug approved by disease/ indication ○ Diagnosed disease or condition ○ Severity of condition ○ Line of treatment/ place in therapy Tested in clinical trial cohort, used in population ○ Broad inclusion of patients with disease of interest Empiric drug selection ○ Lack of information to select optimal drug Within drug class or between classes ○ Known inter-patient variability in efficacy However, different patients react differently to these drugs that are selected empirically. Precision Medicine Definition: medical treatment tailored to the individual patient Selection of an effective agent ○ Drugs designed based on knowledge of disease ○ Treatment based on specific knowledge of the condition it is treating (based on the subtype of a disease) Attributes of bacteria Attributes of genetics of tumor Genetics of patients that cause disease (ie. cystic fibrosis) Examples: ○ Infectious Disease ○ Cystic Fibrosis ○ Cancer ○ Gene Therapy Origin of “Precision Medicine” Paul Ehrlich credited for coining “magic bullet” ○ 1870s research staining cells with colored dyes Acidic, neutral, and basic dyes stained different cell structures ○ Chemistry is critical for drug distribution/ action Searched for “magic bullet” drugs ○ Drugs that go straight to the organism they targeted ○ Attack pathogen yet harmless to healthy tissues 1908 screening hundreds of compounds for syphilis ○ Arsphenamine (Salvarsan) highly active and well tolerated Precision medicine has existed for many years, we just didn’t realize it (ie. antibiotics that target specific bacteria) Infectious Disease (1920s) Alexander Fleming ○ Microbiologist studying staphylococci (Accidentally) left petri dishes with staphylococci in lab ○ One dish had a fungus, around which staphylococci were dead ○ Figured out the mold grew penicillin Penicillin is an effective antibiotic mainly in gram-positive bacteria Bacterias evolve (resistance pathogens) → only use the strongest drugs in specific patients with known highly resistant pathogens. ○ Reduce antibiotics in livestock feed to prevent resistant strains from developing We still use empiric (usually on life-threatening diseases) and precision treatment within anti-infective and infectious disease treatments.  ○ Empiric selection (starts immediately): Select antibiotic based on the suspected organism and predicted sensitivity Ex: what tissue, where the patient has been prior ○ Definitive selection (24 - 72 hrs): Culture organisms and select antibiotics based on sensitivity testing Cystic Fibrosis (2000s) CF: pulmonary condition caused by genetic CFTR mutations ○ CFTR protein transports fluids and ions in sweat and mucus (lungs) Without CFTR lung fluid thickens causing infections and breathing difficulties ○ ~2000 CFTR variants that cause CF Variants found in patient’s inherited genes CF defined by class of defect ○ From thousands of mutations → cause at least 6 classes of defect TLDR: Because many different types of mutations cause CF (ex: misfolding, non-existent CFTR), we have different treatments for different classes of mutations (ie. precise medicine) Drugs developed to match CF mechanisms ○ Ivacaftor makes dysfunctional CFTR proteins open to transport ions ○ Lumacaftor corrects CFTR protein misfolding Drugs tested and approved in patients with specific mutations ○ Ivacaftor approved for patients carrying CFTR-G551D ○ Lumacaftor used with ivacaftor in patients carrying FTR-F5008del N of 1 clinical trials are done on patients that may be in a subtype but don’t necessarily have that certain gene mutation (drug is not FDA approved for the different mutation in that subtype) ○ Give the patient the drug that’s usually used in that subtype → if it works → stay on the drug → considered FDA approved Cancer (1980s) Disease of cellular replication Tumors defined by location (very broad): ○ “Lung”, “Breast”, “Ovarian”, etc. ○ Drugs approved by tumor type Aberrant signaling mechanisms for some tumor types (precision medicine approach): ○ Estrogen-receptor +ve breast cancer Addicted to estrogen signaling ○ Develop drugs that compete with estrogen (ie. tamoxifen) ○ Estrogen-receptor -ve Cancer (1990s) Figured out specific genetic variance causes certain tumors to occur Disease of aberrant genetics ○ Transform healthy cells into cancer Mutations, rearrangements, deletions, etc. Found in the TUMOR cells only ○ Activate oncogene/ inactivate tumor suppressor Cause uncontrolled cellular replication Philadelphia Chromosome ○ Rearrangement of BCR and ABL genes Mutant protein with permanent ABL signaling ○ Found in several leukemias (CML, ALL, AML) Imatinib (Gleevec) inhibits ABL signaling ○ Highly effective in Philadelphia+ tumors TLDR: Healthy cells become cancer cells because something happens in their genetics that lose their ability to properly regulate their cellular divisions. Create drugs that are tailored to specific mechanisms allows us to make highly effective drugs for different cancer subtypes Cancer (2000s) The Cancer Genome Atlas (TCGA) ○ Landscape of tumor genomes ○ samples from cancer patients that go through a lot of testings Wide diversity of oncogenic aberrations ○ Mutations ○ Translocations ○ Amplifications ○ Expression changes ○ Methylation patterns, etc Limited number of shared signaling pathways ○ RAS-RAF-MEK-ERK pathway ○ PI3K-AKT-mTOR pathway TLDR: Finding out lots of different tumors have shared oncogenic pathways Cancer (2010s) Develop inhibitors targeted at every step of pathway ○ Incredible scope and success of research (as of 2016) ○ 548 targeted agents in clinical development for 185 unique targets ○ 72 FDA-approved targeted agents TLDR: Discovery of shared oncogenic pathways leads to the development of drugs that inhibit every step of the pathway (break the chain of signaling) Tumor genomics (different mutations) determines clinical trial eligibility ○ BATTLE trial (umbrella trial) → diagnose by anatomical location (ex: non-small cell tumor) → figure out which oncogenic mutations they have → give them drugs specifically designed for that tumor subtype ○ NCI-MATCH trial (basket trial) → all cancer patients enroll in a single trial (same testings) → group patients by different oncogenic mutations (RAF mutations) → goes into trial with specific inhibitors (RAF inhibitor) → if effective, the drug is approved based on specific mutation, not location (ex: lung cancer) TLDR: basically subtyping cancer based on mechanism, not location Tumore genomics determines treatment selection ○ Profiling patients (profiling subtypes), figuring out which patient has an amplification of which mutation, and go onto appropriate therapy → very precise Cancer (2020s) Precision immunotherapy (CAR-T therapy) 1) Collect the patient’s immune cells 2) And 3) Activate immune cells ex vivo 4) And 5) Reintroduce immune cells Immune cells destroy cancer cells First-in-class drug recommended for FDA approval in July 2017 Gene Therapy (2020s) Another approach to deliver or fix genes ○ Replace broken/missing gene ○ Activate gene expression ○ Fix mutations (“Gene editing”/ CRISPR) Progress ○ 1990s: fatal toxicity in phase I study slowed research progress ○ 2010s: hundreds of clinical trials underway but no FDAP approvals 2017: FDA approves gene therapy for RPE65-mutation-associated retinal dystrophy Inactivated virus carries healthy genes into retina to replace defective gene ○ 2020s-30s: perhaps dozens-hundreds of approved agents Precision Medicine Framework Goal: all patients get some treatment that is effective to their disease state Look at patients holistically: health data, microbiomes, environmental impact, exposures, behaviors NIH Precision Medicine Initiative Large-scale data collection (+1M patients) ○ Genetics ○ Environment ○ Medical information Discovery of: ○ Predictors of disease ○ Predictors of treatment response ○ Disease sub-classifcations Development of: ○ Targeted therapies ○ Patient engagement in health ○ Mobile health (mHealth)/ technology Summary: Genetics has revolutionized the understanding of diseases Precision medicine is the standard of care for some diseases ○ Infectious diseases Agent selection based on bacterial sensitivity/ genetics ○ Cystic fibrosis Agent selection based on patient’s genetics ○ Cancer Agent selection based on tumor’s genetics Targeted agents for many other diseases in development ○ Gene therapy research ongoing for hundreds of conditions ___ Lecture 8: The Dose Makes the Poison Amit Pai Toxicology Toxicology is driven by the amount or dose that enters the body Goal: Maximize therapeutic range ○ Maximum effect with lowest amount of toxicity Sources of exposure to Chemicals Environmental, including home and school Occupational Therapeutic Dietary Accidental Deliberate Ex: lead in turmeric, lead in paint Route of exposure The route of exposure is an important determinant of the ultimate dose— different routes may result in different rate of absorption ○ Dermal (skin) ○ Inhalation (lung) ○ Oral Ingestion (gastrointestinal) ○ Injection The route of exposure may be important if there are tissue-specific toxic responses Toxic effects may be local or systemic Exotic Toxins Novichok- combat grade nerve agent used against Aleksei Navalny (2020) - applied to inner seam of his underwear [skin contact] Carfentanyl- Moscow Theater Hostages (2002) - Chenchen separatists - 120 hostages died [inhaled] Polonium-210 - laced teapot in a London restaurant, political assassination [ingested] Any chemical can be toxic Any chemical can be toxic if someone eats, drinks, or absorbs very high doses Vitamin pills can be lethal if someone swallows too many in too short of a time Higher than recommended Vitamin D can cause kidney stones, high blood pressure, deafness, and death Even water can be lethal if someone drinks too much too quickly! (lower sodium concentration in water) Are natural products safer? Natural products can range from relatively harmless to highly toxic Some plants and animals can create toxic chemicals either for self-defense or for assistance in catching their prey For example, snakes, scorpions, and poison ivy- each produces a natural toxin that is hazardous to humans as well as to other organisms From snake venom to captopril - first antihypertensive drug in the class of angiotensin-converting enzyme (ACE) inhibitors. Captopril was developed from a peptide found in the venom from Bothrops jararaca, a poisonous viper endemic to Brazil, which uses its venom to make its prey lose consciousness from a drop in blood pressure Toxins can be medicines Botox- a form of botulinum toxins Risks associated with dietary supplements Dietary supplements are not inspected by the FDA before they are marketed ○ Under Food and Trade Commision (FDC) not FDA They are considered “unusually toxic”, and therefore, are not adequately tested in preclinical safety assessment studies. Many supplements contain active ingredients that have strong biological effects Not necessarily standardized for active substances Lack of rigor in the synthetic chemistry and manufacture process Impurities and additives have been found in supplements, which offered risks for consumers. How much is too much A key concept in Toxicology is the quantitative relationship between the concentration of a xenobiotic in the body and the magnitude of the biological effect it produces. Therapeutic VS. Toxic effects: Vitamin A Hormesis: process that exhibits a biphasic response to exposure to increasing amounts of a substance. ○ Low dosage have beneficial effects and high dosage are harmful. Dose-response relationship Dose-response bioassays are carried out to measure a chemical’s short-term toxicity Exposure to a single dose of a chemical occurs on day 1, but the experiment continues for 14 days in order to give the organism time to react The experiment must include control group At the end of the study, the number of dead mice are counted and any health-related responses are noted for those that survive. Lethal Dose 50% (LD50)  LD50 : stands for the dose that causes the death of 50% of the treated organisms Expressed in milligrams of the chemical per kilogram of body weight (mg/ kg) Death doesn’t need to be the Lethal endpoint Intraspecies variability Within any species, some individuals will die at lower doses than others When mice are fed caffeine, some may die after only 100mg, while others may tolerate 20 or 30 times this amount In humans, a cup of coffee at bedtime may keep someone awake through the whole night, but have no effect on someone else Toxicity tests are based on group responses, rather than relying on individuals (we have to figure out what’s the safest dose for the population as some are sensitive and some are resistant) The more individuals tested, the better the chance of accurately estimating the LD50. Why do some individuals respond differently? ○ Fast metabolizers Interspecies variability LD50 values can vary broadly from one species to another For example, the LD50 for digoxin is 5000 times higher for hamsters than for guinea pigs Factors influencing the interspecies variability: ○ Size ○ Cannot scale LD50 to bigger species (not proportional) Ex: dogs with chocolate (accumulation of theobromines) Short-term (Acute) Toxicity Oxalic acid is the most common component of kidney stones Members of spinach family and brassicas (cabbage, broccoli, and brussels sprouts) are high in oxalic acid Although the amount of oxalic acid found in a small proportion of spinach is harmless, it can result in kidney damage, or even death if someone eats 10-20 lbs of spinach at one meal Ex: too many alcoholic drinks in a short period of time may be lethal due to acute alcohol poisoning Evaluation: give maximum tolerated dose and see where do we get to see acute toxicity Long-term (Chronic) Toxicity Lead is present in a wide variety of products including: paint, ceramics, pipes, plumbing materials, gasoline, batteries, and cosmetics Exposure to lead can occur by contaminated air, water, dust, food, or consumer products Lead accumulates in the body over time and is associated with long-term toxicity, expressed by stunted growth and mental retardation in children or kidney failure and neurological effects in adults. Ex: at the rate of one drink per day for several years, some individuals may develop hepatic cirrhosis  Evaluation is hard as we are giving low exposure over long periods of time Evaluating chronic toxicity To test for chronic toxicity, lab animals are given relatively low doses of a test chemical for months or even years The experiments look for various effects such as lowered growth rates, changes in behavior, increased susceptibility to disease, or reduced reproductive ability Since lab animals have much shorter lives than humans, it is possible to study effects on lifespan and reproduction without having to wait decades for the results Ex: evaluation of osteoporosis ___ Lecture 9: It’s in Your DNA Dan Hertz Inter-patient Response Variability Patient’s inherited genetics’ effects on what their body does to the drug (PK) and what the drug does to the body (PD) Variability in drug action attributable to variability in: ○ Exposure → PK (absorption, distribution, metabolism, excretion) ○ Sensitivity → PD (target, mechanism of action, drug response) Determines clinical outcome → CO (efficacy, toxicity) Pharmacogenetics investigates the influence of genetic variants on drug outcomes (and the processes - PK and PD) Principles of Pharmacogenetics Genetic variants in DNA cause differences in mRNA that’s produced, leading to differences in protein produced in the body. Ex: cystic fibrosis → variants in DNA causing proteins to have different amino acids → dysfunctional proteins ○ Or a change in DNA that causes mRNA to not even be transcribed Pharmacogenetics Examples Prodrugs - compound is inactive until it is metabolized into an active drug in the body. 6-mercaptopurine (commonly used in pediatric cancer) ○ Metabolically eliminated from the patient by TPMT enzyme or will cause side-effects ○ A single code change of adenine causes defective TPMT ○ Causes high toxicity in patients who lack TPMT or have defective TPMT Clopidogrel ○ CYP2C19 needed for metabolic activation for efficacy ○ If lack enzyme → no response Allergic reactions to HIV medication, Abacavir (red splotchy welts) ○ Has nothing to do with pharmacokinetics, it’s all pharmacodynamics (what drug does to body) effects on genetically altered HLA region Pharmacogenetics Implementation For a successful clinical practice:  ○ Find genetic variations in patients → create genotyping assays that someone can run in lab to find what variations patients have → approach a physician and create plan for course of actions if there are variants (ex: this patient has high toxicity, you should give them 10% of the dose) ○ But it’s very complex to genotype every patient ___ Lecture 10: The Internet of Health Dan Hertz Hierarchy of Medical Evidence A randomized controlled trial is the highest quality evidence to generate information. Fundamentals of Clinical Trials 1) Control - comparator for treatment effect 2) Randomization - random allocation of subjects to treatment arms 3) Blinding - prevent participant bias in effect reporting & investigator bias in effect analyzing Evaluating Health Claims Attributes of high quality health claims: ○ Multiple studies with consistent findings ○ Large, well-conducted clinical trials Randomized, controlled, blinded ○ Expertise  Science consensus >> individual scientist/ doctor >> non-expert Attributes of low-quality health claims: ○ Rely on personal experience or tradition (anecdotes) ○ Rely on “experts” with conflict of interest (financial) ○ Rely on results of uncontrolled studies (no comparison group) ○ Rely on the result of a single study (typically small & poorly conducted) Health Information on the Internet Common Mistakes in Lay Press Extrapolate a single finding ○ Bias toward “new” findings that ignore large bodies of evidence Extrapolate correlation to causation ○ Two associated variables are not necessarily causally linked ○ Ex: vaccine DO NOT cause autism Extrapolate pre-clinical findings ○ Findings in cells or animals do not necessarily translate to humans. Purchasing Medications on the Internet Real medications from licensed US pharmacies, requiring a valid prescription ○ Legal and properly regulated (Purportedly) real medications from other countries, requiring a valid prescription ○ Concern: medication is fake or not made or stored properly (Purportedly) real medications from other countries, not requiring a valid prescription ○ Concern: patient is taking medication without medical professional's oversight ○ ConernL medication is fake or not made or stored properly Dangers of Online Medication Purchasing Supplements (unproven efficacy) disguised to be real medications Mobile Health (mHealth) Smartphones are nearly ubiquitous ○ Estimated 90% of world population by 2020 Platform for two-way data transfer and communication ○ Overcome geographic and socioeconomic disparities mHealth applications ○ Health data collection and monitoring Tracking of glucose (diabetes) or blood pressure (HTN) Patient input or wearable sensors (ie. fitbit) ○ Health data access Mobile electronic medical records or patient portals ○ Health recommendations Medication adherence reminders Ex: games ○ Health care delivery Telemedicine