BIOM 570 Exam 3: Pharmacokinetics and Biotransport

ADME

Absorption

cross gut membrane; not too polar, not too big

ADME

Distribution

enter bloodstream; not stuck in fat or urine

ADME

Metabolism

interaction with body; cannot be destroyed by digestive enzymes (immediately), not reactive/unstable

ADME

Excretion

not too fast, tiny & polar

Lipinsk’s Rule of 5

1. <= 5 H-bond donors (more donors => more polar => poor absorption)

2. <= 10 H-bond acceptors (more acceptors => more polar => poor absorption)

3. MW <= 500 Da (too large => poor absorption)

4. log(P_ict/water)=log([solute]_oct/[solute]_un-ionized water) <= 5 (increase hydrophobicity => sticks in fat)

Methods of Data Collection for Small Molecule Variants

Assay/HTS - Brute Force

testing a large number of biochemical screens showing small-molecule target interaction; pros: reproducible, controlled, practical, low cost; cons: need large amount of target & test compounds, false-positives

Methods of Data Collection for Small Molecule Variants

Fragment-based Design

connecting known fragments that bind to the target; slightly more targeted than Assays, but still sort of brute-forced

Methods of Data Collection for Small Molecule Variants

Structure Activity Relationships (SARs)

take variations of molecules and run through the assay; learn which molecules increase/decrease activity; step to improve compound designs

Methods of Data Collection for Small Molecule Variants

Pharmacore

identify chemical motifs of reference molecule and match to candidates

Methods of Data Collection for Small Molecule Variants

Docking - More Targeted

modeling to determine interactions of small-molecule variants and target; shape-complementary, but computationally expensive; uses fast Fourier transforms

Challenges of Engineering Small-Molecule Drug Candidates

Scoring

degree in which a small molecule will effectively interact with the target; approximations of energy (sum of 1 and 2 body effects), neglects the role of solvent/water, doesn’t account for entropy, desolvation, polarization, surface area

Challenges of Engineering Small-Molecule Drug Candidates

Sampling

ensuring all forms are accounted for; positions of small molecule, rotamers, backbone flexibility (assumed rigid)

Engineering Therapeutic Biomolecules

Experimental Screen - Brute Force

quantify performance of (many) isolated variants; assay; pros: datasets, focus/control; cons: low capacity (hundreds to thousands)

Engineering Therapeutic Biomolecules

Experimental Selection

link variant performance to natural selection, apply condition to library of variants —> recover and sequence survivors; pros: high capacity (millions to trillions); cons: no data, complex setup

Engineering Therapeutic Biomolecules

Antibody Development

choose target —> inject purified target into animal model —> isolate b-cells which produce unique antibody —> screen and test —> humanization —> manufacturing (scaffold, injection)

Engineering Therapeutic Biomolecules

Antibody Development - Pros & Cons

pros: mouse does work for you => no computational model, clinical success; cons: less control over epitope, large molecules, expensive, low patient response

Engineering Therapeutic Biomolecules

Computational Protein Design - Most Targeted

generates protein shapes, then fits amino acids to stabilize; given sequence —> predict structure, given structure —> predict sequence; invent new shapes => create perfect binding protein for almost any target instead of searching for one

Engineering Therapeutic Biomolecules

Computational Protein Design - Pros & Cons

pros: targeted, smaller => easier to manufacture and administer, no animal model; cons: energy function accuracy, slow validation, reliability, large design/search space

Macromolecular Therapeutic Molecules

Most Commonly used

proteins/peptides, monoclonal antibodies (-mab, cell receptors), enzymes, pathogen ribosomes (for antibiotics, cannot make proteins)

Macromolecular Therapeutic Molecules

Immunogenicity

solve via humanization: replace bits of mouse antibody with human equivalent, keep parts that recognizes target

Challenges of Large Macromolecules as Drugs

Production

growing mammalian cells are harder and more time-consuming, proper glycosylation, purification

Challenges of Large Macromolecules as Drugs

Formulation

many shapes and rotations; stabilize native protein shape for long periods of time, at high concentrations, and varying temperatures

Challenges of Large Macromolecules as Drugs

Delivery

difficult to deliver sufficient doses of large molecules => long injection times or large needles

Drug Development Process

Discovery

target identification (selecting known or hypothesizing) —> target validation (critical to disease, modulation of target have effects, in vitro/vivo) —> assay development —> hits to leads (solubility, specificity, stability, toxicity) —> IND filling

Drug Development Process

Development - Clinical Trials

Phase I: toxicity, single ascending dose (SAD, one dose each of increasing doses), MAD (repeated doses); Phase II: measurable effect and correct dosing

Drug Development Process

Full Development - Clinical Trials

Phase III: compare to the best alternative or placebo, some may be marketed; Phase IV: post-market surveillance and unique populations

Mass Transport

Flux/Diffusion

dependent on the diffusion coefficient and concentration gradient, moves down the concentration gradient

Mass Transport

Non-Biological (in Vitro)

lower chemical concentrations and fewer chemical species; defined reaction pathways; uniform flux

Mass Transport

Biological (In Vivo)

many chemical species; nonuniform concentrations, sizes, and properties; many reaction pathways that change over time and different in different locations;

Momentum Transport

Non-Biological

uniform flow rates; uniform and rigid pipes; external control systems (valves, sensors)

Momentum Transport

Biological

pulsatile flow; microscale interactions; flexible and inconsistant vessels; complex control systems

Fluid Dynamics

Non-Biological

simple, Newtonian fluids

Fluid Dynamics

Biological

complex aqueous fluids (cells, proteins) => non-Newtonian

Transport Modes

Diffusion

movement of molecules down a concentration gradient

Transport Modes

Convection

bulk fluid motion

Transport Modes

Active Transport

requires energy/ATP; against concentration gradient; through proteins and/or pumps

Transport Modes

Passive Transport

membrane mediated; down gradient

Transport Modes

Vesicular Transport

endo and exocytosis; large molecules

Transport Modes

Filtration

pressure-driven across membranes

Transport Modes

Energy Transport

heat conduction/dissipation

Pharmacokinetics

what the body does to the drug; study of the uptake of drugs, their biotransformation, distribution, metabolism, and elimination

Pharmacodynamics

what the drug does to the body; study of the biochemical and physiological effects of the drug, mechanisms of drug action, and the relationship between drug concentration and effect

Pharmacokinetics

Key Physiological Processes

ADME

Pharmacokinetics

Central Volume of Distribution (Vc)

hypothetical volume into which a drug initially distributes upon administration

Pharmacokinetics

Peripheral Volume (Vt)

sum of all tissue spaces outside the central compartment

Pharmacokinetics

Apparent Volume of Distribution (Vd)

volume of fluid that would be required to account for all the drug in the body

Pharmacokinetics

Simple Compartment Models

if a drug rapidly equilibriates; only uses Vd, half-life

Pharmacokinetics

Two-Compartment Models

if a drug exhibits a slow equilibration with peripheral tissues; distribution phase: drug is moving from the central volume to the tissue; the elimination phase: predominant process, looks straight on log plot because it is a first-order (exponential) process

Pharmacokinetics

Physiologically-Based Pharmacokinetic (PBPK) Models

compartments represent tissues connected by flows (Q); generate material balance equations for species of interest, accounting for effects like metabolism, diffusion, etc.; example: BBB

Cardio Transport

Components Relative to Conservation of Mass Transport

mass transport = diffusion + convection + reaction

Cardio Transport

Fick’s Law

flux of molecules move down the concentration gradient, and relies on the diffusion coefficient

Cardio Transport

What Influences the Diffusion Coefficient

concentration, size, medium, temperature

Cardio Transport

Measuring Diffusivity

track molecule and measure mean square displacement (disregards left or right movement, <x>²=2Dt); measure distance traveled and time

Cardio Transport

Reaction Rates - 1st Order

A —k1—> B + C; exponential decay (log(C) vs t)

Cardio Transport

Reaction Rates - 2nd Order

A + A/B —k2—> C + D; hyperbolic decay for two of the same components (1/C vs t)

Cardio Transport

Oxygen Transport in Insects

large surface area of air ducts compared to volume; 1 or 2-way ventilation; mostly diffusion with some pumping => low metabolic demands

Cardio Transport

Oxygen Transport in Salamanders/Small Organisms

large surfcace area to body volume => breath through skin => diffusion => dries out -=> release mucous; cold blooded => less O2 => less metabolic demand

Cardio Transport

Oxygen Transport in Fish

1-way gas exchange; diffusion and convection

Cardio Transport

Cilia

carry mucous up airways

Cardio Transport

Mucous

keeps cells moist and captures particles; gel and sol layers

Cardio Transport

Surfactant

lowers surface tension => equilibriates air flow and stabilizes alveoli => reduces effort to inflate

Cardio Transport

Partial Pressure

mole fraction*total pressure; essentially gives concentration

Cardio Transport

Partial Pressure through the Body in mmHg

air: Po2=40, Pco2=46 —> alveoli: Po2=105, Pco2=40 —> Po2=100, Pco2=40 —> Po2<40, Pco2>46 —> Po2=40, Pco2=46

Cardio Transport

Filtration Pressures

dominated by BHP; BHP = 35 mmHg, IFOP = 1 mmHg

Cardio Transport

Absorption Pressures

dominated by BCOP; BCOP = 26 mmHg. IFHP = 0 mmHg

Cardio Transport

Net Transport

NFP = BHP+IFOP-BCOP-IFHP (filtration-absorption)

Cardio Transport

Purpose of Lymphatic System

maintain tissue fluid balance; immune cell trafficking (B and T cells); lipid transport