Search Results for: kinetics

Estimating Metabolite/Protein Concentrations from RNAseq Data

Under steady-state conditions, it is possible to estimate the concentration of a metabolite from the amount of protein and the amount of protein from the amount of mRNA (see figure above). In general, the conversion factors used for these calculations … Continue reading

A Complete Aerobic Model of Marathon Performance

The equation above is one of the simplest and most accurate predictors of marathon performance (having been shown to account for ~70% of the variability in individual marathon performance).1 In the figures below I delve more deeply into each of … Continue reading

What do “PEG-linkers” do to drugs?

Where synthetic chemistry has given us many molecules that bind (and inhibit) many different proteins, chemical biology endeavors to “attach” new function to these “classical” drugs. Examples of chemical biological applications include: (1) attaching toxins or imaging agents for targeted … Continue reading

Estimating Metabolite Concentrations at Steady State

In a follow up to our post on sequential biochemical pathways, we next wanted to present an method to approximate the concentration of a metabolic intermediate in a biosynthetic pathway. In general, under steady state conditions, the steady state concentration … Continue reading

Understanding Multivalency (aka Avidity)

Making a Ligand or Drug multivalent is a common method to try to improve the potency or EC50 of that drug from that predicted by the Hill Equation. Below we summarize the full spectrum of multivalent enhancement for the n … Continue reading

The Thermodynamic Limits on Small Molecule Drug Affinity

Not too long ago, some really cool papers1,3 sought to examine “The Maximal Affinity of Ligands” by compiling a list of known small-molecule drugs and comparing their affinities (in kcal/mol or Kd‘s see post on the Hill Equation) with various … Continue reading

Kinetic Limits on Engineering Agonist Drugs

There are many drugs that act as agonists ligands (L) which means they “turn on” their target receptor (RL) so that it induces its normal down-stream signalling. Examples of such drugs include: growth hormones, insulin, steroids and G-protein coupled Recetor(GCPR) … Continue reading

Binding #3: Competitive Inhibition

While many drugs act like agonists and “turn on” their target/receptor (see posts on Hill Equation and Agonist Limits), many more drugs act like antagonists and “turn off” their target/receptor. One of the most common mechanisms by which drugs “turn … Continue reading

Binding #2: The Michaelis-Menton Equation

The Michaelis-Menton Equation has a very similar form to the Hill Equation but the key difference is that it deals with enzyme rates not ligand/receptor or drug/target interactions per se. Basically, it describes how fast an enzyme (E) makes its … Continue reading

Binding#1: Understanding the Hill Equation

If you want to understand how drugs work/behave (or just how 2 molecules interact with each other) then you need to understand one of the oldest and most useful theories in biochemistry: the Hill Equation. The Hill Equation mathematically models … Continue reading

A Single pKa Chart: Visualizing Reactivity Trends

The pKa¬†value of a chemical functional group (Figure 1A) is very useful because it can directly give you the approximate charged state of that functional group (in the context of drugs, proteins, membranes, DNA, etc.) at a specific solution pH. … Continue reading