nucleic lec 12

Structural Biology in Drug Discovery

• Drug discovery employs structural biology to identify and predict drug function.
• Drugs are chemical entities causing desired therapeutic effects.
• These entities can be small molecules (natural, synthetic, or semi-synthetic) or proteins (from natural sources or recombinant).
• Drugs work by specifically binding and affecting a protein or other biological target.

Drug Targets

• Common targets are proteins, but DNA and RNA may also be targets.
• Effective drugs target only one or a few biological molecules.
• The target is selected so that effective chemical interventions efficiently produce the desired effect.

Historical Example - Aspirin

• Hippocrates recognized willow bark's pain-relieving properties.
• Salicylic acid, extracted from willow bark, was later identified as the active ingredient.
• Researchers modified salicylic acid to form acetyl salicylic acid (aspirin).
• Aspirin has fewer gastrointestinal side effects than salicylic acid.
• Aspirin inhibits the synthesis of prostaglandins through the inhibition of cycloxygenase 2 (COX-2).

How Aspirin Works

• Aspirin inhibits COX-2 by acetylating Ser530.
• COX-2 is an inducible oxygenase that synthesizes prostaglandins, mediators of inflammation and chronic pain.

Aspirin Limitations

• Acetylation can be applied to other natural products, like morphine.
• Early drug development had riskier practices compared to modern standards

Modern Drug Development

• Today, new drugs need extensive in vitro and animal testing before human trials.
• Modern drug development processes ensure that a drug candidate demonstrates safety and efficacy.
• Many compounds fail to meet the stringent criteria set for regulatory approval.

Conceptual Drug Invention

• Drug invention begins with understanding the "disease" state.
• Mechanistic understanding leads to identifying a possible route for therapeutic intervention.
• Systematic search for a chemical that hits the target.

Drug Candidate Development

• Lead discovery involves identifying preliminary molecules with desired activity.
• Lead optimization involves affinity, selectivity, toxicity, property refinement.
• A drug candidate goes through pre-clinical testing and three phases of clinical trials.
• The average drug takes ~15 years and costs ~US$2 billion to develop and approve.

Target Identification

• Drug discovery often focuses on finding compounds affecting specific molecular targets (usually proteins).
• The selected target enables effective chemical intervention for the desired biological outcome.
• Common targets include the first committed step of an enzymatic pathway or the receptor of a signal transduction pathway.
• Protein structure is crucial as it indicates how "druggable" a target is.

High-Throughput Screening (HTS)

• HTS is traditionally the first step in identifying a new drug.
• Screening involves a large library (~10⁵-10⁶) of synthesized organic compounds, for potential drug candidates.
• A biochemical or cell-based assay identifies if a compound binds to the target.

Transforming Hits to Leads

• Hits are compounds exhibiting positive assay results but not necessarily producing the desired pharmacological effect.
• Subsequent testing involves evaluating and eliminating compounds not meeting criteria, such as being toxic, too difficult to synthesize or non-specific
• “Leads” are compounds confirmed to demonstrate the desirable bio-chemical response and eligible for further investigation.

Lead Optimization

• Modifying lead compounds to improve affinity, selectivity, toxicity, and other pharmacokinetic parameters.
• This often requires synthesizing many new compounds, with extensive testing on activity, selectivity, and other qualities.
• Leads may have 10 µM binding constants, and the development candidates need ~1 nM binding constants.

Properties of Orally Available Drugs

• Binding of the drug to the target must be tight with the target (in the low nanomolar range) to ensure effective action at low concentrations.
• The drug needs to be readily absorbed, dissolved into membranes, and transported out of cells efficiently.
• Large molecules often face challenges in crossing cell membranes; optimal size is important
• Favorable chemical properties contribute to greater success during drug development.

Drug Candidate Chemical Properties

• Drug candidates should ideally have few or no chiral centers, for easier synthesis in good yields.
• The presence of chiral centers in the structure impacts the production of a desired quantity and prevents the development of undesired properties.
• Minimizing free rotatable bonds is critical to reducing conformational entropy in a drug molecule.

ADME-Tox

• Assessing the Absorption, Distribution, Metabolism, Excretion, and Toxicity of drug candidates in the body.
• These factors ensure the efficacy and safety of a drug by evaluating its interaction and metabolism within the body.
• Early identification of associated problems are crucial.

Structure-Guided Drug Discovery (SGDD)

• Using structural biology to measure and predict drug function and binding.
• Drug development can leverage protein structures to predict drug binding and guide medicinal chemistry.

Experimental Structures for Rationalization

• Experimental structures (e.g., X-ray crystallography) help rationalize how new compounds bind.

Fragment Screening

• Fragment screening is a "divide and conquer" approach for drug discovery by focusing on small molecules.
• Methods like native mass spectrometry or surface plasmon resonance can identify weak binders.

NMR for Ligand Binding

• Monitoring ligand binding using NMR identifies changes in chemical shifts.

Screening with Crystallography

• Screening drug-like fragments using crystallography assists in understanding how the ligand binds, identifying interactions, and evaluating potential modifications.

Linking Fragments

• Linking pre-identified fragments that bind in close proximity on the targeted protein enables designing an appropriate linker.
• Drug-like molecules, with their size constraints, are prioritized for production.

Computational Chemistry

• Computational methods can estimate binding energies, using force fields and molecular dynamics simulations.

MD in Drug Discovery

• Molecular dynamics (MD) simulations can evaluate molecular interaction details and binding.

Simplified Scoring Functions

• Simplified scoring functions provide quick evaluations for large numbers of molecules by assuming the protein is static.

Approximating Binding Energy

• Estimating energy by integrating van der Waals, electrostatic, and hydrogen bond interactions.

Docking

• Docking computationally analyzes where ligands bind to target proteins with available structural data.

Virtual Screening

• Virtual screening uses iterative docking to examine a large library of candidate molecules.
• Ranking compounds based on energy levels guides drug discovery efforts.

"On-Demand" Molecules

• "On-demand" molecules are available through customized synthesis, expanding chemical libraries for drug testing.

Virtual Fragment Screening

• Focused on testing component fragments, limiting experimentation scope to relevant compounds.

Virtual Screening Against Alphafold Models

• Alphafold models have been used in virtual screening to identify new drug compounds.

Alphafold 3 and Beyond

• Alphafold 3 and its counterparts hold significant promise in drug target evaluation.

Summary

• Computational approaches are powerful tools in circumventing expensive high-throughput screening (HTS).
• Understanding a target's structure allows for 'pre-screening' compounds.
• Computational tools can predict and incorporate off-target interactions into the workflow for drug screening.