Successful Drugs and Targets

The focus of this material shifts from theoretical concepts (agonists, receptor conformations, antagonists, and modulators) to practical considerations in drug development. This means that instead of just understanding the basic science behind how drugs work, we'll explore how to actually create effective drugs in real-life medical settings.

The central objective is to identify strategies and chemical principles that increase the probability of a drug being effective in a clinical setting. For example, this could involve determining how to modify a molecular structure to improve its absorption in the body, or finding the right biological target for the drug to interact with.

Lipinski's Rule of Five

• Lipinski's Rule of Five is considered a cornerstone of pharmacology; knowledge of these rules is often viewed as a marker of expertise in the field. These rules are important because they help scientists understand what makes a drug likely to be absorbed effectively by the body.

• The name "Rule of Five" does not refer to there being five separate rules; rather, it refers to the fact that the parameters involved are based on the number five. Specifically, there are four main criteria, but they are all linked to the relevance of the number five.

• These rules serve as a primary screening tool to eliminate drug candidates likely to fail due to poor pharmacokinetic properties. Pharmacokinetics focuses on how drugs move through the body, so these rules help ensure that drugs will be effective in terms of absorption and distribution.

• The four original criteria are:

  • Molecular Mass: Ideally, the molecular mass should be under $500\text{ Daltons}$. The speaker notes that larger molecules are usually absorbed poorly compared to smaller ones. A Dalton is treated as equivalent to a gram per mole ($g/mol$) or an atomic mass unit ($AMU$), though the choice of unit often depends on whether one is a biologist, chemist, or physicist. This means that lighter molecules are often better at passing through cell membranes.

  • High Lipophilicity: Specifically, a Log $P$ greater than $5$. This suggests the molecule should have a high preference for lipid environments over aqueous ones. In simpler terms, drugs that dissolve well in fats and oils are typically better at getting into cells.

  • Hydrogen Bond Donors: The molecule should contain no more than five hydrogen bond donors. Hydrogen bond donors are groups containing a hydrogen atom bonded to a highly electronegative atom ($O-H$, $N-H$, or $F-H$). In drugs, these usually present as hydroxyl groups ($O-H$) or amino groups ($N-H_2$). Having too many hydrogen bond donors can make a drug less effective.

  • Hydrogen Bond Acceptors: The molecule should possess a high number of hydrogen bond acceptors (typically oxygens, fluorines, and nitrogens). These do not require an attached hydrogen; for example, ketones and esters contain oxygens that act as acceptors. This property helps the drug interact with the target in the body.

Partition Coefficient ($P$) and Log $P$

• The partition coefficient ($P$) measures whether a molecule prefers a lipophilic (oil) or hydrophilic (water) environment. This means it tells us how well a drug can move between different environments in the body.

• Experimental Determination: To find out how much a drug likes oil versus water:

  • A separatory funnel is filled with water and octanol (which serves as the representative oil).

  • The drug molecule is added to the funnel and shaken.

  • After the phases separate, the concentration of the drug in each phase is measured.

  • The coefficient is the ratio of concentration in the oil phase versus the water phase. This process helps determine how effective the drug will be in the body.

• Log $P$ Definition: Because the range of lipophilicity across different drugs can be massive, a logarithmic scale (base $10$) is used to condense the data into manageable numbers.

  • Formula: $\text{Log } P = \text{log}_{10}(P)$.

  • Most viable drugs fall within a Log $P$ range of $0$ to $10$. This means that if we calculate the Log $P$ of a drug and it falls within this range, it's likely a good candidate for further testing.

Modern Improvements to Lipinski's Rules

• While Lipinski's rules are dogmatic, they are considered narrow because they only address four parameters. Over the years, scientists have found that there are more factors that contribute to how effective a drug is.

• Updated parameters for drug-likeness:

  • Partition Coefficient (Log $P$): Adjusted to a range between $-0.4$ and $5.6$. This means we now accept a wider variety of drugs than before.

  • Molar Refractivity: Values between $40$ and $130$. This factor considers how polar (charged) a molecule is, influencing how it behaves in the body.

  • Molecular Weight: Refined to a range of $160$ to $500$. This emphasizes that a drug should not be too small, as well as not too large.

  • Number of Atoms: Ideally between $20$ and $70$. This count excludes hydrogens and focuses on "heavy atoms" (any atom other than hydrogen).

  • Polar Surface Area (PSA): Should be no greater than $140\text{ square angstroms}$. This metric requires computer modeling to determine the molecular surface area that is polar.

CNS Drug Design and the Blood-Brain Barrier

• The target of a drug dictates how strictly these rules are applied. Drugs targeting the Central Nervous System (CNS) must cross the Blood-Brain Barrier (BBB). The BBB is a highly selective barrier that protects the brain from harmful substances but also makes it difficult for beneficial drugs to enter.

• The BBB is significantly more permeable to smaller, more lipophilic molecules. This means that drugs designed to treat brain disorders must be able to pass through this barrier more effectively.

• Comparisons of drugs that have reached at least Phase II clinical trials show distinct differences:

  • Average Non-CNS Drug PSA: Approximately $70\text{ square angstroms}$. This shows the average size of drugs that work outside of the brain.

  • Average CNS Drug PSA: Approximately $40\text{ square angstroms}$. This smaller average suggests that drugs targeting the CNS typically have properties that allow for better penetration of the BBB.

• Therefore, standard rules must be tweaked when designing drugs intended for the brain or spinal cord, emphasizing the need for specific adaptations when creating these types of drugs.

Chemical Reactivity in Drug Molecules

• Whether chemical reactivity is beneficial or detrimental depends on the context and selectivity. This means that the same chemical property can either help or harm the effectiveness of a drug based on how and where it reacts in the body.

• Detrimental Effects:

  • Non-selective modification of proteins or nucleic acids can cause systemic toxicity. For example, non-selective nucleic acid modification is a mechanism of chemotherapy, which is notoriously toxic. Chemotherapy drugs can attack healthy cells as well, leading to side effects.

  • Unanticipated selective modification leads to side effects. This means that if a drug accidentally interacts with the wrong target in the body, it could cause unwanted reactions.

• Beneficial Effects:

  • Selective modification can lead to irreversible inhibition. Unlike competitive inhibitors, which can be washed out or overcome by increased agonist concentration, covalent modification "kills" the protein.

  • To recover activity after irreversible inhibition, the body must synthesize new enzymes, which provides a longer-lasting effect. This indicates that certain types of chemical modifications can make drugs more powerful and longer-lasting.

Labile and Reactive Functional Groups

• Labile Functional Groups: These are prone to breaking down naturally within biological systems. This can be good or bad depending on the goal of the treatment. Common examples include:

  • Esters: These can be broken down quickly but can also be useful in prodrugs.

  • Amides: These are also broken down in the body, and their stability can be important for drug design.

  • Disulfides: These can sometimes break apart too quickly, affecting drug efficacy.

  • These groups often lead to a short half-life and frequent dosing requirements unless they are specifically intended for a prodrug approach. A prodrug is a substance that becomes active in the body after undergoing chemical conversion.

• Highly Reactive Functional Groups:
  

  • Epoxides: Extremely reactive and often associated with carcinogenicity, making them risky for drug development.

  • Michael Acceptors: Defined as a carbonyl group conjugated with a double bond. The double bond is separated from the oxygen double bond by exactly one single bond, allowing electrons to move freely. This makes one of the carbons highly susceptible to nucleophilic attacks, often reacting with thiol groups in cysteines found in proteins. Such reactivity needs to be well understood to avoid harmful effects in the drug.

Prodrug Strategies

• A prodrug is an inactive or less active version of a drug designed to overcome barriers like poor absorption or the Blood-Brain Barrier.

• Process:

  1. A "pro-moiety" is added to the drug to change its properties (e.g., making it less polar).

  2. The prodrug crosses the biological barrier.

  3. Enzymes on the other side of the barrier break the pro-moiety off, releasing the active drug.

• This approach highlights the complexity of drug design and the importance of creating drugs that can successfully navigate the body’s barriers.

• Common Functional Groups in Prodrugs:

  • Esters are the most frequently used group for making prodrugs because the body contains many esterases (enzymes that break down esters).

  • Example: A carboxylic acid, which is partially charged at physiological pH and poorly absorbed, can be converted into an ester. Once inside the target area, esterases convert it back into the active carboxylic acid form, showcasing how adjustments can lead to improved drug delivery.

Target Selection: Druggable vs. Undruggable

• Easily Druggable Targets: These typically have active sites or are designed to bind ligands:

  • Enzymes: Targets like kinases, phosphatases, deacetylases, and metabolic enzymes are easier to target with competitive inhibitors that act like a "door jam" in the active site. This means they have defined areas where drugs can easily interact.

  • Receptors: GPCRs (G-Protein Coupled Receptors), tyrosine kinases, and cytokine receptors are examples of targets designed to accept ligands, making them easy to target with small molecules or antibodies. They can be manipulated with agonists (activators), antagonists (blockers), or inverse agonists, which counteract the effects of agonists.

• Undruggable Targets (Traditional View):

  • Transcription Factors: These are often considered too challenging to target because they do not have clear binding sites.

  • Structural Proteins: These can play crucial roles in maintaining the shape of cells and tissues, but they can be hard for drugs to access due to their complexity.

  • Protein-Protein Interactions (PPI): These are difficult because they often involve large, flat surface areas. Inhibiting them is compared to trying to prevent two flat surfaces from being glued together; a small drug molecule (like a bottle cap) may not be enough to prevent the large surfaces from sticking around it.

  • Missing or Deleted Genes: A drug cannot easily fix a cell that is sick because it simply lacks a specific protein. These complexities contribute to challenges in developing therapies.

Advanced Strategies for "Undruggable" Targets

• Higher Order Complex Formation: This involves targeting specific small surface interactions needed for complex formation, aided by computer modeling and in silico molecular docking. Advanced technology allows researchers to simulate how drugs interact with targets, improving the design process.

• RNA interference (RNAi) / Antisense RNA: This technique prevents the formation of a protein by degrading the mRNA before translation occurs, representing a novel way to disrupt harmful pathways in diseases like cancer.

• CRISPR-Cas9: Editing the genome directly represents a cutting-edge approach to drug design. While promising, it currently faces significant moral and technical hurdles for human use, and its broader applications are still being researched.

• SAR by NMR (Structure Activity Relationship by Nuclear Magnetic Resonance): Using NMR to detect conformational changes in a protein when a drug binds, even if the binding site was not rationally predicted, adds another layer of precision in drug development. This technique allows scientists to visualize how drugs are physically interacting with their targets.

Synthetic Lethality

• Synthetic lethality occurs when the loss of either Gene A or Gene B individually does not kill the cell, but the loss of both simultaneously is fatal. This means that while individual genes may not be essential for survival, targeting both can lead to cell death.

• This is a powerful tool for targeting cancer cells that have already lost a specific gene function, allowing for more precise treatments.

• Mechanism:

  • Normal cells have redundant pathways (e.g., Pathway A to D and Pathway B to D). This means they have multiple ways to accomplish the same function.

  • Cancer cells often eliminate one pathway (e.g., Gene A is mutated or deleted) to maintain their mutated state. This vulnerability can be exploited by drug therapies.

  • By using a drug to inhibit the remaining pathway (Gene B), the cancer cell dies, while normal cells (which still have a functional Gene A) survive. This highlights the potential of using new therapeutic strategies to selectively target cancer cells.

• Example: PARP Inhibitors and BRCA Mutations:

  • PARP is a protein involved in DNA repair.

  • Normal cells are "homologous recombination proficient" (using BRCA or p10). If PARP is inhibited, they use homologous recombination to repair DNA and survive.

  • Cancer cells often have BRCA or p10 mutations (making them homologous recombination deficient) to prevent the cell from fixing its own mutations.

  • When a PARP inhibitor is given to these patients, the cancer cell has no remaining way to fix DNA damage. This results in massive, lethal DNA damage (indicated by the absence of Rad51 foci), leading to cell death.

• Screening for Synthetic Lethality: Researchers compare wild-type cells (normal) with mutant cells (cancerous). They look for drugs that kill only the mutant cells, ensuring that the therapy is highly targeted with minimal effects on healthy tissue. This strategy helps to provide more effective treatments with fewer side effects, particularly in cancer therapy where maintaining the health of surrounding normal cells is crucial.