Drug Discovery Exam 2

Toxicity

Part of ADMET or ADME/Tox.

Currently finding predictors of toxicity. Major one: Cardiotoxicity

Cardiotoxicity

Major predictor of toxicity. hERG is one aspect that is tested to evaluate. FDA requires hERG eval for any IND application. Biochemical and cellular assays available. (Electrophysiology/patch clamp). Langendorff heart model.

Seldane (terfenadine)

Widely-used antihistamine allergy medication. Metabolized CYP 3A4. Co-administered with ketoconazole (inhibitor of 3A4 and antifungal) led to incidents of severe cardiac arrhythmia.

Terfenadine is inhibitor of hERG (Human Ether-a-gogo Related Gene), so too much K+ gets out and QT interval elongated.

FDA pulled drug from market in 1997.

hERG

(Human Ether-a-gogo Related Gene)

Potassium and calcium ion channel. Contracts heart. Outward K+ mediated by channel. QT interval impacted

hERG activity routinely tested. FDA required for any IND application.

Langendorff heart model

Pig heart made to function electrically, can test drug effect on heart with this.

Electrophysiology/patch clamp.

Hit generation

A compound that demonstrates activity in assay that meets a threshold set by investigator. Mast majority of “hits” are derived from Screening. Modification of standard, Literature/Patent mining, Docking.

Screening

Been doing forever. Figuring out the chemical is effective for what you want.

Folklore/Word of Mouth

Natural products/chemical defense (natural sponges

Synergistic effects

Microbial/Soil Samples

Repetition allows for some levels of simplification. Assay plates (96,384, 1536 well). Liquid handling - Robotics, Automated Detection.

Modification of Standard

Assays require a standard in order to show that the assay works.

Can start with known standard and modify to get desired effect.

Analogs/mimics of natural substrates and modulators is another method.

Literature/Patent Mining

Most common hit generation method. “New and improved” drugs that are modified versions of older ones. Penicillin v amoxicillin, for example. Slight structure changes.

Docking

Screening resources

Now collections of compounds available for screening (screening libraries)

NIH has Molecular Libraries Program to help screen their compounds against assays.

Companies create their own, proprietary screening collections based on historical compounds, commerial acquisitions, academic collaborations.

CPAS at USF.

Screening limitiations

Reagents (cost/availability). Not all assays able to be performed in a high throughput manner. Lead optimization strategy dictates what/whether hits warrant additional investigation

Screening pooling strategies

Helps with costs

Staurosporine

Inhibitor for all but two kinases. Modified to be a more selective kinase inhibitor - Becaterin.

Modification of Standard Examples

Staurosporine.

Literature/patent mining changes

Exposure, half-life, metabolism, side effects.

Concerns about “me-too” drugs

Cost of development. Intellectual Property. Raises ethical dilemma - what if you discovered a potential new therapeutic agent that was considered someone else’s IP?

Patent

Acknowledgement of a novel invention and legal right to exclude other parties from practicing that invention. Open to debate.

NOT the same as legal right to practice invention. Just legal right to exclude other parties from practicing. No patent agency can grant inventor freedom to operate. A patent whose claims cannot be practiced without violating IP is said to be dominated by other patent. Individual claims in a patent can be licensed.

4 main types for drug discovery: composition of matter, method of use, article of manufacture (aka process), device

Composition of matter

can be requested if you created something that has never been created before.

Method of use

Can be requested for any matter if new use has been discovered.

AZT - discovered in 1965, found to be active against HIV in 1985.

Article of Manufacture

Can be requested for any matter if a new method for manufacturing has been discovered. Zoplicone vs lunestar (racemic vs single enantiomer ver)

Claim

Specific statement of a discovery that defines what the inventors claimed to have discovered. All claims are at the end of the patent application.

Patent v patent application

Patent application submitted to WIPO

Claims published, but not indicative of if those claims will be granted by patenting agency. Does not preclude any party from practicing potential invention

Each country’s patent office must rule on what claims it will or will not grant. WIPO does not examine or award patents.

Device

Machine, tool for delivering drug.

Patent Agencies

WIPO - follow patent cooperation treaty (PCT)

USPTO - patent application for protection in US

EPO - patent protection for the EU, Intellectual Property Office

Regular (nonprovisional) patent application

Expires 20 years after filing date, requires full examination, published by the WIPO 6 months after filing date. Reveals legitamate reason to limit broad claims, the length of time of an examiner requires to make a decision is still 20 years regardless.

Provisional

Establishes an invention date. Does not require an examination or even claims. Must be converted into a nonprovisional application by the 1 year anniversary of the provisional filing date. Or, a new provisional application can be filed.

Examiner does what

Restrictions - claims that re constitute more than one invention or violate patent law

US Patent code

a) if invention was known or used by others in this country, or patented or described in a printed publication inside or outside the US, before the invention by the applicant, cannot patent

b) you can patent something for a year after its been published

c) if you did not invent it yourself, then you can’t patent.

March 16th, 2013

America Invents Act. Changed the prioritization of inventions from “first to invent” to “first to file”. Until then, US was the only one that use the “first to invent” to establish invention priority. If someone claims they invented before this date, they can prevent you from getting patent, though.

6 basic requirements for patentability

Usefulness, novelty, nonobviousness, a written description, enablement, best mode

Usefulness

Novelty

Examiner must deterine if any claiims have been previously published or claims in another patent application. In drug discovery, need to see if compound falls under another “generic” compounds that has a claimed use in another patent.

Nonobviousness

Cannot claim something that could have been obviously anticipated by someone who has “ordinary skill in the art” of the subject matter.

Improved PK, or activity against a different target are nonobvious, so accepted.

Still an effective mechanism for preventing simply adding a methyl group to a known drug to avoid patent infringement a la designer drugs.

Enablement

Must demonstrate with adequate detail and specifications how they made and prepared

…

If they didn’t enable a specific compound, their right to claim the compound is in question

Now common to include NMR data for each claimed compound

Best Mode

In order for patent claim to be valid, have to disclose best mode contemplated for enablement of patent. Cannot intentionally hide best synthesis of a potential drug to slow down competitors. Can’t play dumb, if judge thinks someone in the field would have contemplated it, your claim can be invalidated. Leads to one of the most common methods used by legal challengers to claims.

Patent trolls

People who buy up patents or have patents for the purpose of suing and extorting people for infringing on it. Intellectual Ventures, Landmark Technologies.

TRAIL (Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand)

Novel target for cancer. Compounds that induce TRAIL are called TRAIL inducing compounds or TIC. Found TIC10. Argument over who owns patent for it.

CRISPR technology

Patent lawsuit for CRISPR on mammalian cells vs a broader patent on CRISPR for gene editing.

Who writes patents

Patents are written by either patent attorneys or patent agent. An agent is someone who patent bar exam. Any person with technical degree (natural or physical science or engineering) is qualified to take patent bar examination.

Docking

For targets with structural biology assets, docking is fourth alternative. Biomolecule modeling using tech can be used to identify homology models. Structural biology assets include:

X-ray crystallography

Protein NMR

Cryo-electron Microscopy (2017 Nobel)

fourth emerging.

Alphafold

AI that helps identify protein structures. Predicts protein structure, allowing docking to the know purely hypothetical structure. Too early to say whether this will truly be effective. And extremely risky. But opens possibility of targeting proteins for which there is no structural info.

Docking Databases

Repositories of crystallographic data such as the Protein Data Bank (PDB). Armed with a target to model, programs such as DOCK allow a search of known chemicals that could serve as hits. Databases of chemicals including structural info, like ZINC are available. AutoDock lets you consider any molecule you can imagine.

Screening drawbacks

Natural products often have poor PK

Commercial libraries - heavily mined areas

Modification of standard drawbacks

Typically synthetically complex

Literature/patent mining drawbacks

Creating novel IP is hard

Docking drawbacks

Binding pockets are dynamic

Lack of hard data

Lead optimization

Confirm hit is real. Then what interactions are critical dor activity. Try to accomplish this in the simplest manner possible. Make simplest compounds first

…

Molecular interactions

Bonding

• Covalent bonds - > 200 kj/mol

• Ionic bonds - 30

• Hydrogen bonds - 20

Interactions

Ionic

Van der Waals

…

Systematically probe the hit

Every change you make to a potential drug can have big impact.

How do you determine what changes to make, whether you have structural biology assets, ….

SAR

Structure activity relationship. Making single changes allows you to directly relate those changes to activity.

Sulfur

Easily oxidized, typically not good for potential drug candidate

Alcohols and amines

Can be bioconjugated or oxidized, typically not good to have in drug candidate

Floppy molecules

Tend to bind to albumin, so not as good at entering cells. Fixing this in drug candidate improves its PK.

Benzene rings

Attract CYPs for oxidation. Minaprine. Not good for PK

Topliss Tree

Systematic method for examining trends for systematically probing the hit.

Decision tree. For an unsubstituted benzene ring in a molecule. If you have the activity of a molecule with an unsubstituted phenyl ring, you would then make a 4-chlorophenyl analog and compare activities. If less active, do 4-methoxy analog. If more active, make the …, if the same, …