1. Biotech

Design and R&D of Covalent Drugs

Disclaimer: This is a user generated content submitted by a member of the WriteUpCafe Community. The views and writings here reflect that of the author and not of WriteUpCafe. If you have any complaints regarding this post kindly report it to us.

For a long time, electrophilic groups have been a minefield in drug development. Therefore, in the classic medicinal chemistry textbooks of the past, it is always recommended to avoid introducing functional groups such as epoxide, acridine and Michael receptor into the structure of drug molecules, because these functional groups are highly reactive and may interact with a wide range of biological macromolecules and cause serious toxic side effects.

Aspirin, Lansoprazole and Clopidogrel have all been found in recent studies to act as covalent bonds with their targets. Inspired by this, the research and development of covalent drugs are slowly entered people’s field of vision. It has shown advantages that non-covalent combination drugs are difficult to achieve, such as longer-lasting efficacy, lower therapeutic doses and less resistance to drugs.

Due to the different mechanisms of covalent and non-covalent binding, it is difficult to truly reflect their efficacy and safety by using traditional evaluation indicators such as dissociation constants, IC50, EC50 during the research and development process. The formation of covalent bonds between drug molecules and their targets is influenced by the reaction rate, whereas non-covalent is only a thermodynamic equilibrium process that shows the activity of a compound within a short period of time. Therefore, the use of traditional evaluation indicators often leads to misjudgments.

Covalently drugs and natural products

Discovering new drugs from natural products is a common strategy in new drug research and development projects. Many drugs are discovered based on this approach, such as paclitaxel, xylophone, morphine, etc. Another approach is to structurally modify natural products to obtain compounds that are more effective, such as salicylic acid to aspirin, morphine to methadone. According to statistics, about 60% of the drugs in clinical practice are obtained based on the above strategy.

Although covalently drugs have only become popular in recent years, the concept is not uncommon in nature. Many antibiotics, such as penicillin, showdomycin and fosfomycin, interact with their targets in bacteria in the form of covalent bonds. Lipstatin is an irreversible inhibitor of pancreatolipase isolated from streptomyces.

The above examples of natural products prove that covalent binding interactions are an overlooked treasure trove in drug design. Most of the drug targets are proteins. Residues such as serine, lysine, cysteine and histidine contain nucleophilic active functional groups (hydroxyl, sulfhydryl, amino, etc.), so the protein can act as an excellent nucleophile and can interact with electrophilic active groups to form covalent bonds. The greatest difficulty in the design of such compounds lies in the selectivity, which is prone to serious side reactions, resulting in failure of research and development.

Currently, around 30% of drugs targeting enzymes are in the form of covalent binding, mainly because this design concept has only been accepted in recent years. Prior to this, active reactive groups were structures that were avoided wherever possible in drug design. Telaprevir, developed by Merck and approved for marketing by the FDA in 2011, achieves its antiviral effect by forming a hemiacetal with the catalytic serine residue (hydroxyl group) in the HCV protease and inhibiting its activity. Initially, the compound showed poor activity in the standard IC50 test and was nearly abandoned, however, in a specially designed activity test, it performed well. The development of Telaprevir is a profound example, which highlights that the development of covalent drugs requires a different set of evaluation methods that are different from traditional non-covalently bound drugs.

Another classic example is the development of Afatinib. It is an irreversible inhibitor of the EGFR receptor (launched in 2013). The electrophilic active group acrylamide in its structure forms a covalent bond with a cysteine residue (sulfhydryl group) in the active site of the EGFR receptor, which overcomes the resistance problems of the first generation of EGFR (gefitinib, erlotinib, etc.) receptor inhibitors, and shows good activity against non-resistant EGFR receptors. These two successful cases demonstrate the potential of covalent drugs. On the other hand, their development process provides valuable lessons for the development of other covalent drugs.

Drug-target binding process

Similar to non-covalent drugs, the covalent drug first interacts with the target to form a drug-target conjugate. Since this process is thermodynamic, equilibrium can be reached very quickly and its affinity can be described by parameters such as dissociation constant Ki or IC50. The difference lies in the formation of covalent bonds in the second step, which is formed at a slower rate compared to the first step, and exists a reaction equilibrium constant Ki*. Therefore, the overall binding of the covalently bound drug requires consideration of two parameters: Ki and Ki*. When Krea is much larger than Krev-rea, the reaction equilibrium constant tends to infinity, and the binding between the drug and the target can be regarded as irreversible covalent binding. When the difference between Krea and Krev-rea is not very large, i.e. Ki* is within a reasonable value range, the binding between the drug and the target can be regarded as reversible covalent binding.

Binding Mechanisms

Most of the drug targets are proteins, which can essentially act as nucleophilic reagents because their structures are rich in functional groups such as hydroxyl, sulfhydryl and amino groups. Covalent binding compounds usually contain electrophilic functional groups in their structures, such as Michael receptors, epoxy, halogen, carbonyl, isocyanine and other structures (Figure 5), which can act as electrophiles, and the two react with each other to form new covalent bonds. The main types of reactions involved are: acylation reactions, alkylation reactions, Michael addition, disulfide bonding, Pinner reactions, etc. The choice of covalent bond formation method depends on the nature of the target binding site.

Toxicity issues

Covalent drug design strategies are now becoming more and more sophisticated, and the risks should not be underestimated, especially the irreversible covalent binding effects. The formation of a new covalent bond between a small molecule and a target can cause changes in the structure of the protein and produce an immune response, but such reports are relatively rare. Off-target effects are also an important cause of toxicity, and improving the selectivity of compounds and lowering therapeutic doses are effective solutions to this problem.

The majority of covalent binding drugs are currently focused on the anti-cancer field, but with the continuous development of technology and theories, such drugs will become available in more and more disease areas.


Welcome to WriteUpCafe Community

Join our community to engage with fellow bloggers and increase the visibility of your blog.
Join WriteUpCafe