Design and development of covalently bound drugs [reprint]

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Design and development of valence-binding drugs

order

Figure 1 Classical * * * Valence Binding Drugs

For a long time, electrophilic groups have been a minefield in drug development. Therefore, it is always recommended to avoid introducing such functional groups into the molecular structure of drugs, such as epoxy group, acridine group, Michael receptor and so on. Because of its high reactivity, it may interact with a variety of biological macromolecules, causing serious toxic and side effects. Earlier aspirin, lansoprazole and clopidogrel (Figure 1) were all discovered in recent years, and all of them acted on the target in the form of * * * valence bonds. Inspired by this, the development of * * valence drugs has gradually entered people's field of vision, showing incomparable advantages of non * * valence drugs in many fields such as anti-cancer, anti-virus, diabetes and so on. Such as long-lasting curative effect, lower therapeutic dose and less drug resistance.

Because the * * * valence binding mechanism is different from the non * * valence binding mechanism, it is difficult to truly reflect its efficacy and safety with traditional evaluation indexes, such as dissociation constant, IC50, EC50, etc. The main reason is that the formation of * * valence bond between drug molecules and targets is affected by the reaction rate, while the non-* * valence bond is only a thermodynamic equilibrium process, which can be manifested in a short time.

* * * valence combines drugs and natural products.

Fig. 2 Natural products with electrophilic activity

Discovering new drugs from natural products is a common strategy in new drug development projects. Many drugs are discovered in this way, such as paclitaxel, camptothecin and morphine. Another method is to modify the structure of natural products to obtain better compounds, such as salicylic acid to aspirin, morphine to methadone. According to statistics, about 60% of drugs in clinic are obtained based on the above strategy. Although * * * valence-binding drugs have only become popular in recent years, this concept is not uncommon in nature. Some antibiotics such as penicillin, oxytetracycline and fosfomycin all interact with the target in bacteria in the form of valence bond. Lipstatin is an irreversible inhibitor of pancreatic lipase isolated from Streptomyces. Based on this natural product, Roche developed a new weight-loss drug orlistat, and there are many other examples.

The above examples of many natural products prove that valence combination is a neglected treasure in drug design! Most drug targets are protein, in which serine, lysine, cysteine, histidine and other residues contain nucleophilic functional groups (hydroxyl, sulfhydryl, amino, etc. Therefore, protein can be used as an excellent nucleophile and can interact with electrophilic groups to form valence bonds. For the design of this kind of compounds, the biggest difficulty lies in selectivity, otherwise it will easily cause serious side reactions and lead to development failure.

Figure 3 * * Valuable binding drugs on the market (active reaction sites are marked in yellow)

At present, about 30% of drugs targeting enzymes exist in the form of * * * valence combination, mainly because this design concept has only been accepted in recent years. Prior to this, active reactive groups were the structures that should be avoided in drug design. Telapivir was developed by Merck and approved by FDA on 20 1 1. It forms hemiacetal with serine residue (hydroxyl) which has catalytic effect in HCV protease, thus inhibiting its activity and achieving antiviral effect. At first, in the standard IC50 test, the activity of the compound was very poor and it was almost abandoned. However, it performed well in specially designed activity tests. The research and development process of trapivil profoundly reflects that in the research and development of * * * valence-bound drugs, a set of evaluation methods different from the traditional research and development of non * * valence-bound drugs is needed.

Another classic example is the development of the irreversible EGFR receptor inhibitor alfatinib (listed on 20 13). The electrophilic active group acrylamide in its structure forms valence bond with cysteine residue (sulfhydryl group) in EGFR active site, which overcomes the drug resistance problem of the first generation EGFR (gefitinib, erlotinib, etc.). ) receptor inhibitors, and also showed good resistance to non-drug-resistant EGFR receptors. The above two successful examples prove the potential of * * * valence-binding drugs. On the other hand, its research and development process also provides valuable experience for the research and development of * * * valence combined drugs!

Drug-target binding process

Figure 4 * * * Binding process of precious drugs

Like non-valence-binding drugs, valence-binding drugs first interact with the target to form drug-target conjugates. Because this process belongs to thermodynamic process, it can reach equilibrium quickly, and its affinity can be described by parameters such as dissociation constant Ki or IC50. The difference is that in the second step, compared with the first step, the formation rate of * * * valence bond is relatively slow, and there is a reaction equilibrium constant Ki*. Therefore, the overall combination of * * valence-binding drugs needs to consider two parameters, Ki and Ki*. When krea is much larger than krev-rea, the reaction equilibrium constant tends to infinity, which can be regarded as irreversible valence binding. When there is little difference between krea and krev-rea, that is, Ki* is within a reasonable numerical range, it can be regarded as a reversible valence combination.

binding mechanism

Fig. 5 Common active functional groups

The target of drug action is mostly protein, which is rich in hydroxyl, sulfhydryl, amino and other functional groups, and can be used as a nucleophile in essence. The structure of * * valence binding compounds usually contains electrophilic functional groups, such as Michael acceptor, epoxy, halogen, carbonyl, isonitrile and other structures (Figure 5), which can be used as electrophilic reagents, and they react with each other to form new * * * valence bonds. The main types of reactions involved are acylation reaction, alkylation reaction, Michael addition reaction, disulfide bond reaction, Pinner reaction and so on. Which valence bond formation method is adopted depends on the nature of the target binding site. Generally speaking, there is a lot of choice.

Fig. 6 Mechanism of action of esomeprazole

20 14 among the top ten best-selling drugs in the United States, one is esomeprazole (racemic omeprazole). Omeprazole was developed in1970s, and was marketed in 1988 after many optimization and clinical studies. Two years later, it was discovered that its proton pump inhibition was based on * * * valence bond. Omeprazole is activated near the target under acidic conditions to form active sulfenamide derivatives, and then forms a valence bond with cysteine residues (sulfhydryl groups) in the target.

Fig. 7 Action principle of clopidogrel

Another popular drug is clopidogrel, which needs to be activated by P450 oxidase in the liver to generate sulfur-containing compounds, and then form disulfide bonds with cysteine residues in P2Y 12 receptors, thus inhibiting platelet aggregation. At present, the above two drugs are widely used. At first, they did not exist in the form of * * * valence bond, but in the later mechanism research, they were found to bind to the target through * * * valence bond, resulting in irreversible inhibition.

Fig. 8 saxagliptin mechanism of action.

Compounds containing cyano groups usually react with nucleophilic functional groups in protein, such as hydroxyl groups and sulfhydryl groups, to form imine ester bonds, which are usually reversible. Successful examples, such as saxagliptin and Viglitazone, are used to treat DPP4 type II diabetes. In addition, ondancatex is used to treat osteoporosis in postmenopausal women. However, due to its potential risk of stroke, Merck announced on 20 16 that it would abandon this compound.

As for other valence binding mechanisms, such as alkylation, acylation, Michael addition, etc. , not listed here. Their essence is the interaction between nucleophilic groups in biological macromolecules and electrophilic groups in drug molecules.

Selective control

Fig. 9 development of ocetinib (Teresa)

* * * The selectivity of valence binding drugs is very important! On the issue of selectivity, the commonly used strategy at present is to design a non-valent bonded precursor with high selectivity to the target, and then optimize the design of active functional groups on the basis of this compound, that is, first find the appropriate "shell" and then add the appropriate "warhead". A typical example is the development of oxytinib. The initial lead compound 1 showed excellent binding ability in vitro, but its affinity plummeted by nearly 70 times in cell experiments, which may be due to the combination of high concentration ATP with its competitive target. Therefore, the third generation targeted drug for lung cancer, oxitinib, was successfully developed by irreversible valence binding strategy, and was released in 2065438. In addition to the strategies mentioned above, we can also achieve selectivity through the physical and chemical characteristics of different tissues in the human body, such as omeprazole, which can selectively act on proton pumps because it needs to be activated under strong acid conditions.

Figure 10 design of * * * valence drugs with stable non-* * valence effect

In addition, selectivity can also be achieved through carefully designed electrophilic groups. As shown in figure 10, the Michael addition of α-cyano-substituted acrylamide with mercapto group is a reversible process. In a specific target, the addition product can be stable due to the noncovalency of other amino acid residues, while other non-target targets cannot achieve this effect, thus achieving selectivity. Of course, this strategy needs very strong bioinformatics support, otherwise it will be difficult to achieve.

Toxicity problem

Although the drug design strategy of * * * valence combination is becoming more and more mature, its risks should not be underestimated, especially the irreversible * * * valence combination. Because small molecular compounds form new valence bonds with the target, it will lead to the change of protein structure and the possibility of immune reaction, but this kind of report is rare. The off-target effect is also an important cause of toxicity. In order to solve this problem, improving the selectivity of compounds and reducing the therapeutic dose are effective solutions.

summary

At present, most of the valence-binding drugs are concentrated in the field of anti-cancer, but with the maturity of technology and theory, such drugs will show their talents in more and more disease fields.

reference data

1, Cescau, Stephane de, et al., Design and Discovery of Covalent Inhibitors, European Journal of Medicinal Chemistry138 (2017): 96-114.

Rand M. Miller，Ville O. Paavilainen，Shyam Krishnan，Iana M. Serafimova，Jack Taunton。 "Design of reversible covalent kinase inhibitors based on electrophilic fragments." Journal of American Chemical Society135.14 (2013): 5298.

Targeted covalent inhibitors in drug design, Angewandte Chemie International Edition 55.43 (2016):13408-13421.

Lagoutte, r, r pa tourette and n Wensinger. "Covalent inhibitors: an opportunity for rational target selectivity." Latest viewpoint of chemical biology 39(20 17):54-63.

Development of covalent inhibitors of epidermal growth factor receptor (EGFR) activation and gatekeeper mutant based on structure and activity Journal of Pharmaceutical Chemistry 56.17 (2017): 7025-48.