Dual-acting macromolecules: new ideas for cancer drug design

A fundamental challenge in drug development is how to balance
"optimizing the drug's match to the target" with "the drug's ability to cross the cell membrane and reach the target.
" In traditional drug design, the study of cell-penetrating drugs prioritizes compounds that may cross the cell membrane, and thus focuses on molecules with low molecular weight and rigid, non-polar chemical structures
。 However, in a study published December 8, 2022 in the journal Science, UCSF researchers Kevin Lou, MD candidate, Dr.
Luke Gilbert and Dr.
Kevan Shokat, revealed an important cellular uptake pathway, in which large, complex molecules can bind to targets in unconventional ways and be efficiently absorbed by target cells, an idea that could be used to make new drugs to treat cancer and other diseases It is expected to be used to develop novel drugs/therapies that use larger, flexibly connected chemical entities and break the traditional rules of drug design
.

Most conventional medicines are small molecules that follow simple molecular rules, including limiting the size of the molecule and the number of sticky chemical groups on the surface of the
molecule.
Many key drug targets, such as kinase enzymes, which often involve cancer, are difficult to target selectively with conventional drugs
.
In the new study, the authors used a combination of functional genomics and chemical methods to discover an endogenous pathway involving interferon-induced transmembrane proteins (IFITMs) that promote cellular uptake of different related molecules
.
IFITM proteins are found in the plasma membrane and normally provide cells with resistance to viruses
.

Kevin Lou, lead author of the study, said: "There are more than 500 human kinase enzymes that are very similar in the region where the drug binds, which makes it a challenge
to selectively target a member of this family.
" There are many important intracellular drug targets that researchers cannot target with small, compact and rigid molecules
.
To address this challenge, scientists began to ligand ligands into a single chemical entity (linkage chemotype).

These connections form chemical entities that can have enhanced potency, greater selectivity, and the ability to
induce multiple target associations.

"Given the difference between the good biological activity of many large, bivalent molecules and the traditional concept of passive permeability, we infer that chemical entities that connect constituents may hijack cellular processes to help pass through cell membranes
," Lou said.

The team chose RapaLink-1, a bitopic inhibitor of the signaling protein mTOR, as an example that is active in vivo but whose molecular weight far exceeds the usual guidelines and cannot be considered a drug-like drug
.
The researchers demonstrated with chemogenetics that Rapalink-1 activity relies on interferon-induced transmembrane proteins (IFITMs).

IFITMs promote cellular uptake by different "linkage chemical macromolecules," and they also explored the role
of linker length in uptake pathways.
This work may guide the development of
dual-action drugs.

To demonstrate this mechanism, the team designed two new linker drugs, one of which is to link two known leukemia protein BCL-ABL1 inhibitors (dasatinib and asciminib) with linkers to generate DasatiLink-1 — because each drug binds to different sites on the target protein, the researchers reasoned that the linked version could fix itself to two contact points, like inserting a double-ended key into two locks.
Enhanced its specificity and effectiveness
.
The second is BisRoc-1, which is additionally designed to bridge two molecules of the chemotherapy drug rocaglamide (neemamide), allowing it to bind to the drug's
two protein targets.

Although both drugs violate traditional drug design principles, the team showed that both drugs enter cells, bind tightly to the intended target, and are just as effective as
the unbound version.
The linkage version relies solely on IFITM protein expression in target cells, and the results show that the IFITM pathway plays a role
in many types of linker molecules.
DasatiLink-1 is specific only for the BCL-ABL1 kinase, and is more specific than its two components
.
They also found that IFITMs moderately assisted some chimeras targeting proteolysis
.

"Connectivity inhibitors need to be multi-pronged and more selective
," Lou explains.
"As long as they can effectively enter the cell, they have a huge advantage
.
"

"We found that the IFITM protein enables dual-targeted inhibitors to enter cells, which may allow us to target previously untargeted proteins in disease," said Luke Gilbert, Ph.
D.
, co-corresponding author and the Goldberg-Benioff Professor of
Prostate Cancer Translational Biology at UCSF.
"Hopefully, our study will provide new clues
for drug design scientists and virologists to study the mechanisms of the IFITM protein.
"

Scientists are working to chemically optimize the properties of the relevant BCR-ABL inhibitors to improve their potency and position them as the next generation of therapies
for BCR-ABL-mutant cancers.
"We are also excited to expand the range of intracellular targets to accommodate dual inhibition
.
"

Journal Reference:

1. Kevin Lou, Douglas R.
   Wassarman, Tangpo Yang, YiTing Paung, Ziyang Zhang, Thomas A.
   O’ Loughlin, Megan K.
   Moore, Regina K.
   Egan, Patricia Greninger, Cyril H.
   Benes, Markus A.
   Seeliger, Jack Taunton, Luke A.
   Gilbert, Kevan M.
   Shokat.
   IFITM proteins assist cellular uptake of diverse linked chemotypes.
   Science, 2022; 378 (6624): 1097 DOI: 10.
   1126/science.
   abl5829