Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin with tubulin degradation effect

Abstract

Microtubules, composed of αβ-tubulin heterodimers, have remained popular anticancer targets for decades. Six known binding sites on tubulin dimers have been identified thus far, with five sites on β-tubulin and only one site on α-tubulin, hinting that compounds binding to α-tubulin are less well characterized. Cevipabulin, a microtubule-active antitumor clinical candidate, is widely accepted as a microtubule-stabilizing agent by binding to the vinblastine site. Our x-ray crystallography study reveals that, in addition to binding to the vinblastine site, cevipabulin also binds to a new site on α-tubulin. We find that cevipabulin at this site pushes the αT5 loop outward, making the nonexchangeable GTP exchangeable, which reduces the stability of tubulin, leading to its destabilization and degradation. Our results confirm the existence of a new agent binding site on α-tubulin and shed light on the development of tubulin degraders as a new generation of antimicrotubule drugs targeting this novel site.

Microtubule Targeting Agents in Disease: Classic Drugs, Novel Roles

“…Accordingly, the simplest classification of these drugs is into two groups: MT-stabilizing agents (MSAs) and MT-destabilizing agents (MDAs). All MTAs bind to one of these seven sites in the tubulin dimers [9][10][11] (Figure 2).…”

“…Accordingly, the simplest classification of these drugs is into two groups: MT-stabilizing agents (MSAs) and MT-destabilizing agents (MDAs). All MTAs bind to one of these seven sites in the tubulin dimers [9][10][11] (Figure 2). − Vinca domain (MDA, orange in Figure 2): this domain is located in the β tubulin monomer at the inter-dimer interface between two longitudinally aligned tubulin dimers.…”

“…− Gatorbulin site (MDA, yellow in Figure 2): this new site has been described in 2021, is located in the α-tubulin subunit (between αand β-tubulin) close to the colchicine site, and it functions in a similar way to the vinca site, creating a wedge between two longitudinally aligned tubulin dimers at the end of MTs [10]. Recently, a new compound called Cevipabulin has been described to also bind to this pocket [11].…”

Structure-Based Design and Synthesis of N-Substituted 3-Amino-β-Carboline Derivatives as Potent αβ-Tubulin Degradation Agents

“…MTs play pivotal roles in many biological functions such as the formation of mitotic spindles, intracellular transportation, and the establishment and maintenance of cell morphology and cell motility. − To date, seven distinct ligand-binding sites on tubulin have been identified and characterized by structural biology . Among them, two sites (taxane and laulimalide/peloruside A sites) are targeted by microtubule-stabilizing agents (MSAs); four sites (colchicine, vinca, maytansine, and pironetin sites) are targeted by microtubule-destabilizing agents (MDAs). − The newly discovered seventh site is targeted by cevipabulin (a widely accepted MSA that binds to the vinca site), which can promote tubulin degradation. , MSAs stabilize microtubules by strengthening lateral and/or longitudinal tubulin contacts in microtubules. , MDAs destabilize microtubules by either inhibiting the formation of native tubulin contacts or hindering the curved-to-straight conformational change of tubulin accompanying microtubule formation. , However, the molecular mechanism of tubulin degradation promoted by tubulin-targeting compounds is not yet well understood.…”

Discovery of Novel 3,4-Dihydro-2(1H)-Quinolinone Sulfonamide Derivatives as New Tubulin Polymerization Inhibitors with Anti-Cancer Activity

“…Among them, five binding sites are located on the β subunit of tubulin, including the paclitaxel binding site, laulimalide binding site, vinblastine binding site, maytansine binding site and colchicine binding site. Meanwhile, two binding sites are located on the α subunit of tubulin, including the evipabulin binding site and pironetin binding site [ 10 , 13 , 14 , 15 ]. Colchicine can bind to the dimer β subunit in the microtubule lattice and has a strong anti-tumor activity.…”