8RCX | pdb_00008rcx

Crystal structure of the Mycobacterium tuberculosis regulator VirS (N-terminal fragment 4-208) in complex with the drug candidate alpibectir

• PDB DOI: https://doi.org/10.2210/pdb8RCX/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-07 Released: 2025-10-29 
• Deposition Author(s): Edoo, Z., Frita, R., Grosse, C., Bourotte, M., Moune, M., Antoine, R., Trebosc, V., Schellhorn, B., Dreneau, A., Hofmann, L., Kemmer, C., Lociuro, S., Dale, G.E., Jung, F., Perez-Herran, E., Mendoza, A., Rebollo Lopez, M.J., Ghidelli-Disse, S., Drewes, G., Mathys, V., Soetaert, K., Megalizzi, V., Wintjens, R., Barros Aguirre, D., Remuinan, M.D., Gitzinger, M., Deprez, B., Willand, N., Pieren, M., Baulard, A.R.
• Funding Organization(s): Fonds National de la Recherche Scientifique (FNRS), Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.204 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.181 (DCC) 

Starting Model: in silico

Literature

Alpibectir-Ethionamide combination (AlpE) for the treatment of tuberculosis.

Edoo, Z., Grosse, C., Maitre, T., Frita, R., Chauffour, A., Fournier Le Ray, L., Godmer, A., Aubry, A., Bourotte, M., Antoine, R., Tawk, L., Slupek, S., Trebosc, V., Schellhorn, B., Dreneau, A., Hofmann, L., Kemmer, C., Lociuro, S., Dale, G.E., Jung, F., Perez-Herran, E., Mendoza, A., Rebollo Lopez, M.J., Ghidelli-Disse, S., Werner, T., Ballell, L., Barros-Aguirre, D., Mathys, V., Soetaert, K., Megalizzi, V., Wintjens, R., Gitzinger, M., Deprez, B., Veziris, N., Remuinan, M.J., Willand, N., Pieren, M., Baulard, A.R.

(2026) Nat Commun 

• PubMed: 41946736 
• DOI: https://doi.org/10.1038/s41467-026-71460-6
• Primary Citation Related Structures: 
  8RCX


• PubMed Abstract: 
  

  Ethionamide (Eto) and prothionamide (Pto) are second-line antibiotics used for tuberculosis (TB) treatment. Both are prodrugs whose antibacterial activity depends on bioactivation by oxidases in Mycobacterium tuberculosis, including the Baeyer-Villiger monooxygenase MymA. Through biophysical, genetic, and cellular assays, we show that the clinical candidate alpibectir (Alp, BVL-GSK098) binds the transcriptional regulator VirS, increasing MymA expression and potentiating Eto and Pto activity. Alpibectir also boosts the activity of the corresponding host-derived sulfoxide metabolites. We additionally show that alpibectir exhibits intrinsic antibacterial activity via overexpression of the mymA operon. The alpibectir/Eto (AlpE) combination is rapidly bactericidal in vitro and in mice, lowers the frequency of spontaneous resistance of Eto, and remains active on Eto- and isoniazid-resistant strains, including isolates with inhA promoter mutations. Alpibectir was safe in a Phase 1 human clinical trial. Together with the potentiation data presented here, these findings highlight its potential to optimize TB chemotherapy by reducing Eto/Pto doses, which can minimize dose-related side effects, enhancing adherence.

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Organizational Affiliation: 
• Univ. Lille, CNRS, Inserm, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France.
BioVersys SAS, Lille, France.
Research Department in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, ULB, Bruxelles, Belgium.
Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses, CIMI, F-75013, Paris, France.
APHP. Sorbonne Université, Hôpital Tenon, Service de Pneumologie et d'Oncologie Thoracique, Centre de Référence Maladie Rares, GRC Sorbonne Université SOLID, Paris, France.
APHP. Sorbonne Université, Hôpital Saint-Antoine, Département de Bactériologie, Centre National de Référence des Mycobactéries, Paris, France.
APHP. Sorbonne-Université, Hôpital Pitié Salpêtrière, Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries et de la résistance des mycobactéries aux antituberculeux, Paris, France.
BioVersys AG, Basel, Switzerland.
GSK, Tres Cantos R&D, PTM, Tres Cantos, Madrid, Spain.
Cellzome GmbH. A GSK Company, Heidelberg, Germany.
National Reference Center for Tuberculosis and Mycobacteria, Sciensano, Brussels, Belgium.
Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, Lille, France.
Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France.
Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, Lille, France. [e-mail].
BioVersys AG, Basel, Switzerland. [e-mail].
Univ. Lille, CNRS, Inserm, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France. [e-mail].
Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.81 kDa 
• Atom Count: 3,492 
• Modeled Residue Count: 410 
• Deposited Residue Count: 806 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator VirS	A, B	403	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: virS
UniProt
Find proteins for P9WMJ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMJ3  Go to UniProtKB:  P9WMJ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YPQ (Subject of Investigation/LOI)	C [auth A], D [auth B]	4,4,4-tris(fluoranyl)-1-[3-(trifluoromethyl)-1-oxa-2,8-diazaspiro[4.5]dec-2-en-8-yl]butan-1-one C12 H14 F6 N2 O2 ZEAVKHMQTZBUND-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.204 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.181 (DCC) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.313	α = 90
b = 115.313	β = 90
c = 70.713	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
STARANISO	data scaling
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Edoo, Z., Frita, R., Grosse, C., Bourotte, M., Moune, M., Antoine, R., Trebosc, V., Schellhorn, B., Dreneau, A., Hofmann, L., Kemmer, C., Lociuro, S., Dale, G.E., Jung, F., Perez-Herran, E., Mendoza, A., Rebollo Lopez, M.J., Ghidelli-Disse, S., Drewes, G., Mathys, V., Soetaert, K., Megalizzi, V., Wintjens, R., Barros Aguirre, D., Remuinan, M.D., Gitzinger, M., Deprez, B., Willand, N., Pieren, M., Baulard, A.R.

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Funding Organization	Location	Grant Number
Fonds National de la Recherche Scientifique (FNRS)	Belgium	CR40003580
Agence Nationale de la Recherche (ANR)	France	ANR-20-PAMR-0005

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release
  
• Version 1.1: 2026-05-13
  Changes: Database references