8WGM | pdb_00008wgm

Quadruple mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S, N51I+C59R+S108N+I164L) complexed with LA1, NADPH and dUMP

PDB DOI: https://doi.org/10.2210/pdb8WGM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Plasmodium falciparum VS/1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-09-22 Released: 2024-09-11
Deposition Author(s): Vanichtanankul, J., Saeyang, T., Vitsupakorn, D., Arwon, U., Decharuangsilp, S., Yuthavong, Y., Kamchonwongpaisan, S.
Funding Organization(s): National Science and Technology Development Agency (NSTDA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.190 (Depositor), 0.194 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Flexible 2,4-diaminopyrimidine bearing a butyrolactone as Plasmodium falciparum dihydrofolate reductase inhibitors.

Decharuangsilp, S., Arwon, U., Hoarau, M., Vanichtanankul, J., Saeyang, T., Jantra, T., Rattanajak, R., Thiabma, R., Sooksai, N., Kongkasuriyachai, D., Kamchonwongpaisan, S., Yuthavong, Y.

(2024) Bioorg Chem 153: 107789-107789

PubMed: 39250850 Search on PubMed
DOI: https://doi.org/10.1016/j.bioorg.2024.107789
Primary Citation Related Structures:
8WGM, 8WGN

PubMed Abstract:
Recently, P218, a new flexible antifolate targeting Plasmodium falciparum dihydrofolate reductase (PfDHFR), has entered its clinical trial with good safety profile and effective Pf infection prevention. However, it carries a free carboxyl terminal, which is hydrophilic and prone to metabolic glucuronidation. Here, a new series of P218 analogues carrying butyrolactone has been synthesized with the purpose of enhancing lipophilicity and minimizing metabolic instability. The inhibition constants against the mutant PfDHFR enzymes are in sub-nanomolar level and the antimalarial activity against antifolate-resistant parasites are in the low micromolar range. The crystal structure of the most potent analogue LA1 bound enzyme complex indicates interaction with multiple residues, including Arg122 and Phe116 in the active site. In vitro log D _7.4 and kinetic solubility confirmed a higher lipophilicity of this butyrolactone series as compared to P218. These outcomes suggest the possibility to further develop butyrolactone derivatives as non-carboxyl antiplasmodial antifolates.

Organizational Affiliation

National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand. Electronic address: sasithorn.dec@biotec.or.th.

Macromolecule Content

Total Structure Weight: 146.49 kDa
Atom Count: 9,780
Modeled Residue Count: 1,060
Deposited Residue Count: 1,216
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional dihydrofolate reductase-thymidylate synthase	A, B	608	Plasmodium falciparum VS/1	Mutation(s): 4 Gene Names: DHFR-TS EC: 2.1.1.45 (UniProt), 1.5.1.3 (UniProt)
UniProt
Find proteins for P13922 (Plasmodium falciparum (isolate K1 / Thailand)) Explore P13922 Go to UniProtKB: P13922
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13922
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
WCQ (Subject of Investigation/LOI) Query on WCQ Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	(3~{E})-3-[[2-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]oxypropoxy]phenyl]methylidene]oxolan-2-one C₂₀ H₂₄ N₄ O₄ IYGGQEQHKUVGBG-WYMLVPIESA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
UMP Query on UMP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]