María P. C. Mora-Gamboa

Pontificia Universidad Javeriana

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Leidy D. Ardila-Leal

Francisco de Paula Santander University

Balkys Quevedo-Hidalgo

Pontificia Universidad Javeriana

Raúl A. Poutou‐Piñales

Pontificia Universidad Javeriana

Aura M. Pedroza-Rodríguez

Pontificia Universidad Javeriana

Johan F. Galindo

Universidad Nacional de Colombia

Sandra M. Rincón-Gamboa

Pontificia Universidad Javeriana

María C. Ferrucho-Calle

Pontificia Universidad Javeriana

Lina M. Rojas-Ojeda

Universidad Nacional de Colombia

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Pontificia Universidad Javeriana

Universidad Nacional de Colombia

Francisco de Paula Santander University

AgroBio

Instituto Politécnico Nacional

Universidad de La Sabana

University of Quindío

University of Florida

Fundación Instituto de Inmunología de Colombia

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“In Silico” prediction of antibiotics biodegradation by Ganoderma lucidum GILCC 1 laccase

Deleted Journal (2024)

María P. C. Mora-Gamboa Leidy D. Ardila-Leal Johan F. Galindo Raúl A. Poutou‐Piñales Balkys Quevedo-Hidalgo

Abstract Antibiotics present a pressing environmental challenge as emerging pollutants due to their persistence and role in promoting antibiotic-resistant bacteria. To model the utilization of Ganoderma lucidum GlLCC1 laccase in degrading antibiotics, a 3D homology model of GILCC1, based on Lentinus tigrinus mushroom laccase, was utilized. Five broad-spectrum WHO-designated antibiotics with molecular weights between 100 and 500 Da were selected. Molecular dynamics simulations were conducted at pH 3.0 and 7.0 to evaluate the interactions between GILCC1 and antibiotics in a TIP3P water box, with system behaviour assessed at 300 °K using an NPT assembly. ABTS (2,2ʹ-Azino-bis (3-ethylbenzthiazoline-6-sulfonic Acid)) served as the comparison molecule. The binding free energy indicated a strong affinity between 3D GILCC1 and various ligands. At pH 3.0, GILCC1 exhibited significant Gibbs free energy (ΔG), indicating a high affinity for Levofloxacin (LVX; −8.2 kcal mol −1 ), Sulfisoxazole (SFX; −7.8 kcal mol −1 ), Cefuroxime (CXM; −7.5 kcal mol −1 ), Cephradine (CFD; −7. 5 kcal mol −1 ), ABTS (−7.6 kcal mol −1 ), and Tetracycline (TE; −7.5 kcal mol −1 ), attributed to pocket topology and interactions such as hydrogen bonds and van der Waals forces. Electron transfer in GILCC1 involved a chain of residues, including His 395 and Phe 239 . Although the affinity decreased at pH 7.0, the potential of GILCC1 to degrade antibiotics remained plausible. This study accurately predicted the behaviour of the laccase-antibiotic system, providing atomic-level insights into molecular interactions and emphasizing the importance of experimental assays and assessments of antibiotic degradation in wastewater, considering various chemical compounds. The use of ABTS as a mediator was suggested to enhance molecule affinity. Graphical abstract

Tetracycline antibiotics

ABTS

10.1007/s42452-024-06128-1

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Statistical Improvement of rGILCC 1 and rPOXA 1B Laccases Activity Assay Conditions Supported by Molecular Dynamics

Molecules (2023)

María P. C. Mora-Gamboa María C. Ferrucho-Calle Leidy D. Ardila-Leal Lina M. Rojas-Ojeda Johan F. Galindo

Laccases (E.C. 1.10.3.2) are glycoproteins widely distributed in nature. Their structural conformation includes three copper sites in their catalytic center, which are responsible for facilitating substrate oxidation, leading to the generation of H2O instead of H2O2. The measurement of laccase activity (UL−1) results may vary depending on the type of laccase, buffer, redox mediators, and substrates employed. The aim was to select the best conditions for rGILCC 1 and rPOXA 1B laccases activity assay. After sequential statistical assays, the molecular dynamics proved to support this process, and we aimed to accumulate valuable insights into the potential application of these enzymes for the degradation of novel substrates with negative environmental implications. Citrate buffer treatment T2 (CB T2) (pH 3.0 ± 0.2; λ420nm, 2 mM ABTS) had the most favorable results, with 7.315 ± 0.131 UL−1 for rGILCC 1 and 5291.665 ± 45.83 UL−1 for rPOXA 1B. The use of citrate buffer increased the enzyme affinity for ABTS since lower Km values occurred for both enzymes (1.49 × 10−2 mM for rGILCC 1 and 3.72 × 10−2 mM for rPOXA 1B) compared to those obtained in acetate buffer (5.36 × 10−2 mM for rGILCC 1 and 1.72 mM for rPOXA 1B). The molecular dynamics of GILCC 1–ABTS and POXA 1B–ABTS showed stable behavior, with root mean square deviation (RMSD) values not exceeding 2.0 Å. Enzyme activities (rGILCC 1 and rPOXA 1B) and 3D model–ABTS interactions (GILCC 1–ABTS and POXA 1B–ABTS) were under the strong influence of pH, wavelength, ions, and ABTS concentration, supported by computational studies identifying the stabilizing residues and interactions. Integration of the experimental and computational approaches yielded a comprehensive understanding of enzyme–substrate interactions, offering potential applications in environmental substrate treatments.

ABTS

Enzyme Kinetics

10.3390/molecules28217263

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Impact of Antibiotics as Waste, Physical, Chemical, and Enzymatical Degradation: Use of Laccases

Molecules (2022)

María P. C. Mora-Gamboa Sandra M. Rincón-Gamboa Leidy D. Ardila-Leal Raúl A. Poutou‐Piñales Aura M. Pedroza-Rodríguez

The first traces of Tetracycline (TE) were detected in human skeletons from Sudan and Egypt, finding that it may be related to the diet of the time, the use of some dyes, and the use of soils loaded with microorganisms, such as Streptomyces spp., among other microorganisms capable of producing antibiotics. However, most people only recognise authors dating between 1904 and 1940, such as Ehrlich, Domagk, and Fleming. Antibiotics are the therapeutic option for countless infections treatment; unfortunately, they are the second most common group of drugs in wastewaters worldwide due to failures in industrial waste treatments (pharmaceutics, hospitals, senior residences) and their irrational use in humans and animals. The main antibiotics problem lies in delivered and non-prescribed human use, use in livestock as growth promoters, and crop cultivation as biocides (regulated activities that have not complied in some places). This practice has led to the toxicity of the environment as antibiotics generate eutrophication, water pollution, nutrient imbalance, and press antibiotic resistance. In addition, the removal of antibiotics is not a required process in global wastewater treatment standards. This review aims to raise awareness of the negative impact of antibiotics as residues and physical, chemical, and biological treatments for their degradation. We discuss the high cost of physical and chemical treatments, the risk of using chemicals that worsen the situation, and the fact that each antibiotic class can be transformed differently with each of these treatments and generate new compounds that could be more toxic than the original ones; also, we discuss the use of enzymes for antibiotic degradation, with emphasis on laccases.

10.3390/molecules27144436

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