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1. UNRAVELING MOLECULAR MECHANISMS OF ANTIBIOTIC RESISTANCE THROUGH MULTISCALE SIMULATIONS AND EXPLAINABLE MACHINE LEARNING

   Song, Zilin (May 2022, SMU Scholar)

   Pathogen resistance to β-lactam antibiotics compromises effective treatments of superbug infections. One major source of β-lactam resistance is the bacterial production of β-lactamases, which could effectively hydrolyze β-lactam drugs. In this thesis, the hydrolysis of various β-lactam antibiotics by class A serine-based β-lactamases (ASβLs) were investigated using hybrid Quantum Mechanical / Molecular Mechanical (QM/MM) minimum energy pathway (MEP) calculations and explainable machine learning (ML) approaches. The TEM-1/benzylpenicillin acylation reaction with QM/MM chain-of-states reaction pathways was firstly revisited. I proposed two decomposition methods for energy contribution analysis based on perturbing ML regression models. Both methods were shown to be model implementation invariant and successfully bridged the discrepancies between two pioneering mechanistic studies. The Toho-1 ASβL acylations of ampicillin and cefalexin were then investigated. I reported that the acylation pathway selection can be ligand dependent: ampicillin could undergo acylation via Lys73 or Glu166 acting as the general base while cefalexin acylation is limited to Lys73 as the general base. An explainable artificial intelligence (XAI) method, the Boltzmann-weighted Cumulative Integrated Gradients (BCIG), was developed to explain the different acylation pathway viability found for ampicillin and cefalexin. Lastly, conformational factors determining the GES-5/imipenem deacylation activity was investigated using edge-conditioned convolutional graph-learning (GL) methods. Critical mechanistic insights were derived from perturbative response of the GL latent representations, which explained the different deacylation reactivity between the two imipenem pyrroline tautomer states and identified the orientation of the carbapenem 6α-hydroxyethyl as the key factor that impacts the deacylation barrier heights. In summary, my thesis focuses on bridging QM/MM chain-of-states reaction pathway calculations and explainable ML to derive essential mechanistic insights into β-lactam resistance driven by ASβLs. 

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2. Beta-Lactam Antibiotic Discrimination Using a Macromolecular Sensor in Water at Neutral pH

   https://doi.org/10.3390/s21196384  

   Xu, Yifei; Bonizzoni, Marco (October 2021, Sensors)

   Penicillins and cephalosporins belong to the β-lactam antibiotic family, which accounts for more than half of the world market for antibiotics. Misuse of antibiotics harms human health and the environment. Here, we describe an easy, fast, and sensitive optical method for the sensing and discrimination of two penicillin and five cephalosporin antibiotics in buffered water at pH 7.4, using fifth-generation poly (amidoamine) (PAMAM) dendrimers and calcein, a commercially available macromolecular polyelectrolyte and a fluorescent dye, respectively. In aqueous solution at pH 7.4, the dendrimer and dye self-assemble to form a sensor that interacts with carboxylate-containing antibiotics through electrostatic interaction, monitored through changes in the dye’s spectroscopic properties. This response was captured through absorbance, fluorescence emission, and fluorescence anisotropy. The resulting data set was processed through linear discriminant analysis (LDA), a common pattern-base recognition method, for the differentiation of cephalosporins and penicillins. By pre-hydrolysis of the β-lactam rings under basic conditions, we were able to increase the charge density of the analytes, allowing us to discriminate the seven analytes at a concentration of 5 mM, with a limit of discrimination of 1 mM. 

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3. Probing the Fate of Different Structures of Beta-Lactam Antibiotics: Hydrolysis, Mineral Capture, and Influence of Organic Matter

   https://doi.org/10.1021/acsearthspacechem.1c00064  

   Klein, A.R.; Sarri, E.; Kelch, S.E.; Basinski, J.J.; Vaidya, S.; Aristilde, L. (June 2021, ACS earth and space chemistry)

   Beta-lactam antibiotics, which are used extensively in human and veterinary applications, are commonly detected in surface waters. To examine how the distinct structures of different generations of beta-lactam antibiotics can influence their persistence or degradation in environmental aqueous media, we examined the fate of two penams (amoxicillin and cloxacillin) and two cephems (cephalexin and ceftriaxone) at pH 5.0 and pH 7.0. By contrast to the lack of hydrolysis of the penam antibiotics at both pHs, we observed hydrolysis of cephalexin at pH 7.0 (t1/2 = 12 d) and ceftriaxone at pH 5.0 (t1/2 = 2.8 d). Using high-performance liquid chromatography coupled with a diode array detector or a high-resolution mass spectrometer, we were able to confirm thiotriazinone and 3-desacetyl cefotaxime as major hydrolysis products of ceftriaxone, and propose the hydrolytic cleavage of the benzene and cephem moieties from cephalexin. In addition, we studied the effects of smectite clay particles suspended in solutions without or with dissolved organic matter. The adsorption capacity of the clay was 4- to 9-fold higher at pH 7.0 than at pH 5.0. Subsequent X-ray diffraction analysis revealed that the antibiotic adsorption was not within the clay interlayer nanopores but occurred primarily on the external clay surfaces. The addition of dissolved organic matter interfered with the adsorption of a cephem antibiotic (ceftriaxone) on the clay, but the adsorption of a penam antibiotic (amoxicillin) remained unaffected. We employed molecular modeling simulations to probe the mechanisms of adsorption on the mineral surface. Our findings offer new insights on how the compound structures can dictate different fates of the beta-lactam class of antibiotics in environmental media. 

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4. Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity

   https://doi.org/10.1038/s41467-021-22089-0  

   Modi, Tushar; Risso, Valeria A.; Martinez-Rodriguez, Sergio; Gavira, Jose A.; Mebrat, Mubark D.; Van Horn, Wade D.; Sanchez-Ruiz, Jose M.; Banu Ozkan, S. (March 2021, Nature Communications)

   Abstract TEM-1 β-lactamase degrades β-lactam antibiotics with a strong preference for penicillins. Sequence reconstruction studies indicate that it evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency. This generalist to specialist conversion involved more than 100 mutational changes, but conserved fold and catalytic residues, suggesting a role for dynamics in enzyme evolution. Here, we develop a conformational dynamics computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism. By deliberately weighting and altering the conformational dynamics of a putative Precambrian β-lactamase, we engineer enzyme specificity that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements. Our conformational dynamics design thus re-enacts the evolutionary process and provides a rational allosteric approach for manipulating function while conserving the enzyme active site. 

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5. Time-resolved β-lactam cleavage by L1 metallo-β-lactamase

   https://doi.org/10.1038/s41467-022-35029-3  

   Wilamowski, M.; Sherrell, D. A.; Kim, Y.; Lavens, A.; Henning, R. W.; Lazarski, K.; Shigemoto, A.; Endres, M.; Maltseva, N.; Babnigg, G.; et al (December 2022, Nature Communications)

   Abstract Serial x-ray crystallography can uncover binding events, and subsequent chemical conversions occurring during enzymatic reaction. Here, we reveal the structure, binding and cleavage of moxalactam antibiotic bound to L1 metallo-β-lactamase (MBL) from Stenotrophomonas maltophilia . Using time-resolved serial synchrotron crystallography, we show the time course of β-lactam hydrolysis and determine ten snapshots (20, 40, 60, 80, 100, 150, 300, 500, 2000 and 4000 ms) at 2.20 Å resolution. The reaction is initiated by laser pulse releasing Zn 2+ ions from a UV-labile photocage. Two metal ions bind to the active site, followed by binding of moxalactam and the intact β-lactam ring is observed for 100 ms after photolysis. Cleavage of β-lactam is detected at 150 ms and the ligand is significantly displaced. The reaction product adjusts its conformation reaching steady state at 2000 ms corresponding to the relaxed state of the enzyme. Only small changes are observed in the positions of Zn 2+ ions and the active site residues. Mechanistic details captured here can be generalized to other MBLs. 

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