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Mycobacterium tuberculosis is the single most important global infectious disease killer and a World Health Organization critical priority pathogen for development of new antimicrobials. M. tuberculosis DNA gyrase is a validated target for anti-TB agents, but those in current use target DNA breakage-reunion, rather than the ATPase activity of the GyrB subunit. Here, virtual screening, subsequently validated by whole-cell and enzyme inhibition assays, was applied to identify candidate compounds that inhibit M. tuberculosis GyrB ATPase activity from the Specs compound library. This approach yielded six compounds: four carbazole derivatives (1, 2, 3, and 8), the benzoindole derivative 11, and the indole derivative 14. Carbazole derivatives can be considered a new scaffold for M. tuberculosis DNA gyrase ATPase inhibitors. IC50 values of compounds 8, 11, and 14 (0.26, 0.56, and 0.08 µM, respectively) for inhibition of M. tuberculosis DNA gyrase ATPase activity are 5-fold, 2-fold, and 16-fold better than the known DNA gyrase ATPase inhibitor novobiocin. MIC values of these compounds against growth of M. tuberculosis H37Ra are 25.0, 3.1, and 6.2 µg/mL, respectively, superior to novobiocin (MIC > 100.0 µg/mL). Molecular dynamics simulations of models of docked GyrB:inhibitor complexes suggest that hydrogen bond interactions with GyrB Asp79 are crucial for high-affinity binding of compounds 8, 11, and 14 to M. tuberculosis GyrB for inhibition of ATPase activity. These data demonstrate that virtual screening can identify known and new scaffolds that inhibit both M. tuberculosis DNA gyrase ATPase activity in vitro and growth of M. tuberculosis bacteria.
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Antituberculosos , Girasa de ADN , Evaluación Preclínica de Medicamentos , Indoles , Mycobacterium tuberculosis , Inhibidores de Topoisomerasa II , Mycobacterium tuberculosis/enzimología , Mycobacterium tuberculosis/efectos de los fármacos , Inhibidores de Topoisomerasa II/farmacología , Inhibidores de Topoisomerasa II/química , Girasa de ADN/metabolismo , Girasa de ADN/química , Ligandos , Indoles/farmacología , Indoles/química , Antituberculosos/farmacología , Antituberculosos/química , Adenosina Trifosfatasas/antagonistas & inhibidores , Adenosina Trifosfatasas/metabolismo , Simulación del Acoplamiento Molecular , Descubrimiento de Drogas , Pruebas de Sensibilidad MicrobianaRESUMEN
Amikacin and piperacillin/tazobactam are frequent antibiotic choices to treat bloodstream infection, which is commonly fatal and most often caused by bacteria from the family Enterobacterales. Here we show that two gene cassettes located side-by-side in and ancestral integron similar to In37 have been "harvested" by insertion sequence IS26 as a transposon that is widely disseminated among the Enterobacterales. This transposon encodes the enzymes AAC(6')-Ib-cr and OXA-1, reported, respectively, as amikacin and piperacillin/tazobactam resistance mechanisms. However, by studying bloodstream infection isolates from 769 patients from three hospitals serving a population of 1.2 million people in South West England, we show that increased enzyme production due to mutation in an IS26/In37-derived hybrid promoter or, more commonly, increased transposon copy number is required to simultaneously remove these two key therapeutic options; in many cases leaving only the last-resort antibiotic, meropenem. These findings may help improve the accuracy of predicting piperacillin/tazobactam treatment failure, allowing stratification of patients to receive meropenem or piperacillin/tazobactam, which may improve outcome and slow the emergence of meropenem resistance.
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Antibacterianos , Elementos Transponibles de ADN , Humanos , Antibacterianos/farmacología , Elementos Transponibles de ADN/genética , Farmacorresistencia Bacteriana Múltiple/genética , Piperacilina/farmacología , Amicacina/farmacología , Pruebas de Sensibilidad Microbiana , Infecciones por Enterobacteriaceae/microbiología , Infecciones por Enterobacteriaceae/tratamiento farmacológico , Infecciones por Enterobacteriaceae/genética , Enterobacteriaceae/genética , Enterobacteriaceae/efectos de los fármacos , Integrones/genética , Bacteriemia/microbiología , Bacteriemia/tratamiento farmacológico , Bacteriemia/genéticaRESUMEN
Quantum chemical calculations of the ground-state properties of positron-molecule complexes are challenging. The main difficulty lies in employing an appropriate basis set for representing the coalescence between electrons and a positron. Here, we tackle this problem with the recently developed Fermionic neural network (FermiNet) wavefunction, which does not depend on a basis set. We find that FermiNet produces highly accurate, in some cases state-of-the-art, ground-state energies across a range of atoms and small molecules with a wide variety of qualitatively distinct positron binding characteristics. We calculate the binding energy of the challenging non-polar benzene molecule, finding good agreement with the experimental value, and obtain annihilation rates which compare favourably with those obtained with explicitly correlated Gaussian wavefunctions. Our results demonstrate a generic advantage of neural network wavefunction-based methods and broaden their applicability to systems beyond the standard molecular Hamiltonian.
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DNA gyrases catalyze negative supercoiling of DNA, are essential for bacterial DNA replication, transcription, and recombination, and are important antibacterial targets in multiple pathogens, including Mycobacterium tuberculosis, which in 2021 caused >1.5 million deaths worldwide. DNA gyrase is a tetrameric (A2B2) protein formed from two subunit types: gyrase A (GyrA) carries the breakage-reunion active site, whereas gyrase B (GyrB) catalyzes ATP hydrolysis required for energy transduction and DNA translocation. The GyrB ATPase domains dimerize in the presence of ATP to trap the translocated DNA (T-DNA) segment as a first step in strand passage, for which hydrolysis of one of the two ATPs and release of the resulting inorganic phosphate is rate-limiting. Here, dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations of the dimeric 43 kDa N-terminal fragment of M. tuberculosis GyrB show how events at the ATPase site (dissociation/hydrolysis of bound nucleotides) are propagated through communication pathways to other functionally important regions of the GyrB ATPase domain. Specifically, our simulations identify two distinct pathways that respectively connect the GyrB ATPase site to the corynebacteria-specific C-loop, thought to interact with GyrA prior to DNA capture, and to the C-terminus of the GyrB transduction domain, which in turn contacts the C-terminal GyrB topoisomerase-primase (TOPRIM) domain responsible for interactions with GyrA and the centrally bound G-segment DNA. The connection between the ATPase site and the C-loop of dimeric GyrB is consistent with the unusual properties of M. tuberculosis DNA gyrase relative to those from other bacterial species.
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Adenosina Trifosfatasas , Girasa de ADN , Simulación de Dinámica Molecular , Mycobacterium tuberculosis , Mycobacterium tuberculosis/enzimología , Mycobacterium tuberculosis/genética , Girasa de ADN/metabolismo , Girasa de ADN/química , Girasa de ADN/genética , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/genética , Dominios Proteicos , Adenosina Trifosfato/metabolismo , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Transducción de SeñalRESUMEN
Resistance to antibiotics is a public health crisis. Although carbapenems are less susceptible to resistance than other ß-lactam antibiotics, ß-lactamases mediating resistance against these drugs are spreading. Here, we dissect the contributions of electric fields to carbapenemase activity in class A ß-lactamases. We perform QM/MM molecular dynamics simulations of meropenem acyl-enzyme hydrolysis that correctly discriminate carbapenemases. Electric field analysis shows that active-site fields in the deacylation transition state and tetrahedral intermediate are important determinants of activity. The active-site fields identify several residues, some distal, that distinguish efficient carbapenemases. Our field analysis script (www.github.com/bunzela/FieldTools) may help in understanding and combating antibiotic resistance.
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Although vaccines are available for SARS-CoV-2, antiviral drugs such as nirmatrelvir are still needed, particularly for individuals in whom vaccines are less effective, such as the immunocompromised, to prevent severe COVID-19. Here we report an α-ketoamide-based peptidomimetic inhibitor of the SARS-CoV-2 main protease (Mpro), designated RAY1216. Enzyme inhibition kinetic analysis shows that RAY1216 has an inhibition constant of 8.4 nM and suggests that it dissociates about 12 times slower from Mpro compared with nirmatrelvir. The crystal structure of the SARS-CoV-2 Mpro:RAY1216 complex shows that RAY1216 covalently binds to the catalytic Cys145 through the α-ketoamide group. In vitro and using human ACE2 transgenic mouse models, RAY1216 shows antiviral activities against SARS-CoV-2 variants comparable to those of nirmatrelvir. It also shows improved pharmacokinetics in mice and rats, suggesting that RAY1216 could be used without ritonavir, which is co-administered with nirmatrelvir. RAY1216 has been approved as a single-component drug named 'leritrelvir' for COVID-19 treatment in China.
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COVID-19 , Vacunas , Humanos , Animales , Ratones , Ratas , SARS-CoV-2 , Tratamiento Farmacológico de COVID-19 , Cinética , Lactamas , Nitrilos , Ratones TransgénicosRESUMEN
Antimicrobial resistance is a global public health threat. Metallo-ß-lactamases (MBLs) inactivate ß-lactam antibiotics, including carbapenems, are disseminating among Gram-negative bacteria, and lack clinically useful inhibitors. The evolving bisthiazolidine (BTZ) scaffold inhibits all three MBL subclasses (B1-B3). We report design, synthesis, and evaluation of BTZ analogues. Structure-activity relationships identified the BTZ thiol as essential, while carboxylate is replaceable, with its removal enhancing potency by facilitating hydrophobic interactions within the MBL active site. While the introduction of a flexible aromatic ring is neutral or detrimental for inhibition, a rigid (fused) ring generated nM benzobisheterocycle (BBH) inhibitors that potentiated carbapenems against MBL-producing strains. Crystallography of BBH:MBL complexes identified hydrophobic interactions as the basis of potency toward B1 MBLs. These data underscore BTZs as versatile, potent broad-spectrum MBL inhibitors (with activity extending to enzymes refractory to other inhibitors) and provide a rational approach to further improve the tricyclic BBH scaffold.
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Antibacterianos , Inhibidores de beta-Lactamasas , Inhibidores de beta-Lactamasas/farmacología , Inhibidores de beta-Lactamasas/química , Antibacterianos/farmacología , Antibacterianos/química , beta-Lactamasas/química , Carbapenémicos , Bacterias GramnegativasRESUMEN
In this paper, I explore a phenomenon those with visible disabilities are all too familiar with: being stared at for their disabled bodies. Drawing on the interrelated fields of psychology, narrative, autoethnography and philosophy, I argue that staring at disabled bodies morally harms disabled people. This moral harm arises from the fact that not only does staring at disabled people fundamentally treat them as means to ends in which they cannot share, and thus, violates the Kantian formula of humanity, but also because this staring results in further, consequential harms for disabled people as well. In elaborating on these consequential harms, I draw largely on the works of disability ethicists Rosemarie Garland-Thomson and Elizabeth Barnes and argue that staring at disabled people contributes to the hermeneutical injustice disabled people face in their largely ableist world. Having identified these harms, I then explore the ameliorative potential of elevating disability narrative (with various disability narratives largely leading the discussion, including my own), drawing on Hilden Lindemann's Damaged Identities, Narrative Repair, and hope to call attention to the ways in which our broader structurally ableist world contributes to disabled people being stared at for their bodies in such harmful fashion.
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[This corrects the article DOI: 10.1039/D0SC05172A.].
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Deep learning methods outperform human capabilities in pattern recognition and data processing problems and now have an increasingly important role in scientific discovery. A key application of machine learning in molecular science is to learn potential energy surfaces or force fields from ab initio solutions of the electronic Schrödinger equation using data sets obtained with density functional theory, coupled cluster or other quantum chemistry (QC) methods. In this Review, we discuss a complementary approach using machine learning to aid the direct solution of QC problems from first principles. Specifically, we focus on quantum Monte Carlo methods that use neural-network ansatzes to solve the electronic Schrödinger equation, in first and second quantization, computing ground and excited states and generalizing over multiple nuclear configurations. Although still at their infancy, these methods can already generate virtually exact solutions of the electronic Schrödinger equation for small systems and rival advanced conventional QC methods for systems with up to a few dozen electrons.
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Owing to the emergence of antibiotic resistance, the polymyxin colistin has been recently revived to treat acute, multidrug-resistant Gram-negative bacterial infections. Positively charged colistin binds to negatively charged lipids and damages the outer membrane of Gram-negative bacteria. However, the MCR-1 protein, encoded by the mobile colistin resistance (mcr) gene, is involved in bacterial colistin resistance by catalysing phosphoethanolamine (PEA) transfer onto lipid A, neutralising its negative charge, and thereby reducing its interaction with colistin. Our preliminary results showed that treatment with a reference pyrazolone compound significantly reduced colistin minimal inhibitory concentrations in Escherichia coli expressing mcr-1 mediated colistin resistance (Hanpaibool et al. in ACS Omega, 2023). A docking-MD combination was used in an ensemble-based docking approach to identify further pyrazolone compounds as candidate MCR-1 inhibitors. Docking simulations revealed that 13/28 of the pyrazolone compounds tested are predicted to have lower binding free energies than the reference compound. Four of these were chosen for in vitro testing, with the results demonstrating that all the compounds tested could lower colistin MICs in an E. coli strain carrying the mcr-1 gene. Docking of pyrazolones into the MCR-1 active site reveals residues that are implicated in ligand-protein interactions, particularly E246, T285, H395, H466, and H478, which are located in the MCR-1 active site and which participate in interactions with MCR-1 in ≥ 8/10 of the lowest energy complexes. This study establishes pyrazolone-induced colistin susceptibility in E. coli carrying the mcr-1 gene, providing a method for the development of novel treatments against colistin-resistant bacteria.
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Proteínas de Escherichia coli , Pirazolonas , Colistina/farmacología , Colistina/química , Escherichia coli/metabolismo , Antibacterianos/farmacología , Farmacorresistencia Bacteriana/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Pirazolonas/farmacología , Pruebas de Sensibilidad MicrobianaRESUMEN
Mutations in DNA gyrase confer resistance to fluoroquinolones, second-line antibiotics for Mycobacterium tuberculosis infections. Identification of new agents that inhibit M. tuberculosis DNA gyrase ATPase activity is one strategy to overcome this. Here, bioisosteric designs using known inhibitors as templates were employed to define novel inhibitors of M. tuberculosis DNA gyrase ATPase activity. This yielded the modified compound R3-13 with improved drug-likeness compared to the template inhibitor that acted as a promising ATPase inhibitor against M. tuberculosis DNA gyrase. Utilization of compound R3-13 as a virtual screening template, supported by subsequent biological assays, identified seven further M. tuberculosis DNA gyrase ATPase inhibitors with IC50 values in the range of 0.42-3.59 µM. The most active compound 1 showed an IC50 value of 0.42 µM, 3-fold better than the comparator ATPase inhibitor novobiocin (1.27 µM). Compound 1 showed noncytotoxicity to Caco-2 cells at concentrations up to 76-fold higher than its IC50 value. Molecular dynamics simulations followed by decomposition energy calculations identified that compound 1 occupies the binding pocket utilized by the adenosine group of the ATP analogue AMPPNP in the M. tuberculosis DNA gyrase GyrB subunit. The most prominent contribution to the binding of compound 1 to M. tuberculosis GyrB subunit is made by residue Asp79, which forms two hydrogen bonds with the OH group of this compound and also participates in the binding of AMPPNP. Compound 1 represents a potential new scaffold for further exploration and optimization as a M. tuberculosis DNA gyrase ATPase inhibitor and candidate anti-tuberculosis agent.
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Mycobacterium tuberculosis , Tuberculosis , Humanos , Mycobacterium tuberculosis/genética , Girasa de ADN/química , Adenilil Imidodifosfato/uso terapéutico , Adenosina Trifosfatasas/química , Células CACO-2 , Antituberculosos/farmacología , Antituberculosos/química , Inhibidores de Topoisomerasa II/farmacología , Inhibidores de Topoisomerasa II/química , Inhibidores de Topoisomerasa II/uso terapéutico , ADNRESUMEN
The polymyxin colistin is a last line antibiotic for extensively resistant Gram-negative bacteria. Colistin binding to lipid A disrupts the Gram-negative outer membrane, but mobile colistin resistance (mcr) gene family members confer resistance by catalyzing phosphoethanolamine (PEA) transfer onto lipid A, neutralizing its negative charge to reduce colistin interactions. Multiple mcr isoforms have been identified in clinical and environmental isolates, with mcr-1 being the most widespread and mcr-3 being common in South and East Asia. Preliminary screening revealed that treatment with pyrazolones significantly reduced mcr-1, but not mcr-3, mediated colistin resistance. Molecular dynamics (MD) simulations of the catalytic domains of MCR-1 and a homology model of MCR-3, in different protonation states of active site residues H395/H380 and H478/H463, indicate that the MCR-1 active site has greater water accessibility than MCR-3, but that this is less influenced by changes in protonation. MD-optimized structures of MCR-1 and MCR-3 were used in virtual screening of 20 pyrazolone derivatives. Docking of these into the MCR-1/MCR-3 active sites identifies common residues likely to be involved in protein-ligand interactions, specifically the catalytic threonine (MCR-1 T285, MCR-3 T277) site of PEA addition, as well as differential interactions with adjacent amino acids. Minimal inhibitory concentration assays showed that the pyrazolone with the lowest predicted binding energy (ST3f) restores colistin susceptibility of mcr-1, but not mcr-3, expressing Escherichia coli. Thus, simulations indicate differences in the active site structure between MCR-1 and MCR-3 that may give rise to differences in pyrazolone binding and so relate to differential effects upon producer E. coli. This work identifies pyrazolones as able to restore colistin susceptibility of mcr-1-producing bacteria, laying the foundation for further investigations of their activity as phosphoethanolamine transferase inhibitors as well as of their differential activity toward mcr isoforms.
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L1 is a dizinc subclass B3 metallo-ß-lactamase (MBL) that hydrolyzes most ß-lactam antibiotics and is a key resistance determinant in the Gram-negative pathogen Stenotrophomonas maltophilia, an important cause of nosocomial infections in immunocompromised patients. L1 is not usefully inhibited by MBL inhibitors in clinical trials, underlying the need for further studies on L1 structure and mechanism. We describe kinetic studies and crystal structures of L1 in complex with hydrolyzed ß-lactams from the penam (mecillinam), cephem (cefoxitin/cefmetazole), and carbapenem (tebipenem, doripenem, and panipenem) classes. Despite differences in their structures, all the ß-lactam-derived products hydrogen bond to Tyr33, Ser221, and Ser225 and are stabilized by interactions with a conserved hydrophobic pocket. The carbapenem products were modeled as Δ1-imines, with (2S)-stereochemistry. Their binding mode is determined by the presence of a 1ß-methyl substituent: the Zn-bridging hydroxide either interacts with the C-6 hydroxyethyl group (1ß-hydrogen-containing carbapenems) or is displaced by the C-6 carboxylate (1ß-methyl-containing carbapenems). Unexpectedly, the mecillinam product is a rearranged N-formyl amide rather than penicilloic acid, with the N-formyl oxygen interacting with the Zn-bridging hydroxide. NMR studies imply mecillinam rearrangement can occur nonenzymatically in solution. Cephem-derived imine products are bound with (3R)-stereochemistry and retain their 3' leaving groups, likely representing stable endpoints, rather than intermediates, in MBL-catalyzed hydrolysis. Our structures show preferential complex formation by carbapenem- and cephem-derived species protonated on the equivalent (ß) faces and so identify interactions that stabilize diverse hydrolyzed antibiotics. These results may be exploited in developing antibiotics, and ß-lactamase inhibitors, that form long-lasting complexes with dizinc MBLs.
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Antibacterianos , Inhibidores de beta-Lactamasas , beta-Lactamas , Humanos , Antibacterianos/farmacología , Inhibidores de beta-Lactamasas/farmacología , beta-Lactamasas/química , beta-Lactamas/química , beta-Lactamas/metabolismo , beta-Lactamas/farmacología , Carbapenémicos/metabolismo , Cristalografía , Cinética , Stenotrophomonas maltophilia/efectos de los fármacos , Infecciones por Bacterias Gramnegativas/tratamiento farmacológicoRESUMEN
KPC-2 (Klebsiella pneumoniae carbapenemase-2) is a globally disseminated serine-ß-lactamase (SBL) responsible for extensive ß-lactam antibiotic resistance in Gram-negative pathogens. SBLs inactivate ß-lactams via a mechanism involving a hydrolytically labile covalent acyl-enzyme intermediate. Carbapenems, the most potent ß-lactams, evade the activity of many SBLs by forming long-lived inhibitory acyl-enzymes; however, carbapenemases such as KPC-2 efficiently deacylate carbapenem acyl-enzymes. We present high-resolution (1.25-1.4 Å) crystal structures of KPC-2 acyl-enzymes with representative penicillins (ampicillin), cephalosporins (cefalothin), and carbapenems (imipenem, meropenem, and ertapenem) obtained utilizing an isosteric deacylation-deficient mutant (E166Q). The mobility of the Ω-loop (residues 165-170) negatively correlates with antibiotic turnover rates (kcat), highlighting the role of this region in positioning catalytic residues for efficient hydrolysis of different ß-lactams. Carbapenem-derived acyl-enzyme structures reveal the predominance of the Δ1-(2R) imine rather than the Δ2 enamine tautomer. Quantum mechanics/molecular mechanics molecular dynamics simulations of KPC-2:meropenem acyl-enzyme deacylation used an adaptive string method to differentiate the reactivity of the two isomers. These identify the Δ1-(2R) isomer as having a significantly (7 kcal/mol) higher barrier than the Δ2 tautomer for the (rate-determining) formation of the tetrahedral deacylation intermediate. Deacylation is therefore likely to proceed predominantly from the Δ2, rather than the Δ1-(2R) acyl-enzyme, facilitated by tautomer-specific differences in hydrogen-bonding networks involving the carbapenem C-3 carboxylate and the deacylating water and stabilization by protonated N-4, accumulating a negative charge on the Δ2 enamine-derived oxyanion. Taken together, our data show how the flexible Ω-loop helps confer broad-spectrum activity upon KPC-2, while carbapenemase activity stems from efficient deacylation of the Δ2-enamine acyl-enzyme tautomer.
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Antibacterianos , Carbapenémicos , Carbapenémicos/química , Carbapenémicos/farmacología , Meropenem , Isomerismo , Antibacterianos/farmacología , Antibacterianos/química , beta-Lactamasas/metabolismo , Proteínas Bacterianas , beta-Lactamas , Klebsiella pneumoniaeRESUMEN
Deep neural networks have been very successful as highly accurate wave function Ansätze for variational Monte Carlo calculations of molecular ground states. We present an extension of one such Ansatz, FermiNet, to calculations of the ground states of periodic Hamiltonians, and study the homogeneous electron gas. FermiNet calculations of the ground-state energies of small electron gas systems are in excellent agreement with previous initiator full configuration interaction quantum Monte Carlo and diffusion Monte Carlo calculations. We investigate the spin-polarized homogeneous electron gas and demonstrate that the same neural network architecture is capable of accurately representing both the delocalized Fermi liquid state and the localized Wigner crystal state. The network converges on the translationally invariant ground state at high density and spontaneously breaks the symmetry to produce the crystalline ground state at low density, despite being given no a priori knowledge that a phase transition exists.
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We report the development of a python-based auxiliary-field quantum Monte Carlo (AFQMC) program, ipie, with preliminary timing benchmarks and new AFQMC results on the isomerization of [Cu2O2]2+. We demonstrate how implementations for both central and graphical processing units (CPUs and GPUs) are achieved in ipie. We show an interface of ipie with PySCF as well as a straightforward template for adding new estimators to ipie. Our timing benchmarks against other C++ codes, QMCPACK and Dice, suggest that ipie is faster or similarly performing for all chemical systems considered on both CPUs and GPUs. Our results on [Cu2O2]2+ using selected configuration interaction trials show that it is possible to converge the ph-AFQMC isomerization energy between bis(µ-oxo) and µ-η2:η2 peroxo configurations to the exact known results for small basis sets with 105-106 determinants. We also report the isomerization energy with a quadruple-zeta basis set with an estimated error less than a kcal/mol, which involved 52 electrons and 290 orbitals with 106 determinants in the trial wave function. These results highlight the utility of ph-AFQMC and ipie for systems with modest strong correlation and large-scale dynamic correlation.
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Electrones , Método de MontecarloRESUMEN
BACKGROUND: Delirium is an acute syndrome characterized by inattention, disorganized thinking, and an altered level of consciousness. A reliable biomarker for tracking delirium does not exist, but oscillations in the electroencephalogram (EEG) could address this need. We evaluated whether the frequencies of EEG oscillations are associated with delirium onset, severity, and recovery in the postoperative period. METHODS: Twenty-six adults enrolled in the Electroencephalography Guidance of Anesthesia to Alleviate Geriatric Syndromes (ENGAGES; ClinicalTrials.gov NCT02241655) study underwent major surgery requiring general anesthesia, and provided longitudinal postoperative EEG recordings for this prespecified substudy. The presence and severity of delirium were evaluated with the confusion assessment method (CAM) or the CAM-intensive care unit. EEG data obtained during awake eyes-open and eyes-closed states yielded relative power in the delta (1-4 Hz), theta (4-8 Hz), and alpha (8-13 Hz) bands. Discriminability for delirium presence was evaluated with c-statistics. To account for correlation among repeated measures within patients, mixed-effects models were generated to assess relationships between: (1) delirium severity and EEG relative power (ordinal), and (2) EEG relative power and time (linear). Slopes of ordinal and linear mixed-effects models are reported as the change in delirium severity score/change in EEG relative power, and the change in EEG relative power/time (days), respectively. Bonferroni correction was applied to confidence intervals (CIs) to account for multiple comparisons. RESULTS: Occipital alpha relative power during eyes-closed states offered moderate discriminability (c-statistic, 0.75; 98% CI, 0.58-0.87), varying inversely with delirium severity (slope, -0.67; 98% CI, -1.36 to -0.01; P = .01) and with severity of inattention (slope, -1.44; 98% CI, -2.30 to -0.58; P = .002). Occipital theta relative power during eyes-open states correlated directly with severity of delirium (slope, 1.28; 98% CI, 0.12-2.44; P = .007), inattention (slope, 2.00; 98% CI, 0.48-3.54; P = .01), and disorganized thinking (slope, 3.15; 98% CI, 0.66-5.65; P = .01). Corresponding frontal EEG measures recapitulated these relationships to varying degrees. Severity of altered level of consciousness correlated with frontal theta relative power during eyes-open states (slope, 11.52; 98% CI, 6.33-16.71; P < .001). Frontal theta relative power during eyes-open states correlated inversely with time (slope, -0.05; 98% CI, -0.12 to -0.04; P = .002). CONCLUSIONS: Presence, severity, and core features of postoperative delirium covary with spectral features of the EEG. The cost and accessibility of EEG facilitate the translation of these findings to future mechanistic and interventional trials.
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Delirio , Delirio del Despertar , Adulto , Humanos , Anciano , Trastornos de la Conciencia , Electroencefalografía/métodos , CogniciónRESUMEN
Mycobacterium tuberculosis protein kinase B (PknB) is essential to mycobacterial growth and has received considerable attention as an attractive target for novel anti-tuberculosis drug development. Here, virtual screening, validated by biological assays, was applied to select candidate inhibitors of M. tuberculosis PknB from the Specs compound library (www.specs.net). Fifteen compounds were identified as hits and selected for in vitro biological assays, of which three indoles (2, AE-848/42799159; 4, AH-262/34335013; 10, AP-124/40904362) inhibited growth of M. tuberculosis H37Rv with minimal inhibitory concentrations of 6.2, 12.5, and 6.2 µg/mL, respectively. Two compounds, 2 and 10, inhibited M. tuberculosis PknB activity in vitro, with IC50 values of 14.4 and 12.1 µM, respectively, suggesting this to be the likely basis of their anti-tubercular activity. In contrast, compound 4 displayed anti-tuberculosis activity against M. tuberculosis H37Rv but showed no inhibition of PknB activity (IC50 > 128 µM). We hypothesize that hydrolysis of its ethyl ester to a carboxylate moiety generates an active species that inhibits other M. tuberculosis enzymes. Molecular dynamics simulations of modeled complexes of compounds 2, 4, and 10 bound to M. tuberculosis PknB indicated that compound 4 has a lower affinity for M. tuberculosis PknB than compounds 2 and 10, as evidenced by higher calculated binding free energies, consistent with experiment. Compounds 2 and 10 therefore represent candidate inhibitors of M. tuberculosis PknB that provide attractive starting templates for optimization as anti-tubercular agents.
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Mycobacterium tuberculosis , Tuberculosis , Humanos , Proteínas Proto-Oncogénicas c-akt/metabolismo , Antituberculosos/farmacología , Antituberculosos/química , Tuberculosis/tratamiento farmacológico , FosforilaciónRESUMEN
Gerasimov et al. claim that the ability of DM21 to respect fractional charge (FC) and fractional spin (FS) conditions outside of the training set has not been demonstrated in our paper. This is based on (i) asserting that the training set has a ~50% overlap with our bond-breaking benchmark (BBB) and (ii) questioning the validity and accuracy of our other generalization examples. We disagree with their analysis and believe that the points raised are either incorrect or not relevant to the main conclusions of the paper and to the assessment of general quality of DM21.