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1.
Int J Mol Sci ; 19(7)2018 Jul 23.
Artículo en Inglés | MEDLINE | ID: mdl-30041472

RESUMEN

Adipose tissue-derived stem cells (ASCs) in the form of stromal vascular fraction (SVF) and cultured expansion have been applied in clinical settings in some countries to treat osteoarthritis (OA) of knees, one of the most common debilitating, incurable disorders. Since the first report of successful cartilage-like tissue regeneration with autologous adipose SVF containing ASCs, there has been a gradual increase in the number of publications confirming such results. Thus far, most of the reports have been limited to treatments of OA of knees. Recently, successful applications of adipose SVF in treating OA of ankles and hips have been reported. In addition, several groups have reported modified methods of applying adipose SVF, such as combining bone marrow stimulation with adipose SVF or adding additional extracellular matrix (ECM) in treating OA. Here, we present an updated, systematic review of clinical effectiveness and safety in treating OA of knees, ankles, and one hip since 2016 using ASCs in the form of adipose SVF or in cultured expansion, along with a description and suggestion of potential biological mechanisms of cartilage regeneration.


Asunto(s)
Cartílago/fisiología , Trasplante de Células Madre Mesenquimatosas/métodos , Osteoartritis/terapia , Regeneración , Tejido Adiposo/citología , Cartílago/citología , Condrogénesis , Humanos
2.
Antimicrob Agents Chemother ; 59(10): 5967-75, 2015 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-26169415

RESUMEN

Fast detection of ß-lactamase (bla) genes allows improved surveillance studies and infection control measures, which can minimize the spread of antibiotic resistance. Although several molecular diagnostic methods have been developed to detect limited bla gene types, these methods have significant limitations, such as their failure to detect almost all clinically available bla genes. We developed a fast and accurate molecular method to overcome these limitations using 62 primer pairs, which were designed through elaborate optimization processes. To verify the ability of this large-scale bla detection method (large-scaleblaFinder), assays were performed on previously reported bacterial control isolates/strains. To confirm the applicability of the large-scaleblaFinder, the assays were performed on unreported clinical isolates. With perfect specificity and sensitivity in 189 control isolates/strains and 403 clinical isolates, the large-scaleblaFinder detected almost all clinically available bla genes. Notably, the large-scaleblaFinder detected 24 additional unreported bla genes in the isolates/strains that were previously studied, suggesting that previous methods detecting only limited types of bla genes can miss unexpected bla genes existing in pathogenic bacteria, and our method has the ability to detect almost all bla genes existing in a clinical isolate. The ability of large-scaleblaFinder to detect bla genes on a large scale enables prompt application to the detection of almost all bla genes present in bacterial pathogens. The widespread use of the large-scaleblaFinder in the future will provide an important aid for monitoring the emergence and dissemination of bla genes and minimizing the spread of resistant bacteria.


Asunto(s)
Cromosomas Bacterianos/química , Cartilla de ADN/química , Reacción en Cadena de la Polimerasa Multiplex/métodos , Plásmidos/química , Resistencia betalactámica/genética , beta-Lactamasas/genética , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/enzimología , Acinetobacter baumannii/genética , Antibacterianos/farmacología , Cromosomas Bacterianos/metabolismo , Cartilla de ADN/síntesis química , Escherichia coli/efectos de los fármacos , Escherichia coli/enzimología , Escherichia coli/genética , Expresión Génica , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/enzimología , Klebsiella pneumoniae/genética , Plásmidos/metabolismo , Sensibilidad y Especificidad , Serratia marcescens/efectos de los fármacos , Serratia marcescens/enzimología , Serratia marcescens/genética , beta-Lactamasas/metabolismo , beta-Lactamas/farmacología
3.
Appl Environ Microbiol ; 81(5): 1708-14, 2015 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-25548050

RESUMEN

Genome analysis revealed the existence of a putative transcriptional regulatory system governing CO metabolism in Thermococcus onnurineus NA1, a carboxydotrophic hydrogenogenic archaeon. The regulatory system is composed of CorQ with a 4-vinyl reductase domain and CorR with a DNA-binding domain of the LysR-type transcriptional regulator family in close proximity to the CO dehydrogenase (CODH) gene cluster. Homologous genes of the CorQR pair were also found in the genomes of Thermococcus species and "Candidatus Korarchaeum cryptofilum" OPF8. In-frame deletion of either corQ or corR caused a severe impairment in CO-dependent growth and H2 production. When corQ and corR deletion mutants were complemented by introducing the corQR genes under the control of a strong promoter, the mRNA and protein levels of the CODH gene were significantly increased in a ΔCorR strain complemented with integrated corQR (ΔCorR/corQR(↑)) compared with those in the wild-type strain. In addition, the ΔCorR/corQR(↑) strain exhibited a much higher H2 production rate (5.8-fold) than the wild-type strain in a bioreactor culture. The H2 production rate (191.9 mmol liter(-1) h(-1)) and the specific H2 production rate (249.6 mmol g(-1) h(-1)) of this strain were extremely high compared with those of CO-dependent H2-producing prokaryotes reported so far. These results suggest that the corQR genes encode a positive regulatory protein pair for the expression of a CODH gene cluster. The study also illustrates that manipulation of the transcriptional regulatory system can improve biological H2 production.


Asunto(s)
Monóxido de Carbono/metabolismo , Regulación de la Expresión Génica Arqueal/efectos de los fármacos , Hidrógeno/metabolismo , Thermococcus/efectos de los fármacos , Thermococcus/genética , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Aldehído Oxidorreductasas/genética , Aldehído Oxidorreductasas/metabolismo , ADN de Archaea/química , ADN de Archaea/genética , Eliminación de Gen , Perfilación de la Expresión Génica , Prueba de Complementación Genética , Datos de Secuencia Molecular , Complejos Multienzimáticos/genética , Complejos Multienzimáticos/metabolismo , Familia de Multigenes , Análisis de Secuencia de ADN , Thermococcus/crecimiento & desarrollo
4.
Extremophiles ; 19(1): 109-18, 2015 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-25142159

RESUMEN

The F420-reducing hydrogenase has been known as a key enzyme in methanogenesis. Its homologs have been identified in non-methanogenic hyperthermophilic archaea, including Thermococcus onnurineus NA1, but neither physiological function nor biochemical properties have been reported to date. The enzyme of T. onnurineus NA1 was distinguished from those of other methanogens and the members of the family Desulfurobacteriaceae with respect to the phylogenetic distribution of the α and ß subunits, organization of frhAGB genes and conservation of F420-coordinating residues. RT-qPCR and Western blot analyses revealed frhA gene is not silent but is expressed in T. onnurineus NA1 grown in the presence of sulfur, carbon monoxide, or formate. The trimeric enzyme complex was purified to homogeneity via affinity chromatography from T. onnurineus NA1 and exhibited catalytic activity toward the electron acceptors such as viologens and flavins but not the deazaflavin coenzyme F420. This is the first biochemical study on the function of the frhAGB-encoding enzyme from a non-methanogenic archaea.


Asunto(s)
Proteínas Arqueales/genética , Hidrogenasas/genética , Thermococcus/genética , Algoritmos , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Clonación Molecular , Biología Computacional , Electrones , Concentración de Iones de Hidrógeno , Datos de Secuencia Molecular , Familia de Multigenes , Filogenia , Reacción en Cadena de la Polimerasa , Unión Proteica , Temperatura , Thermococcus/enzimología
5.
Int J Mol Sci ; 16(5): 9654-92, 2015 Apr 29.
Artículo en Inglés | MEDLINE | ID: mdl-25938965

RESUMEN

Carbapenems (imipenem, meropenem, biapenem, ertapenem, and doripenem) are ß-lactam antimicrobial agents. Because carbapenems have the broadest spectra among all ß-lactams and are primarily used to treat infections by multi-resistant Gram-negative bacteria, the emergence and spread of carbapenemases became a major public health concern. Carbapenemases are the most versatile family of ß-lactamases that are able to hydrolyze carbapenems and many other ß-lactams. According to the dependency of divalent cations for enzyme activation, carbapenemases can be divided into metallo-carbapenemases (zinc-dependent class B) and non-metallo-carbapenemases (zinc-independent classes A, C, and D). Many studies have provided various carbapenemase structures. Here we present a comprehensive and systematic review of three-dimensional structures of carbapenemase-carbapenem complexes as well as those of carbapenemases. We update recent studies in understanding the enzymatic mechanism of each class of carbapenemase, and summarize structural insights about regions and residues that are important in acquiring the carbapenemase activity.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Farmacorresistencia Microbiana , beta-Lactamasas/química , beta-Lactamasas/metabolismo , Hidrólisis , Modelos Moleculares , Relación Estructura-Actividad , Zinc/metabolismo
6.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 11): 2924-36, 2014 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-25372683

RESUMEN

Outbreaks of multidrug-resistant bacterial infections have become more frequent worldwide owing to the emergence of several different classes of ß-lactamases. In this study, the molecular, biochemical and structural characteristics of an Acinetobacter-derived cephalosporinase (ADC)-type class C ß-lactamase, ADC-68, isolated from the carbapenem-resistant A. baumannii D015 were investigated. The blaADC-68 gene which encodes ADC-68 was confirmed to exist on the chromosome via Southern blot analysis and draft genome sequencing. The catalytic kinetics of ß-lactams and their MICs (minimum inhibitory concentrations) for A. baumannii D015 and purified ADC-68 (a carbapenemase obtained from this strain) were assessed: the strain was resistant to penicillins, narrow-spectrum and extended-spectrum cephalosporins, and carbapenems, which were hydrolyzed by ADC-68. The crystal structure of ADC-68 was determined at a resolution of 1.8 Å. The structure of ADC-68 was compared with that of ADC-1 (a non-carbapenemase); differences were found in the central part of the Ω-loop and the C-loop constituting the edge of the R1 and R2 subsites and are close to the catalytic serine residue Ser66. The ADC-68 C-loop was stabilized in the open conformation of the upper R2 subsite and could better accommodate carbapenems with larger R2 side chains. Furthermore, a wide-open conformation of the R2-loop allowed ADC-68 to bind to and hydrolyze extended-spectrum cephalosporins. Therefore, ADC-68 had enhanced catalytic efficiency against these clinically important ß-lactams (extended-spectrum cephalosporins and carbapenems). ADC-68 is the first reported enzyme among the chromosomal class C ß-lactamases to possess class C extended-spectrum ß-lactamase and carbapenemase activities.


Asunto(s)
Acinetobacter baumannii/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , beta-Lactamasas/química , beta-Lactamasas/metabolismo , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/química , Acinetobacter baumannii/metabolismo , Secuencia de Aminoácidos , Secuencia de Bases , Carbapenémicos/metabolismo , Cefalosporinas/metabolismo , Cristalografía por Rayos X , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , beta-Lactamas/metabolismo
7.
New Microbiol ; 37(4): 525-33, 2014 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-25387290

RESUMEN

Mycobacterium tuberculosis genome contains eleven serine/threonine protein kinases (STPKs). Among these ST- PKs, PknA is a key component of signal transduction pathway that regulates cell shape and possibly cell division in M. tuberculosis via reversible phosphorylation of intracellular proteins. The in vitro peptide library screen showed that Wag31, a putative cell division protein, was a new substrate phosphorylated by PknA. The signal transduction pathway involving Wag31 and PknA plays a unique role in M. tuberculosis growth regulation that may participate in the pathogenesis of tuberculosis. In this study, genes of PknA, wild-type Wag31 (Wag31WT), phosphoablative Wag31T73A, and phosphomimetic Wag31T73E were cloned and expressed. Far-western analyses were performed using partial purified PknA and completely purified Wag31 proteins (Wag31WT, Wag31T73A, and Wag31T73E). Far-western analysis data revealed that the direct interaction between PknA and Wag31 is dependent on the phos- phorylation state of Wag31, which can represent a novel target for the development of new anti-tuberculosis drugs.


Asunto(s)
Proteínas Bacterianas/metabolismo , División Celular , Mycobacterium tuberculosis/enzimología , Proteínas Serina-Treonina Quinasas/metabolismo , Proteínas Bacterianas/genética , Regulación Bacteriana de la Expresión Génica , Mycobacterium tuberculosis/citología , Mycobacterium tuberculosis/genética , Fosforilación , Unión Proteica , Proteínas Serina-Treonina Quinasas/genética
8.
Proteins ; 81(11): 2045-51, 2013 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-23737193

RESUMEN

EstU1 is a unique family VIII carboxylesterase that displays hydrolytic activity toward the amide bond of clinically used ß-lactam antibiotics as well as the ester bond of p-nitrophenyl esters. EstU1 assumes a ß-lactamase-like modular architecture and contains the residues Ser100, Lys103, and Tyr218, which correspond to the three catalytic residues (Ser64, Lys67, and Tyr150, respectively) of class C ß-lactamases. The structure of the EstU1/cephalothin complex demonstrates that the active site of EstU1 is not ideally tailored to perform an efficient deacylation reaction during the hydrolysis of ß-lactam antibiotics. This result explains the weak ß-lactamase activity of EstU1 compared with class C ß-lactamases. Finally, structural and sequential comparison of EstU1 with other family VIII carboxylesterases elucidates an operative molecular strategy used by family VIII carboxylesterases to extend their substrate spectrum.


Asunto(s)
Carboxilesterasa/química , Carboxilesterasa/metabolismo , beta-Lactamasas/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Cefalotina/metabolismo , Unión Proteica , Estructura Secundaria de Proteína , beta-Lactamasas/química
9.
Appl Environ Microbiol ; 79(6): 2048-53, 2013 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-23335765

RESUMEN

Hydrogenogenic CO oxidation (CO + H(2)O → CO(2) + H(2)) has the potential for H(2) production as a clean renewable fuel. Thermococcus onnurineus NA1, which grows on CO and produces H(2), has a unique gene cluster encoding the carbon monoxide dehydrogenase (CODH) and the hydrogenase. The gene cluster was identified as essential for carboxydotrophic hydrogenogenic metabolism by gene disruption and transcriptional analysis. To develop a strain producing high levels of H(2), the gene cluster was placed under the control of a strong promoter. The resulting mutant, MC01, showed 30-fold-higher transcription of the mRNA encoding CODH, hydrogenase, and Na(+)/H(+) antiporter and a 1.8-fold-higher specific activity for CO-dependent H(2) production than did the wild-type strain. The H(2) production potential of the MC01 mutant in a bioreactor culture was 3.8-fold higher than that of the wild-type strain. The H(2) production rate of the engineered strain was severalfold higher than those of any other CO-dependent H(2)-producing prokaryotes studied to date. The engineered strain also possessed high activity for the bioconversion of industrial waste gases created as a by-product during steel production. This work represents the first demonstration of H(2) production from steel mill waste gas using a carboxydotrophic hydrogenogenic microbe.


Asunto(s)
Monóxido de Carbono/metabolismo , Hidrógeno/metabolismo , Ingeniería Metabólica , Redes y Vías Metabólicas/genética , Thermococcus/genética , Thermococcus/metabolismo , Reactores Biológicos , Expresión Génica , Perfilación de la Expresión Génica , Técnicas de Inactivación de Genes , Microbiología Industrial/métodos , Familia de Multigenes , Oxidación-Reducción , Regiones Promotoras Genéticas
10.
Sci Total Environ ; 857(Pt 2): 159497, 2023 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-36257427

RESUMEN

Antibiotic resistance is a major global public health concern. Acinetobacter baumannii is a nosocomial pathogen that has emerged as a global threat because of its high levels of resistance to many antibiotics, particularly those considered as last-resort antibiotics, such as carbapenems. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antibiotic resistance genes (ARGs), including the mobilization of ARGs within and between species. We conducted an in-depth, systematic investigation of the occurrence and dissemination of ARGs associated with MGEs in A. baumannii. We focused on a cross-sectoral approach that integrates humans, animals, and environments. Four strategies for the prevention of ARG dissemination through MGEs have been discussed: prevention of airborne transmission of ARGs using semi-permeable membrane-covered thermophilic composting; application of nanomaterials for the removal of emerging pollutants (antibiotics) and pathogens; tertiary treatment technologies for controlling ARGs and MGEs in wastewater treatment plants; and the removal of ARGs by advanced oxidation techniques. This review contemplates and evaluates the major drivers involved in the transmission of ARGs from the cross-sectoral perspective and ARG-transfer prevention processes.


Asunto(s)
Acinetobacter baumannii , Antibacterianos , Humanos , Animales , Antibacterianos/farmacología , Acinetobacter baumannii/genética , Genes Bacterianos , Farmacorresistencia Microbiana/genética , Secuencias Repetitivas Esparcidas
11.
Appl Microbiol Biotechnol ; 93(2): 623-31, 2012 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-21720822

RESUMEN

To search for novel lipolytic enzymes, a metagenomic library was constructed from the tidal flat sediment of Ganghwa Island in South Korea. By functional screening using tributyrin agar plates, 3 clones were selected from among the 80,050 clones of the fosmid library. The sequence analysis revealed that those clones contained different open reading frames, which showed 50-57% amino acid identity with putative lipolytic enzymes in the database. Based on the phylogenetic analysis, they were identified to encode novel members, which form a distinct and new subfamily in the family IV of bacterial lipolytic enzymes. The consensus sequence, GT(S)SA(G)G, encompassing the active site serine of the enzymes was different from the GDSAG motif, conserved in the other subfamily. The genes were expressed in Escherichia coli and recombinant proteins were purified as active soluble forms. The enzymes showed the highest activity toward p-nitrophenyl valerate (C5) and exhibited optimum activities at mesophilic temperature ranges and slightly alkaline pH. In particular, the enzymes displayed salt tolerance with over 50% of the maximum activity remained in the presence of 3 M NaCl (or KCl). In this study, we demonstrated that the metagenomic approach using marine tidal flat sediment as a DNA source expanded the diversity of lipolytic enzyme-encoding genes.


Asunto(s)
Inhibidores Enzimáticos/metabolismo , Esterasas/genética , Esterasas/metabolismo , Sedimentos Geológicos , Metagenoma , Sales (Química)/metabolismo , Secuencia de Aminoácidos , Análisis por Conglomerados , Estabilidad de Enzimas , Escherichia coli/genética , Escherichia coli/metabolismo , Esterasas/química , Esterasas/aislamiento & purificación , Expresión Génica , Biblioteca de Genes , Concentración de Iones de Hidrógeno , Datos de Secuencia Molecular , Filogenia , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/metabolismo , República de Corea , Análisis de Secuencia de ADN , Homología de Secuencia de Aminoácido , Especificidad por Sustrato , Temperatura
13.
Appl Environ Microbiol ; 77(21): 7830-6, 2011 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-21908637

RESUMEN

It has been proposed that family VIII carboxylesterases and class C ß-lactamases are phylogenetically related; however, none of carboxylesterases has been reported to hydrolyze ß-lactam antibiotics except nitrocefin, a nonclinical chromogenic substrate. Here, we describe the first example of a novel carboxylesterase derived from a metagenome that is able to cleave the amide bond of various ß-lactam substrates and the ester bond of p-nitrophenyl esters. A clone with lipolytic activity was selected by functional screening of a metagenomic library using tributyrin agar plates. The sequence analysis of the clone revealed the presence of an open reading frame (estU1) encoding a polypeptide of 426 amino acids, retaining an S-X-X-K motif that is conserved in class C ß-lactamases and family VIII carboxylesterases. The gene was overexpressed in Escherichia coli, and the purified recombinant protein (EstU1) was further characterized. EstU1 showed esterase activity toward various chromogenic p-nitrophenyl esters. In addition, it exhibited hydrolytic activity toward nitrocefin, leading us to investigate whether EstU1 could hydrolyze ß-lactam antibiotics. EstU1 was able to hydrolyze first-generation ß-lactam antibiotics, such as cephalosporins, cephaloridine, cephalothin, and cefazolin. In a kinetic study, EstU1 showed a similar range of substrate affinities for both p-nitrophenyl butyrate and first-generation cephalosporins while the turnover efficiency for the latter was much lower. Furthermore, site-directed mutagenesis studies revealed that the catalytic triad of EstU1 plays a crucial role in hydrolyzing both ester bonds of p-nitrophenyl esters and amide bonds of the ß-lactam ring of antibiotics, implicating the predicted catalytic triad of EstU1 in both activities.


Asunto(s)
Antibacterianos/metabolismo , Carboxilesterasa/genética , Carboxilesterasa/metabolismo , Metagenoma , beta-Lactamas/metabolismo , Dominio Catalítico , Escherichia coli/genética , Expresión Génica , Biblioteca de Genes , Hidrólisis , Cinética , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Análisis de Secuencia de ADN , Homología de Secuencia , Especificidad por Sustrato
14.
Artículo en Inglés | MEDLINE | ID: mdl-21845199

RESUMEN

Metagenomic library was constructed from a deep-sea sediment sample and screened for lipolytic activity. Open-reading frames of six positive clones showed only 33-58% amino acid identities to the known proteins. One of them was assigned to a new group while others were grouped into Families I and V or EstD Family. By employing a combination of approaches such as removing the signal sequence, coexpression of chaperone genes, and low temperature induction, we obtained five soluble recombinant proteins in Escherichia coli. The purified enzymes had optimum temperatures of 30-35°C and the cold-activity property. Among them, one enzyme showed lipase activity by preferentially hydrolyzing p-nitrophenyl palmitate and p-nitrophenyl stearate and high salt resistance with up to 4 M NaCl. Our research demonstrates the feasibility of developing novel lipolytic enzymes from marine environments by the combination of functional metagenomic approach and protein expression technology.

15.
Pharmaceuticals (Basel) ; 14(5)2021 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-34062812

RESUMEN

ß-Lactam antibiotics target penicillin-binding proteins and inhibit the synthesis of peptidoglycan, a crucial step in cell wall biosynthesis. Staphylococcus aureus acquires resistance against ß-lactam antibiotics by producing a penicillin-binding protein 2a (PBP2a), encoded by the mecA gene. PBP2a participates in peptidoglycan biosynthesis and exhibits a poor affinity towards ß-lactam antibiotics. The current study was performed to determine the diversity and the role of missense mutations of PBP2a in the antibiotic resistance mechanism. The methicillin-resistant Staphylococcus aureus (MRSA) isolates from clinical samples were identified using phenotypic and genotypic techniques. The highest frequency (60%, 18 out of 30) of MRSA was observed in wound specimens. Sequence variation analysis of the mecA gene showed four amino acid substitutions (i.e., E239K, E239R, G246E, and E447K). The E239R mutation was found to be novel. The protein-ligand docking results showed that the E239R mutation in the allosteric site of PBP2a induces conformational changes in the active site and, thus, hinders its interaction with cefoxitin. Therefore, the present report indicates that mutation in the allosteric site of PBP2a provides a more closed active site conformation than wide-type PBP2a and then causes the high-level resistance to cefoxitin.

16.
Front Pharmacol ; 12: 731828, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34512357

RESUMEN

To date, the current COVID-19 pandemic caused by SARS-CoV-2 has infected 99.2 million while killed 2.2 million people throughout the world and is still spreading widely. The unavailability of potential therapeutics against this virus urges to search and develop new drugs. SARS-CoV-2 enters human cells by interacting with human angiotensin-converting enzyme 2 (ACE2) receptor expressed on human cell surface through utilizing receptor-binding domain (RBD) of its spike glycoprotein. The RBD is highly conserved and is also a potential target for blocking its interaction with human cell surface receptor. We designed short peptides on the basis of our previously reported truncated ACE2 (tACE2) for increasing the binding affinity as well as the binding interaction network with RBD. These peptides can selectively bind to RBD with much higher affinities than the cell surface receptor. Thus, these can block all the binding residues required for binding to cell surface receptor. We used selected amino acid regions (21-40 and 65-75) of ACE2 as scaffold for the de novo peptide design. Our designed peptide Pep1 showed interactions with RBD covering almost all of its binding residues with significantly higher binding affinity (-13.2 kcal mol-1) than the cell surface receptor. The molecular dynamics (MD) simulation results showed that designed peptides form a stabilized complex with RBD. We suggest that blocking the RBD through de novo designed peptides can serve as a potential candidate for COVID-19 treatment after further clinical investigations.

17.
Front Microbiol ; 12: 752535, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-35095785

RESUMEN

Metallo-ß-lactamases (MBLs) hydrolyze almost all ß-lactam antibiotics, including penicillins, cephalosporins, and carbapenems; however, no effective inhibitors are currently clinically available. MBLs are classified into three subclasses: B1, B2, and B3. Although the amino acid sequences of MBLs are varied, their overall scaffold is well conserved. In this study, we systematically studied the primary sequences and crystal structures of all subclasses of MBLs, especially the core scaffold, the zinc-coordinating residues in the active site, and the substrate-binding pocket. We presented the conserved structural features of MBLs in the same subclass and the characteristics of MBLs of each subclass. The catalytic zinc ions are bound with four loops from the two central ß-sheets in the conserved αß/ßα sandwich fold of MBLs. The three external loops cover the zinc site(s) from the outside and simultaneously form a substrate-binding pocket. In the overall structure, B1 and B2 MBLs are more closely related to each other than they are to B3 MBLs. However, B1 and B3 MBLs have two zinc ions in the active site, while B2 MBLs have one. The substrate-binding pocket is different among all three subclasses, which is especially important for substrate specificity and drug resistance. Thus far, various classes of ß-lactam antibiotics have been developed to have modified ring structures and substituted R groups. Currently available structures of ß-lactam-bound MBLs show that the binding of ß-lactams is well conserved according to the overall chemical structure in the substrate-binding pocket. Besides ß-lactam substrates, B1 and cross-class MBL inhibitors also have distinguished differences in the chemical structure, which fit well to the substrate-binding pocket of MBLs within their inhibitory spectrum. The systematic structural comparison among B1, B2, and B3 MBLs provides in-depth insight into their substrate specificity, which will be useful for developing a clinical inhibitor targeting MBLs.

18.
Anim Cells Syst (Seoul) ; 25(1): 65-73, 2021 Feb 23.
Artículo en Inglés | MEDLINE | ID: mdl-33717418

RESUMEN

Purple corn extract (PCE) is a nutraceutical, an activator of AMPK, and it has antioxidants and anticancer properties. Therefore, PCE could be a candidate for alleviating cigarette smoke (CS)-induced oxidative DNA damage. This study examined whether PCE can have a protective effect on blood cells in an animal model of cigarette smoke (CS)-induced DNA damage. PCE was orally administered to CS-inhaled Spraque-Dawley (SD) rats, followed by the target cells being examined for markers of DNA damage. The study also sought to elucidate the mechanism of PCE action in the PCE treated animals. SD rat inhalation of CS was for once a day for 30 min, repeated for 7 days. PCE was administered orally before CS inhalation. Pretreatment of the animals with oral PCE kept the numbers of white blood cells (WBC) as well as neutrophils (NE), lymphocytes (LY), monocytes (Mo), eosinophils (EO), abd jasophils (BA) from increasing as those were increased in the CS-inhaling SD rats. The amount of phosphorylated γ-H2AX, a DNA damage marker, was assayed in the circulating blood cells collected from the animals and western blot analysis with anti-Foxo3a, p-Foxo3a, p-AMPK, MnSOD antibodies were performed on those cells. PCE protected the circulating blood cells from CS inhalation-induced DNA damage by 44% as assayed by increases in γ-H2AX. PCE also increased the nuclear localization of Foxo3a by 52% over control cells. Mechanistically, PCE appears to efficiently protect various blood cell types from CS-induced DNA damage through removal of ROS via activation of the AMPK/Foxo3a/MnSOD pathway.

19.
Microbiome ; 8(1): 75, 2020 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-32482165

RESUMEN

BACKGROUND: Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate. RESULTS: We evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and ß-lactamases, were identified. In particular, when a lenient threshold of e value of ≤ 1 × e-5 and query coverage of ≥ 60% were employed in the Resfams database, the novel ß-lactamases blaHRV-1 and blaHRVM-1 were found. These genes had unique sequences, forming distinct clades of class A and subclass B3 ß-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages. CONCLUSION: Our results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions. Video abstract.


Asunto(s)
Bacteriófagos , Metagenoma , Antibacterianos/farmacología , Bacteriófagos/genética , Farmacorresistencia Bacteriana/genética , Escherichia coli/efectos de los fármacos , Escherichia coli/genética , Agua Dulce/virología , Metagenoma/efectos de los fármacos , Metagenómica , Virus/genética
20.
Front Bioeng Biotechnol ; 8: 574010, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33195136

RESUMEN

Hutchinson-Gilford progeria syndrome (HGPS) is a rare, fatal, and genetic disorder in the LMNA gene encoding for prelamin A. Normally, prelamin A is processed to become lamin A protein. In HGPS patients, there is a heterozygous mutation in LMNA gene, in which there is a deletion of genetic codes responsible for 50 amino acids at the C-terminus of prelamin A. The processing of the abnormal prelamin A results in abnormal lamin A protein, called progerin, causing symptoms of accelerated early aging, probably due to the inflammaging process. It is well known that adipose tissue-derived mesenchymal stem cells (MSCs) have anti-inflammatory effects by modulating inflammatory cytokines and by extracellular vesicles. Here, we present a case of an HGPS patient who responded positively to injections of allogeneic haploidentical adipose tissue-derived stromal vascular fractions containing MSCs by showing rapid height and weight growth along with increased blood level of insulin-like growth factor 1.

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