RESUMEN
The novel SARS-CoV-2 is the etiological agent causing the Coronavirus disease 2019 (COVID-19), which continues to become an inevitable pandemic outbreak. Over a short span of time, the structures of therapeutic target proteins for SARS-CoV-2 were identified based on the homology modelled structure of similar virus, SARS-CoV that transmitted rapidly in 2003. Since the outset of the disease, the research community has been looking for a potential drug lead. Out of all the known resolved structures related to SARS-CoV-2; 3-chymotrypsin (3 C) like protease (3CLpro) is considered as an attractive anti-viral drug compound on the grounds of its role in viral replication and probable non-interactive competency to bind to any viral host protein. To the best of our knowledge, till date only one compound has been identified and tested in-vitro as a potent inhibitor of 3CLpro protein, addressed as N3 (PubChem Compound CID: 6323191) and is known to bind irreversibly to 3CLpro suppressing its activity. Using computational approach, we intend to identify a probable natural fungal metabolite to interact and inhibit 3CLpro. Here after performing docking and molecular dynamics of various small molecules derived as a secondary metabolite from fungi, we propose Flaviolin as potent inhibitor of 3CLpro of novel Coronavirus SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Asunto(s)
COVID-19 , Simulación de Dinámica Molecular , Hongos , Humanos , Simulación del Acoplamiento Molecular , Naftoquinonas , Inhibidores de Proteasas , SARS-CoV-2RESUMEN
The non-structural protein (nsp)-3 of SARS-CoV2 coronavirus is sought to be an essential target protein which is also named as papain-like protease (PLpro). This protease cleaves the viral polyprotein, but importantly in human host it also removes ubiquitin-like interferon-stimulated gene 15 protein (ISG15) from interferon responsive factor 3 (IRF3) protein which ultimately downregulates the production of type I interferon leading to weakening of immune response. GRL0617 is the most potent known inhibitor for PLpro that was initially developed for SARS outbreak of 2003. The PLpro of SARS-CoV and CoV2 share 83% sequence identity but interestingly have several identical conserved amino acids that suggests GRL0617 to be an effective inhibitor for PLpro of SARS-CoV2. GRL0617 is a naphthalene-based molecule and interacts with Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro). To identify PLpro inhibitors, we prepared a library of secondary metabolites from fungi with aromatic nature and docked them with PLpro of SARS-CoV and SARS-CoV2. We found six hits which interacts with Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro). More surprisingly the top hit, Fonsecin, has naphthalene moiety in its structure, which recruits Tyr268 of SARS-CoV2-PLpro (and Tyr269 of SARS-CoV-PLpro) and has binding energy at par with control (GRL0617). Molecular dynamics (MD) simulation showed Fonsecin to interact with Tyr268 of SARS-CoV2-PLpro more efficiently than control (GRL0617) and interacting with a greater number of amino acids in the binding cleft of PLpro.
Asunto(s)
Tratamiento Farmacológico de COVID-19 , Simulación de Dinámica Molecular , Compuestos de Anilina , Benzamidas , Hongos/metabolismo , Humanos , Simulación del Acoplamiento Molecular , Naftalenos , Papaína/química , Papaína/metabolismo , Péptido Hidrolasas/metabolismo , ARN Viral , SARS-CoV-2RESUMEN
Microbes possess a tremendous potential to interact with their surroundings and have continued to shape the future of all life forms existing on earth. Of all the groups of microbes, viruses are the most nefarious creatures which cannot be solely classified as living or non-living but still pose the greatest threats to the biosphere. Viruses are minuscule, diverse and are probably the only entities that exhibit non-mutualistic association with other lifeforms while retaining their ability to infect and hijack any of the existing living being on the planet. The latest global devastation, caused by novel SARS-CoV-2, is unparalleled in the last century. This review encompasses the mysterious origin of this virus by tracking its lineage, which may help to decode the conundrum of SARS-CoV-2 and shed more light on its epidemiology. The implications and the challenge posed by this virus to the scientific community to the medical community and the economy at large are reflected. Also discussed is the paradigm shift brought upon by the COVID-19 pandemic on the human psyche and their behaviour.
Asunto(s)
COVID-19 , Pandemias , COVID-19/epidemiología , Humanos , SARS-CoV-2RESUMEN
The latest global outbreak of 2019 respiratory coronavirus disease (COVID-19) is triggered by the inception of novel coronavirus SARS-CoV2. If recent events are of any indicators of the epidemics of past, it is undeniable to state a fact that the SARS-CoV2 viral infection is highly transmissible with respect to its previously related SARS-CoV's. Papain-like protease (PLpro) is an enzyme that is required by the virus itself for replicating into the host system; and it does so by processing its polyproteins into a functional replicase complex. PLpro is also known for downregulating the genes responsible for producing interferons, an essential family of molecules produced in response to viral infection, thus making this protein an indispensable drug target. In this study, PLpro inhibitors were identified through high throughput structure-based virtual screening approach from NPASS natural product library possessing ~ 35,000 compounds. Top five hits were scrutinised based on structural aromaticity and ability to interact with a key active site residue of PLpro, Tyr268. For second level of screening, the MM-GBSA End-Point Binding Free Energy Calculation of the docked complexes was performed, which identified Caesalpiniaphenol A as the best hit. Caesalpiniaphenol A not only possess a double ring aromatic moiety but also has lowest minimum binding energy, which is at par with the control GRL0617, the only known inhibitor of SARS-CoV2 PLpro. Details of the Molecular Dynamics (MD) simulation and ADMET analysis helped to conclusively determine Caesalpiniaphenol A as potentially an inhibitor of SARS-CoV2 PLpro.
Asunto(s)
Tratamiento Farmacológico de COVID-19 , Papaína , Compuestos de Anilina , Benzamidas , Humanos , Naftalenos , Péptido Hidrolasas , ARN Viral , SARS-CoV-2 , Flujo de TrabajoRESUMEN
There persists a constant threat from multidrug resistance being acquired by all human pathogens that challenges the well-being of humans. This phenomenon is predominantly led by Pseudomonas aeruginosa which is already resistant to the current generations of antibiotic by altering its metabolic pathways to survive. Specifically for this microbe the phenomenon of quorum sensing (QS) plays a crucial role in acquiring virulence and pathogenicity. QS is simply the cross talk between the bacterial community driven by signals that bind to receptors, enabling the entire bacterial microcosm to function as a single unit which has led to control P. aeruginosa cumbersome even in presence of antibiotics. Inhibition of QS can, therefore, be of a significant importance to curb such virulent and pathogenic strains of P. aeruginosa. Natural compounds are well known for their antimicrobial properties, of which, information on their mode of action is scarce. There can be many antimicrobial phytochemicals that act by hindering QS-pathways. The rationale of the current study is to identify such natural compounds that can inhibit QS in P. aeruginosa driven by LasR, PhzR, and RhlR dependent pathways. To achieve this rationale, in silico studies were first performed to identify such natural compounds which were then validated by in vitro experiments. Gingerol and Curcumin were identified as QS-antagonists (QSA) which could further suppress the production of biofilm, EPS, pyocyanin, and rhamnolipid along with improving the susceptibility to antibiotics.
Asunto(s)
Antibacterianos/farmacología , Proteínas Bacterianas/metabolismo , Catecoles/farmacología , Curcumina/farmacología , Alcoholes Grasos/farmacología , Fitoquímicos/farmacología , Infecciones por Pseudomonas/metabolismo , Pseudomonas aeruginosa/efectos de los fármacos , Percepción de Quorum/efectos de los fármacos , Transducción de Señal/efectos de los fármacos , Transactivadores/metabolismo , Biopelículas/efectos de los fármacos , Glucolípidos/metabolismo , Pruebas de Sensibilidad Microbiana , Simulación de Dinámica Molecular , Infecciones por Pseudomonas/microbiología , Pseudomonas aeruginosa/metabolismo , Pseudomonas aeruginosa/patogenicidad , Piocianina/metabolismo , Virulencia/efectos de los fármacosRESUMEN
Pseudomonas aeruginosa is recognized as a bacterium with many bullets in its armoury and the Achilles heel of the bacterium is that it exudes several pathways that lead to pathogenicity thereby making the application of the strain cautious since the bacterium is known as a 'superbug' ergo, being resistant to multiple antibiotics. The mechanisms of pathogenicity are mainly driven by quorum sensing (QS), a phenomenon that works on cell-cell communication through classical ligand-receptor interactions. QS-mediated pathways enable control of this organism impossible even with the use of antibiotics. Henceforth, interfering with the QS pathways serves as a new mode of action for futuristic antibiotics to decrease the distress of this microbe. We propose gingerol to interfere with various QS-receptors of P. aeruginosa (LasR, PhzR and RhlR) which were deduced using in silico approach and validated in vitro by assessing its impact on EPS, biofilm, pyocyanin and rhamnolipid of the microbe. Further, gingerol was found to increase the antibacterial potency of the antibiotic when applied in integration with ciprofloxacin. The findings provide an insight about preferring the integrated approach of using QS-inhibitors (QSI) in tandem with antibiotics for holistic strategy in fight against the phenomenon of antibiotic resistance acquired by microbes.
Asunto(s)
Catecoles , Farmacorresistencia Bacteriana , Alcoholes Grasos , Pseudomonas aeruginosa , Percepción de Quorum , Antibacterianos/farmacología , Catecoles/farmacología , Farmacorresistencia Bacteriana/efectos de los fármacos , Alcoholes Grasos/farmacología , Pseudomonas aeruginosa/efectos de los fármacos , Percepción de Quorum/efectos de los fármacosRESUMEN
It is the acquisition of unique traits that adds to the enigma of microbial capabilities to carry out extraordinary processes. One such ecosystem is the soil exposed to radionuclides, in the vicinity of atomic power stations. With the aim to study thorium (Th) tolerance in the indigenous bacteria of such soil, the bacteria were isolated and screened for maximum thorium tolerance. Out of all, only one strain AM3, found to tolerate extraordinary levels of Th (1500 mg L-1), was identified to be belonging to genus Providencia and showed maximum genetic similarity with the type strain P. vermicola OP1T. This is the first report suggesting any bacteria to tolerate such high Th and we propose to term such microbes as 'thoriotolerant'. The medium composition for cultivating AM3 was optimized using response surface methodology (RSM) which also led to an improvement in its Th-tolerance capabilities by 23%. AM3 was found to be a good producer of EPS and hence one component study was also employed for its optimization. Moreover, the EPS produced by the strain showed interaction with Th, which was deduced by Fourier Transform Infrared (FTIR) spectroscopy.
RESUMEN
Peptide Nucleic Acid (PNA) serves as an artificial functional analog of DNA. Being immune to enzymatic degradation and possessing strong affinity towards DNA and RNA, it is an ideal candidate for many medical and biotechnological applications that are of antisense and antigene in nature. PNAs are anticipated to have its application in DNA and RNA detection as well as quantification, to serve as antibacterial and antiviral agents, and silencing gene for developing anticancer strategies. Although, their restricted entry in both eukaryotic and prokaryotic cells limit their applications. In addition, aggregation of PNA in storage containers reduces the quality and quantity of functional PNA that makes it inadequate for their mass production and storage. To overcome these limitations, researchers have modified PNA either by the addition of diverse functional groups at various loci on its backbone, or by synthesizing chimeras with other moieties associated with various delivery agents that aids their entry into the cell. Here, this review article summarizes few of the structural modifications that are performed with PNA, methods used to improve their cellular uptake and shedding light on the applications of PNA in various prospects in biological sciences.
Asunto(s)
ADN/análisis , Ácidos Nucleicos de Péptidos/química , ARN/análisis , ADN/química , ARN/químicaRESUMEN
The current study depicts the isolation of luminescent bacteria from fish and squid samples that were collected from Veraval fish harbour. From Indian mackerel, total 14 and from squid, total 23 bioluminescent bacteria were isolated using luminescence agar medium. Two bioluminescent bacteria with highest relative luminescence intensity PBR1 and PBL1 were selected. These two isolates were subjected to detailed biochemical characterization and were tested positive for 5 out of 13 biochemical tests. Furthermore, both PBR1 and PBL1 were able to ferment cellobiose, dextrose, fructose, galactose, maltose, mannose, sucrose and trehalose with acid production. Based on 16S rRNA partial gene sequence analysis, PBR1 was identified as Vibrio alginolyticus and PBL1 as V. rotiferianus. Antibiotic susceptibility test using paper-disc method showed that PBR1 and PBL1 were sensitive to chloramphenicol, ciprofloxacin, co-trimoxazole, gatifloxacin, levofloxacin, linezolid ad roxithromycin out of 18 antibiotics tested. Moreover, both strains were evaluated for their exopolysachharide (EPS) producing ability where PBR1 and PBL1 were able to yield 1.34 g% (w/v) and 2.45 g% (w/v) EPS respectively from 5 g% (v/v) sucrose concentration. Heavy metal toxicity assessment was carried out using agar well diffusion method with eight heavy metals and both the strains were sensitive to As(III), Cd(II), Ce(II), Cr(III), Cu(II), Hg(II) and while they showed resistance to Pb(II) and Sr(II). Based on these results, a study was conducted to demonstrate bio-removal of Pb and Sr by EPS of PBR1 and PBL1. Fourier transform infrared (FTIR) spectra revealed the functional groups of EPS involved in interaction with the heavy metals. Owing to the sensitivity for the remaining heavy metals, these bioluminescent bacteria can be used further for the development of luminescence-based biosensor.
Asunto(s)
Organismos Acuáticos/microbiología , Metales Pesados/química , Polisacáridos Bacterianos/química , Vibrio alginolyticus/efectos de los fármacos , Vibrio/efectos de los fármacos , Animales , Antibacterianos/farmacología , Biodegradación Ambiental , ADN Bacteriano , Luminiscencia , Mediciones Luminiscentes , Pruebas de Sensibilidad Microbiana , Tipificación Molecular , Filogenia , ARN Ribosómico 16S/genética , Espectroscopía Infrarroja por Transformada de Fourier , Vibrio/clasificación , Vibrio/aislamiento & purificación , Vibrio alginolyticus/clasificación , Vibrio alginolyticus/aislamiento & purificaciónRESUMEN
The novel SARS-CoV-2 is the etiological agent causing the Coronavirus disease 2019 (COVID-19), which continues to become an inevitable pandemic outbreak. Over a short span of time, the structures of therapeutic target proteins for SARS-CoV-2 were identified based on the homology modelled structure of similar SARS-CoV transmission of 2003. Since the onset of the disease, the research community has been looking for a potential drug lead. Out of all the known resolved structures related to SARS-CoV, Main protease (Mpro) is considered an attractive anti-viral drug target on the grounds of its role in viral replication and probable non-interactive competency to bind to any viral host protein. To the best of our knowledge, till date only one compound has been identified and tested in-vivo as a potent inhibitor of Mpro protein, addressed as N3 (PubChem Compound CID: 6323191) and is known to bind irreversibly to Mpro suppressing its activity. Using computational approach, we intend to identify a probable natural fungal metabolite to interact and inhibit Mpro. After screening various small molecules for molecular docking and dynamics simulation, we propose Pyranonigrin A, a secondary fungal metabolite to possess potent inhibitory potential against the Main protease (Mpro) expressed in SARS-CoV-2 virus.
Asunto(s)
Antivirales/química , Betacoronavirus/enzimología , Inhibidores de Proteasas/química , Pironas/química , Pirroles/química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Betacoronavirus/patogenicidad , Sitios de Unión , Proteasas 3C de Coronavirus , Cristalografía por Rayos X , Cisteína Endopeptidasas/química , Cisteína Endopeptidasas/genética , Cisteína Endopeptidasas/metabolismo , Descubrimiento de Drogas , Expresión Génica , Enlace de Hidrógeno , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , SARS-CoV-2 , Homología de Secuencia de Aminoácido , Termodinámica , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/genética , Proteínas no Estructurales Virales/metabolismoRESUMEN
Quorum sensing in bacteria is a cell density-dependent phenomenon in which, a community of cells communicate with each other using signalling molecules belonging to various families of which N-acyl homoserine lactone (AHL) is one. AHL acts via ligand-receptor interaction where receptors of AHL differ from species to species, and possess great degree of similarity in conformation at the active site. A macromolecule, LasR, is a receptor protein that binds to N-(3-oxododecanoyl)-L-homoserinelactone (OdDHL), a type of AHL, viz. responsible for biofilm formation in Pseudomonas aeruginosa. Similar macromolecule LuxR, like LasR, found in Vibrio sp. identifies a different AHL, N-(3-oxohexanoyl)-L-homoserine lactone (OhHSL), responsible for the phenomenon of bioluminescence. In silico study depicted that curcumin could bind to both LasR and LuxR by unique sets of hydrogen bonding and hydrophobic interactions that can lead to the inactivation of these proteins, enabling this plant-derived organic AHL antagonist to be categorized as a quorum sensing inhibitor (QSI). To prove this hypothesis, curcumin was treated on P. aeruginosa to access the reduction in biofilm formation and on V. alginolyticus to check its efficacy to reduction in bioluminescence by inhibition of QS. The results of these studies proved curcumin to be an efficient QSI.
Asunto(s)
Bacterias/efectos de los fármacos , Proteínas Bacterianas/química , Curcumina/farmacología , Percepción de Quorum/efectos de los fármacos , Proteínas Represoras/química , Transactivadores/química , Acil-Butirolactonas/química , Bacterias/química , Biopelículas , Redes y Vías Metabólicas , Modelos Moleculares , Simulación del Acoplamiento Molecular , Unión Proteica , Pseudomonas aeruginosa/fisiologíaRESUMEN
The phenomenon of bioluminescence is the most widely investigated model of quorum sensing (QS) that occurs in various strains of Vibrio. Of lately, most of the virulence exhibited by other microbes is also attributed by similar quorum sensing pathways. Any leap towards blocking of such mechanisms is the need of the hour which is hypothesized to be achieved by interfering with normal QS interactions between ligands and their receptors. Gingerol, a pungent oil easily available from ginger is a structural analog of N-acylhomoserine lactone (AHL), which is an actual signalling ligand of QS-receptor LuxR responsible for initiating a cascade of reactions leading to bioluminescence. In-silico study suggested the antagonistic binding of gingerol to LuxR by hydrogen bonding and hydrophobic interactions which should, in theory, reduce bioluminescence. This was corroborated experimentally by rigorous image analysis of luminescence using hue, saturation and luminescence (HSL) values. Hence, we conclude gingerol as a potent QS-inhibitor for LuxR that may also inhibit the other members of AHL-receptor family.
Asunto(s)
Catecoles/farmacología , Alcoholes Grasos/farmacología , Mediciones Luminiscentes , Percepción de Quorum/efectos de los fármacos , Proteínas Represoras/antagonistas & inhibidores , Transactivadores/antagonistas & inhibidores , Vibrio/efectos de los fármacos , Catecoles/química , Relación Dosis-Respuesta a Droga , Alcoholes Grasos/química , Ligandos , Modelos Moleculares , Estructura Molecular , Proteínas Represoras/química , Proteínas Represoras/metabolismo , Relación Estructura-Actividad , Transactivadores/química , Transactivadores/metabolismo , Vibrio/metabolismoRESUMEN
Currently, radioactive waste is disposed primarily by burial in a deep geological repository. Microorganisms thriving in such contaminated environment show tolerance to radionuclides. In the present study the bacterial flora, from soil sample collected from an area around atomic power station exposed to radionuclides and heavy metals, was cultivated and assessed for thorium (Th) tolerance. Of all the isolates, strain AM7 identified as O. intermedium was selected since it could thrive at high levels of Th (1000â¯mgâ¯L-1). AM7 was characterized physico-chemically and its culture medium was optimized using central composite design of response surface methodology for assessing its growth properties in presence of Th. The strain also showed exceptional exopolysaccharide (EPS) production and its yield was further analyzed using one factor study to investigate the influence of each medium component. On supplementing the EPS medium with Th, no significant decrease in yield was observed. FTIR spectroscopy revealed the functional groups of EPS involved in EPS-Th binding. To the best of our knowledge, this is the first report showing exceptional Th-tolerance by any bacteria. Such study will help other researchers to strategize an environment-friendly way of radwaste disposal.
Asunto(s)
Biopolímeros/metabolismo , Ochrobactrum/efectos de la radiación , Polisacáridos Bacterianos/metabolismo , Tolerancia a Radiación , Contaminantes Radiactivos del Suelo/farmacología , Compuestos de Torio/farmacología , Consorcios Microbianos , Ochrobactrum/genética , Ochrobactrum/crecimiento & desarrollo , Ochrobactrum/metabolismo , ARN Ribosómico 16SRESUMEN
There has been a significant surge in consumption of radionuclides for various academic and commercial purposes. Correspondingly, there has been a considerable amount of generation of radioactive waste. Bacteria and archaea, being earliest inhabitants on earth serve as model microorganisms on earth. These microbes have consistently proven their mettle by surviving extreme environments, even extreme ionizing radiations. Their ability to accept and undergo stable genetic mutations have led to development of recombinant mutants that are been exploited for remediation of various pollutants such as; heavy metals, hydrocarbons and even radioactive waste (radwaste). Thus, microbes have repeatedly presented themselves to be prime candidates suitable for remediation of radwaste. It is interesting to study the behind-the-scenes interactions these microbes possess when observed in presence of radionuclides. The emphasis is on the indigenous bacteria isolated from radionuclide containing environments as well as the five fundamental interaction mechanisms that have been studied extensively, namely; bioaccumulation, biotransformation, biosorption, biosolubilisation and bioprecipitation. Application of microbes exhibiting such mechanisms in remediation of radioactive waste depends largely on the individual capability of the species. Challenges pertaining to its potential bioremediation activity is also been briefly discussed. This review provides an insight into the various mechanisms bacteria uses to tolerate, survive and carry out processes that could potentially lead the eco-friendly approach for removal of radionuclides.
Asunto(s)
Bacterias/metabolismo , Biodegradación Ambiental , Residuos Radiactivos , Radioisótopos/metabolismoRESUMEN
This work explores the problem of exercise quality measurement since it is essential for effective management of diseases like cerebral palsy (CP). This work examines the assessment of quality of large amplitude movement (LAM) exercises designed to treat CP in an automated fashion. Exercise data was collected by trained participants to generate ideal examples to use as a positive samples for machine learning. Following that, subjects were asked to deliberately make subtle errors during the exercise, such as restricting movements, as is commonly seen in cases of patients suffering from CP. The quality measurement problem was then posed as a classification to determine whether an example exercise was either "good" or "bad". Popular machine learning techniques for classification, including support vector machines (SVM), single and double-layered neural networks (NN), boosted decision trees, and dynamic time warping (DTW), were compared. The AdaBoosted tree performed best with an accuracy of 94.68% demonstrating the feasibility of assessing exercise quality.