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1.
J Biol Chem ; 300(7): 107438, 2024 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-38838778

RESUMO

HIV-1 integration into the human genome is dependent on 3'-processing of the viral DNA. Recently, we reported that the cellular Three Prime Repair Exonuclease 1 (TREX1) enhances HIV-1 integration by degrading the unprocessed viral DNA, while the integration-competent 3'-processed DNA remained resistant. Here, we describe the mechanism by which the 3'-processed HIV-1 DNA resists TREX1-mediated degradation. Our kinetic studies revealed that the rate of cleavage (kcat) of the 3'-processed DNA was significantly lower (approximately 2-2.5-fold) than the unprocessed HIV-1 DNA by TREX1. The kcat values of human TREX1 for the processed U5 and U3 DNA substrates were 3.8 s-1 and 4.5 s-1, respectively. In contrast, the unprocessed U5 and U3 substrates were cleaved at 10.2 s-1 and 9.8 s-1, respectively. The efficiency of degradation (kcat/Km) of the 3'-processed DNA (U5-70.2 and U3-28.05 pM-1s-1) was also significantly lower than the unprocessed DNA (U5-103.1 and U3-65.3 pM-1s-1). Furthermore, the binding affinity (Kd) of TREX1 was markedly lower (∼2-fold) for the 3'-processed DNA than the unprocessed DNA. Molecular docking and dynamics studies revealed distinct conformational binding modes of TREX1 with the 3'-processed and unprocessed HIV-1 DNA. Particularly, the unprocessed DNA was favorably positioned in the active site with polar interactions with the catalytic residues of TREX1. Additionally, a stable complex was formed between TREX1 and the unprocessed DNA compared the 3'-processed DNA. These results pinpoint the mechanism by which TREX1 preferentially degrades the integration-incompetent HIV-1 DNA and reveal the unique structural and conformational properties of the integration-competent 3'-processed HIV-1 DNA.

2.
BMC Bioinformatics ; 24(1): 358, 2023 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-37740175

RESUMO

BACKGROUND: Helicobacter pylori is a prominent causative agent of gastric ulceration, gastric adenocarcinoma and gastric lymphoma and have been categorised as a group 1 carcinogen by WHO. The treatment of H. pylori with proton pump inhibitors and antibiotics is effective but also leads to increased antibiotic resistance, patient dissatisfaction, and chances of reinfection. Therefore, an effective vaccine remains the most suitable prophylactic option for mass administration against this infection. RESULTS: We modelled a multi-chimera subunit vaccine candidate against H. pylori by screening its secretory/outer membrane proteins. We identified B-cell, MHC-II and IFN-γ-inducing epitopes within these proteins. The population coverage, antigenicity, physiochemical properties and secondary structure were evaluated using different in-silico tools, which showed it can be a good and effective vaccine candidate. The 3-D construct was predicted, refined, validated and docked with TLRs. Finally, we performed the molecular docking/simulation and immune simulation studies to validate the stability of interaction and in-silico cloned the epitope sequences into a pET28b(+) plasmid vector. CONCLUSION: The multiepitope-constructed vaccine contains T- cells, B-cells along with IFN-γ inducing epitopes that have the property to generate good cell-mediated immunity and humoral response. This vaccine can protect most of the world's population. The docking study and immune simulation revealed a good binding with TLRs and cell-mediated and humoral immune responses, respectively. Overall, we attempted to design a multiepitope vaccine and expect this vaccine will show an encouraging result against H. pylori infection in in-vivo use.


Assuntos
Adenocarcinoma , Helicobacter pylori , Vacinas , Humanos , Epitopos , Simulação de Acoplamento Molecular
3.
Clin Endocrinol (Oxf) ; 97(1): 43-51, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35170787

RESUMO

OBJECTIVES: To describe Asian Indian patients with 17ß hydroxysteroid dehydrogenase 3 (17ßHSD3) deficiency and to perform a systematic review to determine the factors influencing gender role in 46,XY disorder of sex development (DSD) due to 17ßHSD3 deficiency. PATIENTS AND DESIGN: We present the phenotypic and genotypic data of 10 patients (9 probands and 1 affected family member) with 17ßHSD3 deficiency from our 46,XY DSD cohort (N = 150; Western India) and a systematic review of 152 probands with genetically proven, index 17ßHSD3 deficiency patients from the world literature to identify the determinants of gender role. RESULTS: 17ßHSD3 deficiency was the third most common (6%) cause of non-dysgenetic 46,XY DSD in our cohort. Five patients each had prepubertal (atypical genitalia) and pubertal (primary amenorrhoea) presentations. Six patients were initially reared as female of whom two (one each in prepubertal and pubertal age) changed their gender role. Ten pathogenic molecular variants (six novel) were observed. In the systematic review, initial male sex of rearing was uncommon (10.5%) and was associated with atypical genitalia, higher testosterone/androstenedione (T/A) ratio and Asian origin. Gender role change to male was seen in 10.3% of patients with initial female sex of rearing and was associated with Asian origin but unrelated to pubertal androgens or molecular variant severity. It has not been reported in patients of European origin. CONCLUSIONS: We report the first Indian case series of 17ßHSD3 deficiency, the third most common cause of 46,XY DSD, with six novel molecular variants. Distinct geographical differences in the frequency of initial male sex of rearing and gender role change to male in those initially reared as females in 17ßHSD3 deficiency were noted which needs further evaluation for the underlying molecular mechanisms.


Assuntos
Transtorno 46,XY do Desenvolvimento Sexual , Transtornos do Desenvolvimento Sexual , Androstenodiona , Transtorno 46,XY do Desenvolvimento Sexual/genética , Transtornos do Desenvolvimento Sexual/genética , Feminino , Papel de Gênero , Genótipo , Humanos , Masculino
4.
Phys Chem Chem Phys ; 24(27): 16694-16700, 2022 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-35766982

RESUMO

Microtubules (MTs) are widely targeted for the treatment of various types of cancer due to their essential role in cell division. MTs are polymers made of αß-tubulin heterodimers. These α- and ß-tubulins have 8 and 10 different isotypes, respectively. It is known that a few tubulin isotypes have anti-cancer drug resistance properties, especially ßIII, which shows poor sensitivity to many potent anti-cancer drugs such as eribulin. However, the molecular-level understanding of drug-resistance due to tubulin isotype variation is poorly understood. This paper presents the study of differential binding affinities of different tubulin isotypes with the potent anti-cancer drug eribulin. Eribulin (MT destabilizer) binds at the inter-dimer interface of MTs near the vinca site and induces a lattice deformation, which results in catastrophic events in MT dynamics. In this study, sequence analysis has been done throughway and the binding sites and based on that 2α-tubulin isotypes (αI and αVIII) and 7ß tubulin isotypes (ßI, ßIIa, ßIII, ßIVa, ßVI, ßVII and ßVIII) were selected. In total, 14 combinations were prepared after building homology models of these selected isotypes. Molecular docking and molecular dynamics simulations were performed to deeply understand the binding mode of eribulin at different MT compositions. RMSD, RMSF, radius of gyration, SASA, ligand-protein interactions, and calculations of binding free energy were performed to investigate the eribulin binding variations to tubulin isotypes and it was found that αIßII showed the maximum binding affinity among all 14 systems to eribulin. The ßIII-tubulin isotype, which shows low sensitivity to eribulin in experimental results, had the least binding affinity in the system αVIIIßIII complex and the average binding affinity in the system αIßIII among all 14 systems. Additionally, we performed steered MD simulations and DynDom analysis of the systems with the lowest binding energy (αIßII) and the highest binding energy (αVIIIßIII) and extracted force, displacement, and H-bonding profiles during the pulling simulations to get a better insight.


Assuntos
Antineoplásicos , Tubulina (Proteína) , Antineoplásicos/metabolismo , Furanos , Humanos , Cetonas , Microtúbulos , Simulação de Acoplamento Molecular , Ligação Proteica , Isoformas de Proteínas/metabolismo , Tubulina (Proteína)/química
5.
Exp Parasitol ; 236-237: 108250, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35390313

RESUMO

Visceral leishmaniasis (VL) is the deadliest form of leishmaniasis without a safer treatment option. This study implies drug repurposing to find a novel antileishmanial compound, namely febrifugine dihydrochloride (FFG) targeting Leishmania antioxidant system. Starting with virtual screening revealed the high binding affinity and lead likeness of FFG against the trypanothione reductase (TR) enzyme of Leishmania donovani, followed by experimental validation. The promastigotes inhibition assay gave the IC50 concentration of FFG and Miltefosine (positive control) as 7.16 ± 1.39 nM and 11.41 ± 0.29 µM, respectively. Their CC50 was found as 451 ± 12.73 nM and 135.9 ± 5.94 µM, respectively. FFG has been shown to increase the reactive oxygen species (ROS), leading to apoptosis-like cell death among L. donovani promastigotes. Spleen touch biopsy resulted in 62% and 55% decreased parasite load with FFG and miltefosine treatment, respectively. Cytokine profiling has shown an increased proinflammatory cytokine response post-FFG treatment. Moreover, FFG is safe on the liver toxicity parameter in mice post-treatment.


Assuntos
Antiprotozoários , Leishmania donovani , Leishmaniose Visceral , Animais , Antiprotozoários/uso terapêutico , Antiprotozoários/toxicidade , Citocinas/metabolismo , Leishmaniose Visceral/parasitologia , Camundongos , Camundongos Endogâmicos BALB C , Piperidinas , Quinazolinas
6.
J Recept Signal Transduct Res ; 37(1): 60-70, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-27147242

RESUMO

Visceral leishmaniasis (VL) is the most fatal form of leishmaniasis and it affects 70 countries worldwide. Increasing drug resistant for antileishmanial drugs such as miltefosine, sodium stibogluconate and pentamidine has been reported in the VL endemic region. Amphotericin B has shown potential antileishmanial activity in different formulations but its cost of treatment and associated nephrotoxicity have limited its use by affected people living in the endemic zone. To control the VL infection in the affected countries, it is necessary to develop new antileishmanial compounds with high efficacy and negligible toxicity. Computer aided programs such as binding free energy estimation; ADMET prediction and molecular dynamics simulation can be used to investigate novel antileishmanial molecules in shorter duration. To develop antileishmanial lead molecule, we performed standard precision (SP) docking for 1160 benzoxaborole analogs along with reference inhibitors against trypanothione reductase of Leishmania parasite. Furthermore, extra precision (XP) docking, ADMET prediction, prime MM-GBSA was conducted over 115 ligands, showing better docking score than reference inhibitors to get potential antileishmanial compounds. Simultaneously, area under the curve (AUC) was estimated using ROC plot to validate the SP and XP docking protocol. Later on, two benzoxaborole analogs with best MM-GBSA ΔG-bind were subjected to molecular simulation and docking confirmation to ensure the ligand interaction with TR. The presented drug discovery based on computational study confirms that BOB27 can be used as a potential drug candidate and warrants further experimental investigation to fight against VL in endemic areas.


Assuntos
Antiprotozoários/química , Antiprotozoários/farmacologia , Compostos de Boro/química , Descoberta de Drogas , Isoxazóis/química , Leishmania donovani/enzimologia , NADH NADPH Oxirredutases/antagonistas & inibidores , Simulação por Computador , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Humanos , Leishmania donovani/efeitos dos fármacos , Leishmaniose Visceral/parasitologia , Leishmaniose Visceral/prevenção & controle , Simulação de Acoplamento Molecular , Estrutura Molecular , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estrutura Terciária de Proteína , Relação Estrutura-Atividade
7.
Adv Protein Chem Struct Biol ; 140: 157-198, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38762269

RESUMO

Chimeric Antigen Receptor (CAR) T cell therapy is a type of adoptive immunotherapy that offers a promising avenue for enhancing cancer treatment since traditional cancer treatments like chemotherapy, surgery, and radiation therapy have proven insufficient in completely eradicating tumors, despite the relatively positive outcomes. It has been observed that CAR-T cell therapy has shown promising results in treating the majority of hematological malignancies but also have a wide scope for other cancer types. CAR is an extra receptor on the T-cell that helps to increase and accelerate tumor destruction by efficiently activating the immune system. It is made up of three domains, the ectodomain, transmembrane, and the endodomain. The ectodomain is essential for antigen recognition and binding, whereas the co-stimulatory signal is transduced by the endodomain. To date, the Food and Drug Administration (FDA) has granted approval for six CAR-T cell therapies. However, despite its remarkable success, CAR-T therapy is associated with numerous adverse events and has certain limitations. This chapter focuses on the structure and function of the CAR domain, various generations of CAR, and the process of CAR-T cell development, adverse effects, and challenges in CAR-T therapy. CAR-T cell therapy also has scopes in other disease conditions which include systemic lupus erythematosus, multiple sclerosis, and myocardial fibrosis, etc.


Assuntos
Neoplasias , Receptores de Antígenos Quiméricos , Humanos , Neoplasias/terapia , Neoplasias/imunologia , Receptores de Antígenos Quiméricos/imunologia , Linfócitos T/imunologia , Linfócitos T/transplante , Linfócitos T/metabolismo , Imunoterapia Adotiva , Animais , Imunoterapia
8.
mBio ; 15(1): e0021222, 2024 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-38085100

RESUMO

IMPORTANCE: HIV-1 capsid protein (CA)-independently or by recruiting host factors-mediates several key steps of virus replication in the cytoplasm and nucleus of the target cell. Research in the recent years have established that CA is multifunctional and genetically fragile of all the HIV-1 proteins. Accordingly, CA has emerged as a validated and high priority therapeutic target, and the first CA-targeting antiviral drug was recently approved for treating multi-drug resistant HIV-1 infection. However, development of next generation CA inhibitors depends on a better understanding of CA's known roles, as well as probing of CA's novel roles, in HIV-1 replication. In this timely review, we present an updated overview of the current state of our understanding of CA's multifunctional role in HIV-1 replication-with a special emphasis on CA's newfound post-nuclear roles, highlight the pressing knowledge gaps, and discuss directions for future research.


Assuntos
Infecções por HIV , Soropositividade para HIV , HIV-1 , Humanos , Capsídeo/metabolismo , Proteínas do Capsídeo/genética , Proteínas do Capsídeo/metabolismo , DNA Viral/genética , DNA Viral/metabolismo , HIV-1/genética , HIV-1/metabolismo , Soropositividade para HIV/metabolismo , Replicação Viral/genética , Integração Viral
9.
bioRxiv ; 2024 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-38562877

RESUMO

HIV-1 integration into the human genome is dependent on 3'-processing of the reverse transcribed viral DNA. Recently, we reported that the cellular Three Prime Repair Exonuclease 1 (TREX1) enhances HIV-1 integration by degrading the unprocessed viral DNA, while the integration-competent 3'-processed DNA remained resistant. Here, we describe the mechanism by which the 3'-processed HIV-1 DNA resists TREX1-mediated degradation. Our kinetic studies revealed that the rate of cleavage (kcat) of the 3'-processed DNA was significantly lower than the unprocessed HIV-1 DNA by TREX1. The efficiency of degradation (kcat/KM) of the 3'-processed DNA was also significantly lower than the unprocessed DNA. Furthermore, the binding affinity (Kd) of TREX1 was markedly lower to the 3'-processed DNA compared to the unprocessed DNA. Molecular docking and dynamics studies revealed distinct conformational binding modes of TREX1 with the 3'-processed and unprocessed HIV-1 DNA. Particularly, the unprocessed DNA was favorably positioned in the active site with polar interactions with the catalytic residues of TREX1. Additionally, a stable complex was formed between TREX1 and the unprocessed DNA compared the 3'-processed DNA. These results pinpoint the biochemical mechanism by which TREX1 preferentially degrades the integration-incompetent HIV-1 DNA and reveal the unique structural and conformational properties of the integration-competent 3'-processed HIV-1 DNA.

10.
Vaccines (Basel) ; 11(7)2023 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-37514998

RESUMO

The JC polyomavirus virus (JCPyV) affects more than 80% of the human population in their early life stage. It mainly affects immunocompromised individuals where virus replication in oligodendrocytes and astrocytes may lead to fatal progressive multifocal encephalopathy (PML). Virus protein 1 (VP1) is one of the major structural proteins of the viral capsid, responsible for keeping the virus alive in the gastrointestinal and urinary tracts. VP1 is often targeted for antiviral drug and vaccine development. Similarly, this study implied immune-informatics and molecular modeling methods to design a multi-epitope subunit vaccine targeting JCPyV. The VP1 protein epitopic sequences, which are highly conserved, were used to build the vaccine. This designed vaccine includes two adjuvants, five HTL epitopes, five CTL epitopes, and two BCL epitopes to stimulate cellular, humoral, and innate immune responses against the JCPyV. Furthermore, molecular dynamics simulation (100 ns) studies were used to examine the interaction and stability of the vaccine protein with TLR4. Trajectory analysis showed that the vaccine and TLR4 receptor form a stable complex. Overall, this study may contribute to the path of vaccine development against JCPyV.

11.
J Biomol Struct Dyn ; 41(9): 3943-3955, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-35382699

RESUMO

The COVID-19 is declared a pandemic by World Health Organization (WHO). It causes respiratory illness which leads to oxygen deficiency; it has affected millions of lives all around the globe. It has also been observed that people with diabetes condition are more likely to have severe symptoms when infected with the SARS-CoV2. So, continued efforts are being taken to design and discover potential anti-covid drugs. Earlier, a study reveals that the acetonitrile (2-phenyl-4H-benzopyrimedo [2,1-b]-thiazol-4-yliden) derivatives have potential anti-diabetic activity. Hence, drugs repurpose approach was used to identify the potential acetonitrile derivative targeting the main protease of SARS-CoV2. Here, ADMET, molecular docking, and molecular dynamics simulation techniques were employed, to identify potential acetonitrile compounds against the main protease. The acetonitrile compounds (A to M) show the drug-likeness properties. Next, the molecular docking and dynamics simulation study reveals that acetonitrile compounds A, F, G, and L show a higher binding affinity and have an effect on the structure and dynamics of the main protease. Furthermore, binding energy calculations reveal that the acetonitrile derivative F has a higher binding affinity with the main protease and derivative L has a lower binding affinity with the main protease. The binding affinity of acetonitrile derivatives decreases in the order of F > A > G > L with the main protease. Thus, our computational modeling study provides valuable structural and energetic information of interaction of potential acetonitrile derivatives with the main protease which could be further used as potential lead molecules against the SARS-CoV2.Communicated by Ramaswamy H. Sarma.


Assuntos
COVID-19 , RNA Viral , Humanos , Simulação de Acoplamento Molecular , SARS-CoV-2 , Proteases 3C de Coronavírus , Simulação de Dinâmica Molecular , Acetonitrilas , Inibidores de Proteases/farmacologia
12.
Gene ; 872: 147443, 2023 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-37105505

RESUMO

Schizophrenia is a complex neuropsychiatric disorder and heritability is as high as 80 % making it the most heritable mental disorder. Although GWAS has identified numerous variants, the pathophysiology is still elusive. Here, an attempt was made to identify genetic risk factors in familial cases of schizophrenia that are associated with a common causative pathway. To achieve this objective, exome sequencing was done in 4 familial cases and identified six unique coding variants in five genes. Among these genes, PIGQ gene has two pathogenic variants, one nonsense and in-frame deletion. One missense variant in GALNT16 and one in GALNT5 have variable damaging score, however, the other variants, in ADAMTS9 and in LTBP4 have the highest damaging score. Further analysis showed that the variant of LTBP4 was not present in the functional domain. The other missense variant in the ADAMTS9 gene was found to be significant and was present in the thrombospondin repeat motif, one of the important motifs. Detailed molecular dynamics simulation study on this variant showed a damaging effect on structural stability. Since, all these genes culminated into the glycosylation process, it was evident that an aberrant glycosylation process may be one of the risk factors. Although, extracellular matrix formation through glycosylation have been shown to be associated, the involvement of ADAMTS9 and PIGQ gene mediated glycosylation has not been reported. In this paper, a novel link between ADAMTS9 and PIGQ gene with schizophrenia have been reported. Therefore, this novel observation has contributed immensely to the existing knowledge on risk factor of Schizophrenia.


Assuntos
Transtornos Psicóticos , Esquizofrenia , Humanos , Esquizofrenia/genética , Glicosilação , Predisposição Genética para Doença , Mutação de Sentido Incorreto , Proteína ADAMTS9/genética , Proteínas de Membrana/genética
13.
Nat Commun ; 14(1): 140, 2023 01 10.
Artigo em Inglês | MEDLINE | ID: mdl-36627272

RESUMO

Species within the Enterobacter cloacae complex (ECC) include globally important nosocomial pathogens. A three-year study of ECC in Germany identified Enterobacter xiangfangensis as the most common species (65.5%) detected, a result replicated by examining a global pool of 3246 isolates. Antibiotic resistance profiling revealed widespread resistance and heteroresistance to the antibiotic colistin and detected the mobile colistin resistance (mcr)-9 gene in 19.2% of all isolates. We show that resistance and heteroresistance properties depend on the chromosomal arnBCADTEF gene cassette whose products catalyze transfer of L-Ara4N to lipid A. Using comparative genomics, mutational analysis, and quantitative lipid A profiling we demonstrate that intrinsic lipid A modification levels are genospecies-dependent and governed by allelic variations in phoPQ and mgrB, that encode a two-component sensor-activator system and specific inhibitor peptide. By generating phoPQ chimeras and combining them with mgrB alleles, we show that interactions at the pH-sensing interface of the sensory histidine kinase phoQ dictate arnBCADTEF expression levels. To minimize therapeutic failures, we developed an assay that accurately detects colistin resistance levels for any ECC isolate.


Assuntos
Colistina , Lipídeo A , Colistina/farmacologia , Colistina/uso terapêutico , Lipídeo A/química , Lipídeo A/farmacologia , Proteínas de Bactérias/metabolismo , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Enterobacter/genética , Farmacorresistência Bacteriana/genética , Testes de Sensibilidade Microbiana
14.
Struct Chem ; : 1-16, 2022 Dec 17.
Artigo em Inglês | MEDLINE | ID: mdl-36570051

RESUMO

SARS-CoV-2 and its variants cause serious health concerns throughout the world. The alarming increase in the daily number of cases has become a nightmare in many low-income countries; although some vaccines are available, their high cost and low vaccine production make them unreachable to ordinary people in developing countries. Other treatment strategies are required for novel therapeutic options. The peptide-based drug is one of the alternatives with low toxicity, more specificity, and ease of synthesis. Herein, we have applied structure-based virtual screening to identify potential peptides targeting the critical proteins of SARS-CoV-2. Non-toxic natural antiviral peptides were selected from the enormous number of peptides. Comparative modeling was applied to prepare a 3D structure of selected peptides. 3D models of the peptides were docked using the ClusPro docking server to determine their binding affinity and peptide-protein interaction. The high-scoring peptides were docked with other crucial proteins to analyze multiple targeting peptides. The two best peptides were subjected to MD simulations to validate the structure stability and evaluated RMSD, RMSF, Rg, SASA, and H-bonding from the trajectory analysis of 100 ns. The proposed lead peptides can be used as a broad-spectrum drug and potentially develop as a therapeutic to combat SARS-CoV-2, positively impacting the current pandemic. Supplementary Information: The online version contains supplementary material available at 10.1007/s11224-022-02113-9.

15.
Biomed Res Int ; 2022: 8221622, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35586806

RESUMO

Staphylococcus aureus is a major human bacterial pathogen that carries a large number of virulence factors. Many virulence factors of S. aureus are regulated by the accessory gene regulator (agr) quorum-sensing system. Phenol-soluble modulins (PSMs) are one of the agr-mediated virulence determinants known to play a significant role in S. aureus pathogenesis. In the present study, the efficacy of thymol to inhibit PSM production including δ-toxin in S. aureus was explored. We employed liquid chromatography-mass spectrometry (LC-MS) to quantify the PSMsα1-PSMα4, PSMß1 and PSMß2, and δ-toxin production from culture supernatants. We found that thymol at 0.5 MIC (128 µg/mL) significantly reduced the PSMα and δ-toxin production in S. aureus WKZ-1, WKZ-2, LAC USA300, and ATCC29213. Downregulation in transcription by quantitative real-time (qRT) PCR analysis of response regulator agrA and receptor histidine kinase agrC upon 0.5 MIC thymol treatment affirmed the results of LC-MS quantification of PSMs. In silico molecular docking analysis demonstrated the binding affinity of thymol with receptors AgrA and AgrC. Transmission electron microscopy images revealed no ultrastructural alterations (cell wall and membrane) in thymol-treated WKZ-1 and WKZ-2 S. aureus strains. Here, we demonstrated that thymol reduces various PSM production in S. aureus clinical isolates and reference strains with mass spectrometry.


Assuntos
Toxinas Bacterianas , Staphylococcus aureus , Timol , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Humanos , Simulação de Acoplamento Molecular , Percepção de Quorum , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/isolamento & purificação , Staphylococcus aureus/metabolismo , Staphylococcus aureus/patogenicidade , Timol/farmacologia , Fatores de Virulência/genética , Fatores de Virulência/metabolismo
16.
Sci Rep ; 12(1): 11526, 2022 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-35798871

RESUMO

A novel tetraphenylethylene (TPE) functionalized aminoglycoside antibiotic kanamycin (TPE-kana 1) has been successfully synthesized and characterized by means of modern analytical and spectroscopic techniques. The probe TPE-kana 1 showed strong affinity towards bovine serum albumin (BSA) compared to its other biological competitors. The recognition of BSA have been investigated employing UV-Vis absorption and fluorescence emission spectroscopy. The significant color change of TPE-kana 1 with BSA can be observed by necked eye, where the role of AIE-active TPE molecule is handle in both optical and colorimetric changes. The quenching of fluorescence of TPE-kana 1 with BSA was characterized by fluorescence spectroscopy, with 71.16% of quenching efficiency. Moreover, the Stern-Volmer quenching constant was calculated and found to be 2.46 × 107 M-1. Probe TPE-kana 1 showed detection limit of 2.87 nM (nM) towards BSA with binding constant 7.56 × 107 M. A molecular docking study is also performed to investigate the detail interactions between TPE-kana 1 with the sites of BSA via non-covalent i.e., H-bonding, π-cation interactions, π-donor hydrogen bonds and π-π interactions. The lowest binding energy conformation was found at - 10.42 kcal/mol.


Assuntos
Sondas Moleculares , Soroalbumina Bovina , Aminoglicosídeos , Antibacterianos , Sítios de Ligação , Canamicina , Simulação de Acoplamento Molecular , Ligação Proteica , Soroalbumina Bovina/química , Espectrometria de Fluorescência , Espectrofotometria Ultravioleta , Estilbenos , Termodinâmica
17.
J Ayurveda Integr Med ; 13(2): 100542, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35228151

RESUMO

BACKGROUND: In Aayurveda, Blumea eriantha DC has been used in the management of various diseases and is found to exhibit antioxidant and anti-hyperlipidemic, hypoglycemic, anti-diarrhoeal, larvicidal, antimicrobial properties. OBJECTIVE: The present study has focused on isolation of the active fraction from B. eriantha DC extract and to investigate its effect as a hair growth promoter along with identification of phytoconstituent(s) responsible for hair growth activity and its probable mechanism of action. MATERIALS AND METHODS: Our work introduces an effective isolation protocol for the active fraction from B. eriantha DC extract using chromatographic techniques. Fraction A was isolated by using mobile phase toluene:acetone (9:1). In-vitro and in-vivo methods were executed for the evaluation of hair growth activity. Moreover, the docked conformations of the isolated phytoconstituent Dimethyl sulfone was compared to Minoxidil for selected proteins namely 2FGF, 2PVC and 4U7P. The PDB identifications 2PVC (DNMT3L recognizes unmethylated histone H3 lysine 4), 4U7P (Crystal structure of DNMT3A-DNMT3L complex and 2FGF (Human Basic Fibroblast Growth Factor) were downloaded from Protein Data Bank. RESULTS: The study data revealed that B. eriantha DC alcoholic extracts exhibited prominent hair growth activity and it was affirmed that Dimethyl sulfone a phyto-constituent isolated from B. eriantha DC alcoholic extract contributed for the same. CONCLUSION: The findings strongly suggest hair growth promotion potential of the extract of B. eriantha DC.

18.
3 Biotech ; 12(3): 66, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-35186663

RESUMO

Potato leafroll virus (PLRV) uses powerful molecular machines to package its genome into a viral capsid employing ATP as fuel. Although, recent bioinformatics and structural studies have revealed detailed mechanism of DNA packaging, little is known about the mechanochemistry of genome packaging in small plant viruses such as PLRV. We have identified a novel P-loop-containing ATPase domain with two Walker A-like motifs, two arginine fingers, and two sensor motifs distributed throughout the polypeptide chain of PLRV capsid protein (CP). The composition and arrangement of the ATP binding and hydrolysis domain of PLRV CP is unique and rarely reported. The discovery of the system sheds new light on the mechanism of viral genome packaging, regulation of viral assembly process, and evolution of plant viruses. Here, we used the RNAi approach to suppress CP gene expression, which in turn prevented PLRV genome packaging and assembly in Solanum tuberosum cv. Khufri Ashoka. Potato plants agroinfiltrated with siRNA constructs against the CP with ATPase domain exhibited no rolling symptoms upon PLRV infection, indicating that the silencing of CP gene expression is an efficient method for generating PLRV-resistant potato plants. In addition, molecular docking study reveals that the PLRV CP protein has ATP-binding pocket at the interface of each monomer. This further confirms that knockdown of the CP harboring ATP-binding domain could hamper the process of viral genome packaging and assembly. Moreover, our findings provide a robust approach to generate PLRV-resistant potato plants, which can be further extended to other species. Finally, we propose a new mechanism of genome packaging and assembly in plant viruses.

19.
J Biomol Struct Dyn ; 39(6): 1990-2002, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32241247

RESUMO

Microtubules (MTs) play an essential role in mitosis; hence they are identified as potential targets to design novel anti-mitotic agents. MT's are composed of α/ß-tubulin isotypes that are associated with differential drug-resistant effects against MT-targeting agents. Peloruside-A (PLA) is a potent anti-mitotic agent showing excellent activity against taxol-resistant carcinoma. PLA alters MT dynamics by binding to the 'non-taxoid' site of ß-tubulin. The abundance of ßII and ßIII tubulin isotypes in human ovarian carcinoma affects the efficacy of PLA. Nevertheless, the mechanism of PLA resistance due to ßII and ßIII tubulin isotype is not well understood. Therefore, we investigated the interactions of PLA with αßIIa, αßIIb, and αßIII tubulin isotypes which are predominantly expressed in the human ovarian carcinoma, using a molecular modeling approach. A sequence analysis study shows that the ßIII isotype has seven residue variations at the 'non-taxoid' site compared to the ßIIa and ßIIb isotypes. Molecular docking and molecular dynamics simulation revealed that residue variation at the 'non-taxoid' site of ßIII isotype affect PLA binding. Furthermore, binding energy calculations showed that αßIIa has the highest binding towards PLA, whereas αßIIb and αßIII isotypes shows weaker associations with PLA. Our computational study provides valuable structural and energetic information to increase understanding into the origin of PLA resistance in human ovarian carcinoma and could be helpful to develop potential PLA analogs against specific ß-tubulin isotypes expressed in cancer cells.Communicated by Ramaswamy H. Sarma.


Assuntos
Antibióticos Antineoplásicos/farmacologia , Compostos Bicíclicos Heterocíclicos com Pontes/farmacologia , Carcinoma , Resistencia a Medicamentos Antineoplásicos , Lactonas/farmacologia , Neoplasias Ovarianas , Carcinoma/metabolismo , Feminino , Humanos , Microtúbulos/metabolismo , Simulação de Acoplamento Molecular , Neoplasias Ovarianas/tratamento farmacológico , Neoplasias Ovarianas/genética , Neoplasias Ovarianas/metabolismo , Ligação Proteica , Tubulina (Proteína)/metabolismo
20.
Immunobiology ; 226(2): 152053, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33517154

RESUMO

Vaccination is the best strategy for the control and prevention of contagious diseases caused by Influenza A viruses. Extraordinary genetic variability and continual evolvability are responsible for the virus having survival and adaptation to host cell immune response, thus rendering the current influenza vaccines with suboptimal effectiveness.Therefore, in the present study, using a novel immunoinformatics approach, we have designed a universal influenza subunit vaccine based on the highly conserved epitopic sequences of rapidly evolving (HA), a moderately evolving (NP) and slow evolving (M1) proteins of the virus. The vaccine design includes 2 peptide adjuvants, 26 CTL epitopes, 9 HTL epitopes, and 7 linear BCL epitopes to induce innate, cellular, and humoral immune responses against Influenza A viruses. We also analyzed the physicochemical properties of the designed construct to validate its thermodynamic stability, hydrophilicity, PI, antigenicity, and allergenicity. Furthermore, we predicted a highly stable tertiary model of the designed subunit vaccine, wherein additional disulfide bonds were incorporated to enhance its stability. The molecular docking and molecular dynamics simulations of the refined vaccine model with TLR3, TLR7, TLR8, MHC-I and MHC-II showed stable vaccine and receptors complexes, thus confirming the immunogenicity of the designed vaccine. Collectively, these findings suggest that our multi-epitope vaccine construct may confer protection against various strains of influenza A virus subtypes, which could prevent the need for annual reformulation of vaccine and alleviate disease burden.


Assuntos
Epitopos de Linfócito B/imunologia , Epitopos de Linfócito T/imunologia , Vírus da Influenza A , Vacinas contra Influenza , Influenza Humana/prevenção & controle , Vacinas de Subunidades Antigênicas , Biologia Computacional , Epitopos de Linfócito B/genética , Epitopos de Linfócito T/genética , Antígenos de Histocompatibilidade Classe I , Antígenos de Histocompatibilidade Classe II/imunologia , Humanos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Receptores Toll-Like/imunologia
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