68 results on '"Sonam Grover"'
Search Results
2. Computational analysis of RNA methyltransferase Rv3366 as a potential drug target for combating drug-resistant Mycobacterium tuberculosis
- Author
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Tasmin Nazim, Vipul Kumar, Faraz Ahmed, Nasreen Z. Ehtesham, Seyed E. Hasnain, Durai Sundar, and Sonam Grover
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Droxidopa ,Levodopa ,MDR ,MTases ,TB ,XDR ,Biology (General) ,QH301-705.5 - Abstract
Mycobacterium tuberculosis (M.tb) remains a formidable global health threat. The increasing drug resistance among M.tb clinical isolates is exacerbating the current tuberculosis (TB) burden. In this study we focused on identifying novel repurposed drugs that could be further investigated as potential anti-TB drugs. We utilized M.tb RNA methyltransferase Rv3366 (spoU) as a potential drug target due to its imperative activity in RNA modification and no structural homology with human proteins. Using computational modeling approaches the structure of Rv3366 was determined followed by high throughput virtual screening of Food and Drug Administration (FDA) approved drugs to screen potential binders of Rv3366. Molecular dynamics (MD) simulations were performed to assess the drug-protein binding interactions, complex stability and rigidity. Through this multi-step structure-based drug repurposing workflow two promising inhibitors of Rv3366 were identified, namely, Levodopa and Droxidopa. This study highlights the significance of targeting M.tb RNA methyltransferases to combat drug-resistant M.tb. and proposes Levodopa and Droxidopa as promising inhibitors of Rv3366 for future pre-clinical investigations.
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- 2024
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3. An immunoinformatics approach to design a multi-epitope vaccine against Mycobacterium tuberculosis exploiting secreted exosome proteins
- Author
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Rahul Sharma, Vikrant Singh Rajput, Salma Jamal, Abhinav Grover, and Sonam Grover
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Medicine ,Science - Abstract
Abstract Tuberculosis is one the oldest known affliction of mankind caused by the pathogen Mycobacterium tuberculosis. Till date, there is no absolute single treatment available to deal with the pathogen, which has acquired a great potential to develop drug resistance rapidly. BCG is the only anti-tuberculosis vaccine available till date which displays limited global efficacy due to genetic variation and concurrent pathogen infections. Extracellular vesicles or exosomes vesicle (EVs) lie at the frontier cellular talk between pathogen and the host, and therefore play a significant role in establishing pathogenesis. In the present study, an in-silico approach has been adopted to construct a multi-epitope vaccine from selected immunogenic EVs proteins to elicit a cellular as well as a humoral immune response. Our designed vaccine has wide population coverage and can effectively compensate for the genetic variation among different populations. For maximum efficacy and minimum adverse effects possibilities the antigenic, non-allergenic and non-toxic B-cell, HTL and CTL epitopes from experimentally proven EVs proteins were selected for the vaccine construct. TLR4 agonist RpfE served as an adjuvant for the vaccine construct. The vaccine construct structure was modelled, refined and docked on TLR4 immune receptor. The designed vaccine construct displayed safe usage and exhibits a high probability to elicit the critical immune regulators, like B cells, T-cells and memory cells as displayed by the in-silico immunization assays. Therefore, it can be further corroborated using in vitro and in vivo assays to fulfil the global need for a more efficacious anti-tuberculosis vaccine.
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- 2021
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4. Predicting phosphorylation sites using machine learning by integrating the sequence, structure, and functional information of proteins
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Salma Jamal, Waseem Ali, Priya Nagpal, Abhinav Grover, and Sonam Grover
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Post-translational modification ,MRMR ,Symmetrical uncertainty ,Random forest ,Support vector machine ,Medicine - Abstract
Abstract Background Post-translational modification (PTM) is a biological process that alters proteins and is therefore involved in the regulation of various cellular activities and pathogenesis. Protein phosphorylation is an essential process and one of the most-studied PTMs: it occurs when a phosphate group is added to serine (Ser, S), threonine (Thr, T), or tyrosine (Tyr, Y) residue. Dysregulation of protein phosphorylation can lead to various diseases—most commonly neurological disorders, Alzheimer’s disease, and Parkinson’s disease—thus necessitating the prediction of S/T/Y residues that can be phosphorylated in an uncharacterized amino acid sequence. Despite a surplus of sequencing data, current experimental methods of PTM prediction are time-consuming, costly, and error-prone, so a number of computational methods have been proposed to replace them. However, phosphorylation prediction remains limited, owing to substrate specificity, performance, and the diversity of its features. Methods In the present study we propose machine-learning-based predictors that use the physicochemical, sequence, structural, and functional information of proteins to classify S/T/Y phosphorylation sites. Rigorous feature selection, the minimum redundancy/maximum relevance approach, and the symmetrical uncertainty method were employed to extract the most informative features to train the models. Results The RF and SVM models generated using diverse feature types in the present study were highly accurate as is evident from good values for different statistical measures. Moreover, independent test sets and benchmark validations indicated that the proposed method clearly outperformed the existing methods, demonstrating its ability to accurately predict protein phosphorylation. Conclusions The results obtained in the present work indicate that the proposed computational methodology can be effectively used for predicting putative phosphorylation sites further facilitating discovery of various biological processes mechanisms.
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- 2021
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5. Cytotoxic T-lymphocyte elicited vaccine against SARS-CoV-2 employing immunoinformatics framework
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Neeraj Kumar, Nikita Admane, Anchala Kumari, Damini Sood, Sonam Grover, Vijay Kumar Prajapati, Ramesh Chandra, and Abhinav Grover
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Medicine ,Science - Abstract
Abstract Development of effective counteragents against the novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains, requires clear insights and information for understanding the immune responses associated with it. This global pandemic has pushed the healthcare system and restricted the movement of people and succumbing of the available therapeutics utterly warrants the development of a potential vaccine to contest the deadly situation. In the present study, highly efficacious, immunodominant cytotoxic T-lymphocyte (CTL) epitopes were predicted by advanced immunoinformatics assays using the spike glycoprotein of SARS-CoV2, generating a robust and specific immune response with convincing immunological parameters (Antigenicity, TAP affinity, MHC binder) engendering an efficient viral vaccine. The molecular docking studies show strong binding of the CTL construct with MHC-1 and host membrane specific TLR2 receptors. The molecular dynamics simulation in an explicit system confirmed the stable and robust binding of CTL epitope with TLR2. Steep magnitude RMSD variation and compelling residual fluctuations existed in terminal residues and various loops of the β linker segments of TLR2-epitope (residues 105-156 and 239-254) to about 0.4 nm. The reduced Rg value (3.3 nm) and stagnant SASA analysis (275 nm/S2/N after 8 ns and 5 ns) for protein surface and its orientation in the exposed and buried regions suggests more compactness due to the strong binding interaction of the epitope. The CTL vaccine candidate establishes a high capability to elicit the critical immune regulators, like T-cells and memory cells as proven by the in silico immunization assays and can be further corroborated through in vitro and in vivo assays.
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- 2021
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6. Computational models for the prediction of adverse cardiovascular drug reactions
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Salma Jamal, Waseem Ali, Priya Nagpal, Sonam Grover, and Abhinav Grover
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Adverse drug reactions ,Machine learning ,Random forest ,Sequential minimization optimization ,Feature selection ,Medicine - Abstract
Abstract Background Predicting adverse drug reactions (ADRs) has become very important owing to the huge global health burden and failure of drugs. This indicates a need for prior prediction of probable ADRs in preclinical stages which can improve drug failures and reduce the time and cost of development thus providing efficient and safer therapeutic options for patients. Though several approaches have been put forward for in silico ADR prediction, there is still room for improvement. Methods In the present work, we have used machine learning based approach for cardiovascular (CV) ADRs prediction by integrating different features of drugs, biological (drug transporters, targets and enzymes), chemical (substructure fingerprints) and phenotypic (therapeutic indications and other identified ADRs), and their two and three level combinations. To recognize quality and important features, we used minimum redundancy maximum relevance approach while synthetic minority over-sampling technique balancing method was used to introduce a balance in the training sets. Results This is a rigorous and comprehensive study which involved the generation of a total of 504 computational models for 36 CV ADRs using two state-of-the-art machine-learning algorithms: random forest and sequential minimization optimization. All the models had an accuracy of around 90% and the biological and chemical features models were more informative as compared to the models generated using chemical features. Conclusions The results obtained demonstrated that the predictive models generated in the present study were highly accurate, and the phenotypic information of the drugs played the most important role in drug ADRs prediction. Furthermore, the results also showed that using the proposed method, different drugs properties can be combined to build computational predictive models which can effectively predict potential ADRs during early stages of drug development.
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- 2019
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7. The Mycobacterium tuberculosis PE_PGRS Protein Family Acts as an Immunological Decoy to Subvert Host Immune Response
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Tarina Sharma, Anwar Alam, Aquib Ehtram, Anshu Rani, Sonam Grover, Nasreen Z. Ehtesham, and Seyed E. Hasnain
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decoy antigens ,glycine ,immune evasion ,latency ,pathogenicity ,TB ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Mycobacterium tuberculosis (M.tb) is a successful pathogen that can reside within the alveolar macrophages of the host and can survive in a latent stage. The pathogen has evolved and developed multiple strategies to resist the host immune responses. M.tb escapes from host macrophage through evasion or subversion of immune effector functions. M.tb genome codes for PE/PPE/PE_PGRS proteins, which are intrinsically disordered, redundant and antigenic in nature. These proteins perform multiple functions that intensify the virulence competence of M.tb majorly by modulating immune responses, thereby affecting immune mediated clearance of the pathogen. The highly repetitive, redundant and antigenic nature of PE/PPE/PE_PGRS proteins provide a critical edge over other M.tb proteins in terms of imparting a higher level of virulence and also as a decoy molecule that masks the effect of effector molecules, thereby modulating immuno-surveillance. An understanding of how these proteins subvert the host immunological machinery may add to the current knowledge about M.tb virulence and pathogenesis. This can help in redirecting our strategies for tackling M.tb infections.
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- 2022
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8. PGRS Domain of Rv0297 of Mycobacterium tuberculosis Is Involved in Modulation of Macrophage Functions to Favor Bacterial Persistence
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Tarina Sharma, Sonam Grover, Naresh Arora, Manjunath P, Nasreen Zafar Ehtesham, and Seyed Ehtesham Hasnain
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apoptosis ,endosomal markers ,lung granulomas ,Mycobacterium smegmatis ,PE_PGRS5 ,phagosome maturation ,Microbiology ,QR1-502 - Abstract
Mycobacterium tuberculosis (M. tb) Rv0297-encoded PE_PGRS5 has been known to be expressed at the later stages of infection and in acidified phagosomes during transcriptome and proteomic studies. The possible role of Rv0297 in the modulation of phagosomal maturation and in providing protection against a microbicidal environment has been hypothesized. We show that Rv0297PGRS is involved in modulating the calcium homeostasis of macrophages followed by impedance of the phagolysosomal acidification process. This is evident from the downregulation of the late endosomal markers (Rab7 and cathepsin D) in the macrophages infected with recombinant Mycobacterium smegmatis (rM.smeg)—M.smeg_Rv0297 and M.smeg_Rv0297PGRS—or treated with recombinant Rv0297PGRS protein. Macrophages infected with rM.smeg expressing Rv0297 produce nitric oxide and undergo apoptosis, which may aid in the dissemination of pathogen in the later stages of infection. Rv0297 was also found to be involved in rescuing the bacterium from oxidative and hypoxic stress employed by macrophages and augmented the survivability of the recombinant bacterium. These results attribute to the functional significance of this protein in M.tb virulence mechanism. The fact that this protein gets expressed at the later stages of lung granulomas during M.tb infection suggests that the bacterium possibly employs Rv0297 as its dissemination and survival strategy.
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- 2020
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9. Alanine mutation of the catalytic sites of Pantothenate Synthetase causes distinct conformational changes in the ATP binding region
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Bharati Pandey, Sonam Grover, Sukriti Goyal, Anchala Kumari, Aditi Singh, Salma Jamal, Jagdeep Kaur, and Abhinav Grover
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Medicine ,Science - Abstract
Abstract The enzyme Pantothenate synthetase (PS) represents a potential drug target in Mycobacterium tuberculosis. Its X-ray crystallographic structure has demonstrated the significance and importance of conserved active site residues including His44, His47, Asn69, Gln72, Lys160 and Gln164 in substrate binding and formation of pantoyl adenylate intermediate. In the current study, molecular mechanism of decreased affinity of the enzyme for ATP caused by alanine mutations was investigated using molecular dynamics (MD) simulations and free energy calculations. A total of seven systems including wild-type + ATP, H44A + ATP, H47A + ATP, N69A + ATP, Q72A + ATP, K160A + ATP and Q164A + ATP were subjected to 50 ns MD simulations. Docking score, MM-GBSA and interaction profile analysis showed weak interactions between ATP (substrate) and PS (enzyme) in H47A and H160A mutants as compared to wild-type, leading to reduced protein catalytic activity. However, principal component analysis (PCA) and free energy landscape (FEL) analysis revealed that ATP was strongly bound to the catalytic core of the wild-type, limiting its movement to form a stable complex as compared to mutants. The study will give insight about ATP binding to the PS at the atomic level and will facilitate in designing of non-reactive analogue of pantoyl adenylate which will act as a specific inhibitor for PS.
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- 2018
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10. PGRS Domain of Rv0297 of Mycobacterium tuberculosis Functions in A Calcium Dependent Manner
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Tarina Sharma, Jasdeep Singh, Sonam Grover, Manjunath P., Firdos Firdos, Anwar Alam, Nasreen Z. Ehtesham, and Seyed E. Hasnain
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mycobacteria ,tuberculosis ,calcium ,cytokine release ,intrinsically disordered proteins ,nitric oxide ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Mycobacterium tuberculosis (M.tb), the pathogen causing tuberculosis, is a major threat to human health worldwide. Nearly 10% of M.tb genome encodes for a unique family of PE/PPE/PGRS proteins present exclusively in the genus Mycobacterium. The functions of most of these proteins are yet unexplored. The PGRS domains of these proteins have been hypothesized to consist of Ca2+ binding motifs that help these intrinsically disordered proteins to modulate the host cellular responses. Ca2+ is an important secondary messenger that is involved in the pathogenesis of tuberculosis in diverse ways. This study presents the calcium-dependent function of the PGRS domain of Rv0297 (PE_PGRS5) in M.tb virulence and pathogenesis. Tandem repeat search revealed the presence of repetitive Ca2+ binding motifs in the PGRS domain of the Rv0297 protein (Rv0297PGRS). Molecular Dynamics simulations and fluorescence spectroscopy revealed Ca2+ dependent stabilization of the Rv0297PGRS protein. Calcium stabilized Rv0297PGRS enhances the interaction of Rv0297PGRS with surface localized Toll like receptor 4 (TLR4) of macrophages. The Ca2+ stabilized binding of Rv0297PGRS with the surface receptor of macrophages enhances its downstream consequences in terms of Nitric Oxide (NO) production and cytokine release. Thus, this study points to hitherto unidentified roles of calcium-modulated PE_PGRS proteins in the virulence of M.tb. Understanding the pathogenic potential of Ca2+ dependent PE_PGRS proteins can aid in targeting these proteins for therapeutic interventions.
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- 2021
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11. Author Correction: An immunoinformatics approach to design a multi-epitope vaccine against Mycobacterium tuberculosis exploiting secreted exosome proteins
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Rahul Sharma, Vikrant Singh Rajput, Salma Jamal, Abhinav Grover, and Sonam Grover
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Medicine ,Science - Published
- 2021
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12. Machine Learning From Molecular Dynamics Trajectories to Predict Caspase-8 Inhibitors Against Alzheimer’s Disease
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Salma Jamal, Abhinav Grover, and Sonam Grover
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Alzheimer’s ,caspase-8 ,machine learning ,molecular dynamics trajectories ,descriptors ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder in which the death of brain cells takes place leading to loss of memory and decreased cognitive ability. AD is a leading cause of death worldwide and is progressive in nature with symptoms worsening over time. Machine learning–based computational predictive models based on 2D and 3D descriptors have been effective in identifying potential active compounds. However, the use of data from molecular dynamics (MD) trajectories for training machine learning models still needs to be explored. In the present study, descriptors have been extracted from the MD trajectories of caspase-8 ligand complexes to train models using artificial neural networks and random forest algorithms. Caspase-8 plays a key role in causing AD by cleaving amyloid precursor proteins during apoptosis leading to increased formation of the amyloid-beta peptide. A total of 43 ligands were docked using the glide module of Schrodinger software, and short MD simulations of 10 ns were performed for the calculation of MD descriptors. The MD descriptors were also combined with the 2D and 3D descriptors of chemical compounds, and individual descriptor based as well as combination models were generated. This study demonstrated that MD descriptors could be effectively used for the characterization of bioactive compounds along with lead prioritization and optimization.
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- 2019
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13. The PGRS Domain of Mycobacterium tuberculosis PE_PGRS Protein Rv0297 Is Involved in Endoplasmic Reticulum Stress-Mediated Apoptosis through Toll-Like Receptor 4
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Sonam Grover, Tarina Sharma, Yadvir Singh, Sakshi Kohli, Manjunath P., Aditi Singh, Torsten Semmler, Lothar H. Wieler, Karsten Tedin, Nasreen Z. Ehtesham, and Seyed E. Hasnain
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calcium homeostasis ,ER localization signal ,granulomas ,unfolded protein response ,Microbiology ,QR1-502 - Abstract
ABSTRACT The genome of Mycobacterium tuberculosis, the causal organism of tuberculosis (TB), encodes a unique protein family known as the PE/PPE/PGRS family, present exclusively in the genus Mycobacterium and nowhere else in the living kingdom, with largely unexplored functions. We describe the functional significance of the PGRS domain of Rv0297, a member of this family. In silico analyses revealed the presence of intrinsically disordered stretches and putative endoplasmic reticulum (ER) localization signals in the PGRS domain of Rv0297 (Rv0297PGRS). The PGRS domain aids in ER localization, which was shown by infecting macrophage cells with M. tuberculosis and by overexpressing the protein by transfection in macrophage cells followed by activation of the unfolded protein response, as evident from increased expression of GRP78/GRP94 and CHOP/ATF4, leading to disruption of intracellular Ca2+ homeostasis and increased nitric oxide (NO) and reactive oxygen species (ROS) production. The consequent activation of the effector caspase-8 resulted in apoptosis of macrophages, which was Toll-like receptor 4 (TLR4) dependent. Administration of recombinant Rv0297PGRS (rRv0297PGRS) also exhibited similar effects. These results implicate a hitherto-unknown role of the PGRS domain of the PE_PGRS protein family in ER stress-mediated cell death through TLR4. Since this protein is already known to be present at later stages of infection in human granulomas it points to the possibility of it being employed by M. tuberculosis for its dissemination via an apoptotic mechanism. IMPORTANCE Apoptosis is generally thought to be a defense mechanism in protecting the host against Mycobacterium tuberculosis in early stages of infection. However, apoptosis during later stages in lung granulomas may favor the bacterium in disseminating the disease. ER stress has been found to induce apoptosis in TB granulomas, in zones where apoptotic macrophages accumulate in mice and humans. In this study, we report ER stress-mediated apoptosis of host cells by the Rv0297-encoded PE_PGRS5 protein of M. tuberculosis exceptionally present in the pathogenic Mycobacterium genus. The PGRS domain of Rv0297 aids the protein in localizing to the ER and induces the unfolded protein response followed by apoptosis of macrophages. The effect of the Rv0297PGRS domain was found to be TLR4 dependent. This study presents novel insights on the strategies employed by M. tuberculosis to disseminate the disease.
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- 2018
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14. Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations.
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Sharad Verma, Sonam Grover, Chetna Tyagi, Sukriti Goyal, Salma Jamal, Aditi Singh, and Abhinav Grover
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Medicine ,Science - Abstract
p53, a tumor suppressor protein, has been proven to regulate the cell cycle, apoptosis, and DNA repair to prevent malignant transformation. MDM2 regulates activity of p53 and inhibits its binding to DNA. In the present study, we elucidated the MDM2 inhibition potential of polyphenols (Apigenin, Fisetin, Galangin and Luteolin) by MD simulation and MM/PBSA free energy calculations. All polyphenols bind to hydrophobic groove of MDM2 and the binding was found to be stable throughout MD simulation. Luteolin showed the highest negative binding free energy value of -173.80 kJ/mol followed by Fisetin with value of -172.25 kJ/mol. It was found by free energy calculations, that hydrophobic interactions (vdW energy) have major contribution in binding free energy.
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- 2016
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15. Potential Repurposed Drug Candidates for Tuberculosis Treatment: Progress and Update of Drugs Identified in Over a Decade
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Khushbu Sharma, Faraz Ahmed, Tarina Sharma, Abhinav Grover, Meetu Agarwal, and Sonam Grover
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General Chemical Engineering ,General Chemistry - Published
- 2023
16. Structure-based drug repurposing to inhibit the replication-associated essential protein DnaG of Mycobacterium tuberculosis
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Waseem Ali, Salma Jamal, Rishabh Gangwar, Faraz Ahmed, Meetu Agarwal, Javaid Ahmad Sheikh, and Sonam Grover
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Background: Mycobacterium tuberculosis (M.tb), the etiological agent of Tuberculosis (TB), is the second leading cause of mortality after COVID-19, with a global death toll of 1.5 million in 2020. The escalating cases of drug-resistant TB are further worsening the current situation and making TB treatment extremely challenging. Thus, it is crucial to look for new anti-TB drugs with novel mechanisms of action and high efficacy. The DnaG of M.tb replication machinery is an essential protein for pathogen survival. Also, its imperative primase activity and lack of structural homology to human proteins, make it a possible target for drug development. Methods: In this presented study, using a computational structure-based drug repurposing approach, Food and drug administration (FDA) approved drugs were virtually screened against M.tb DnaG to identify potential inhibitors. Five drugs viz. Caspofungin, Doxorubicin, Mitoxantrone, Vapreotide, and Zanamivir showed higher molecular docking scores. Further RMSD, RMSF, Rg, SASA, H-bond, and PCA analysis of these drugs and DnaG complexes. Alamar Blue Assay further evaluated the anti-TB activity of these drugs in vitro using H37Ra and H37Rv M.tb strains. Results: The top results for DnaG binding included several FDA-approved drugs, out of which five were selected and subjected to Molecular dynamic simulation and displayed their high binding affinity, stable interaction, more compactness, and reduced atomic motion. The minimum inhibitory concentration of Doxorubicin, Mitoxantrone, and Vapreotide were detected in the range of 0.19-25 µg/ml for both H37Ra, and H37Rv, respectively. Conclusions: Our findings from the study present potential repurposed drug candidates that target DnaG and inhibit M.tb survival. Thorough investigations of these compounds may lead to the discovery of new anti-TB therapeutics.
- Published
- 2023
17. Novel group-based QSAR and combinatorial design of CK-1δ inhibitors as neuroprotective agents.
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Kopal Joshi, Sukriti Goyal, Sonam Grover, Salma Jamal, Aditi Singh, Pawan Dhar, and Abhinav Grover
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- 2016
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18. Multifaceted role of drugs: a potential weapon to outsmart Mycobacterium tuberculosis resistance by targeting its essential ThyX
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Seema Mehra, Sonam Grover, Salma Jamal, Sana Tanweer, Faizan, Najumu Saqib, Faraz Ahmad, and Abhinav Grover
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0303 health sciences ,Tuberculosis ,biology ,business.industry ,In silico ,030303 biophysics ,Human immunodeficiency virus (HIV) ,General Medicine ,Bioinformatics ,medicine.disease ,medicine.disease_cause ,biology.organism_classification ,Food and drug administration ,Mycobacterium tuberculosis ,03 medical and health sciences ,Drug repositioning ,Structural Biology ,medicine ,Risk of death ,business ,Molecular Biology ,Repurposing - Abstract
Tuberculosis (TB) is one of the prominent cause of deaths across the world and multidrug-resistant and extensively drug-resistant TB continues to pose challenges for clinicians and public health centers. The risk of death is extremely high in individuals who have compromised immune systems, HIV infection, or diabetes. Research institutes and pharmaceutical companies have been working on repurposing existing drugs as effective therapeutic options against TB. The identification of suitable drugs with multi-target affinity profiles is a widely accepted way to combat the development of resistance. Flavin-dependent thymidylate synthase (FDTS), known as ThyX, is in the class of methyltransferases and is a possible target in the discovery of novel anti-TB drugs. In this study, we aimed to repurpose existing drugs approved by Food and Drug Administration (FDA) that could be used in the treatment of TB. An integrated screening was performed based on computational procedures: high-throughput molecular docking techniques, followed by molecular dynamics simulations of the target enzyme, ThyX. After performing in silico screening using a library of 3,967 FDA-approved drugs, the two highest-scoring drugs, Carglumic acid and Mesalazine, were selected as potential candidates that could be repurposed to treat TB.Communicated by Ramaswamy H. Sarma.
- Published
- 2021
19. Insights into the mutations leading to capreomycin resistance in S-adenosyl-L-methionine binding motif in TlyA from
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Waseem, Ali, Salma, Jamal, Abhinav, Grover, and Sonam, Grover
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S-Adenosylmethionine ,Methionine ,Bacterial Proteins ,Mutation ,Capreomycin ,Mycobacterium tuberculosis ,Methyltransferases - Abstract
Capreomycin is a second line antibiotic used for the treatment of drug resistant Tuberculosis (TB), primary reason of death from a solo infectious organism
- Published
- 2021
20. An immunoinformatics approach to design a multi-epitope vaccine against Mycobacterium tuberculosis exploiting secreted exosome proteins
- Author
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Abhinav Grover, Sonam Grover, Salma Jamal, Rahul Sharma, and Vikrant Singh Rajput
- Subjects
0301 basic medicine ,Science ,medicine.medical_treatment ,Immunology ,Population ,Epitopes, T-Lymphocyte ,Diseases ,Immune receptor ,Biology ,Exosomes ,Exosome ,Article ,Mycobacterium tuberculosis ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,Antigen ,medicine ,Humans ,Tuberculosis ,Tuberculosis Vaccines ,Author Correction ,education ,education.field_of_study ,Multidisciplinary ,Computational Biology ,biology.organism_classification ,Virology ,Computational biology and bioinformatics ,Molecular Docking Simulation ,030104 developmental biology ,Immunization ,Vaccines, Subunit ,Medicine ,Epitopes, B-Lymphocyte ,Adjuvant ,030215 immunology - Abstract
Tuberculosis is one the oldest known affliction of mankind caused by the pathogen Mycobacterium tuberculosis. Till date, there is no absolute single treatment available to deal with the pathogen, which has acquired a great potential to develop drug resistance rapidly. BCG is the only anti-tuberculosis vaccine available till date which displays limited global efficacy due to genetic variation and concurrent pathogen infections. Extracellular vesicles or exosomes vesicle (EVs) lie at the frontier cellular talk between pathogen and the host, and therefore play a significant role in establishing pathogenesis. In the present study, an in-silico approach has been adopted to construct a multi-epitope vaccine from selected immunogenic EVs proteins to elicit a cellular as well as a humoral immune response. Our designed vaccine has wide population coverage and can effectively compensate for the genetic variation among different populations. For maximum efficacy and minimum adverse effects possibilities the antigenic, non-allergenic and non-toxic B-cell, HTL and CTL epitopes from experimentally proven EVs proteins were selected for the vaccine construct. TLR4 agonist RpfE served as an adjuvant for the vaccine construct. The vaccine construct structure was modelled, refined and docked on TLR4 immune receptor. The designed vaccine construct displayed safe usage and exhibits a high probability to elicit the critical immune regulators, like B cells, T-cells and memory cells as displayed by the in-silico immunization assays. Therefore, it can be further corroborated using in vitro and in vivo assays to fulfil the global need for a more efficacious anti-tuberculosis vaccine.
- Published
- 2021
21. Multifaceted role of drugs: a potential weapon to outsmart
- Author
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Sana, Tanweer, Salma, Jamal, Seema, Mehra, Najumu, Saqib, Faraz, Ahmad, Faizan, Abhinav, Grover, and Sonam, Grover
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Molecular Docking Simulation ,Flavins ,Antitubercular Agents ,Humans ,Tuberculosis ,HIV Infections ,Mycobacterium tuberculosis ,Thymidylate Synthase ,Mesalamine - Abstract
Tuberculosis (TB) is one of the prominent cause of deaths across the world and multidrug-resistant and extensively drug-resistant TB continues to pose challenges for clinicians and public health centers. The risk of death is extremely high in individuals who have compromised immune systems, HIV infection, or diabetes. Research institutes and pharmaceutical companies have been working on repurposing existing drugs as effective therapeutic options against TB. The identification of suitable drugs with multi-target affinity profiles is a widely accepted way to combat the development of resistance. Flavin-dependent thymidylate synthase (FDTS), known as ThyX, is in the class of methyltransferases and is a possible target in the discovery of novel anti-TB drugs. In this study, we aimed to repurpose existing drugs approved by Food and Drug Administration (FDA) that could be used in the treatment of TB. An integrated screening was performed based on computational procedures: high-throughput molecular docking techniques, followed by molecular dynamics simulations of the target enzyme, ThyX. After performing
- Published
- 2021
22. Cytotoxic T-lymphocyte elicited vaccine against SARS-CoV-2 employing immunoinformatics framework
- Author
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Damini Sood, Nikita Admane, Anchala Kumari, Sonam Grover, Abhinav Grover, Vijay Kumar Prajapati, Neeraj Kumar, and Ramesh Chandra
- Subjects
Models, Molecular ,0301 basic medicine ,COVID-19 Vaccines ,Science ,Biophysics ,Epitopes, T-Lymphocyte ,Biology ,Major histocompatibility complex ,medicine.disease_cause ,Epitope ,Article ,03 medical and health sciences ,Immunogenicity, Vaccine ,0302 clinical medicine ,Immune system ,medicine ,Humans ,Computer Simulation ,030212 general & internal medicine ,Coronavirus ,Multidisciplinary ,SARS-CoV-2 ,Immunogenicity ,Viral Vaccine ,COVID-19 ,Computational Biology ,Acquired immune system ,Virology ,Toll-Like Receptor 2 ,Computational biology and bioinformatics ,CTL ,030104 developmental biology ,Spike Glycoprotein, Coronavirus ,biology.protein ,Medicine ,T-Lymphocytes, Cytotoxic - Abstract
Development of effective counteragents against the novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains, requires clear insights and information for understanding the immune responses associated with it. This global pandemic has pushed the healthcare system and restricted the movement of people and succumbing of the available therapeutics utterly warrants the development of a potential vaccine to contest the deadly situation. In the present study, highly efficacious, immunodominant cytotoxic T-lymphocyte (CTL) epitopes were predicted by advanced immunoinformatics assays using the spike glycoprotein of SARS-CoV2, generating a robust and specific immune response with convincing immunological parameters (Antigenicity, TAP affinity, MHC binder) engendering an efficient viral vaccine. The molecular docking studies show strong binding of the CTL construct with MHC-1 and host membrane specific TLR2 receptors. The molecular dynamics simulation in an explicit system confirmed the stable and robust binding of CTL epitope with TLR2. Steep magnitude RMSD variation and compelling residual fluctuations existed in terminal residues and various loops of the β linker segments of TLR2-epitope (residues 105-156 and 239-254) to about 0.4 nm. The reduced Rg value (3.3 nm) and stagnant SASA analysis (275 nm/S2/N after 8 ns and 5 ns) for protein surface and its orientation in the exposed and buried regions suggests more compactness due to the strong binding interaction of the epitope. The CTL vaccine candidate establishes a high capability to elicit the critical immune regulators, like T-cells and memory cells as proven by the in silico immunization assays and can be further corroborated through in vitro and in vivo assays.
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- 2021
23. Computational models for the prediction of adverse cardiovascular drug reactions
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Abhinav Grover, Waseem Ali, Priya Nagpal, Sonam Grover, and Salma Jamal
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0301 basic medicine ,Drug ,Drug-Related Side Effects and Adverse Reactions ,Computer science ,media_common.quotation_subject ,Adverse drug reactions ,lcsh:Medicine ,Feature selection ,Machine learning ,computer.software_genre ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Redundancy (engineering) ,Humans ,Computer Simulation ,Cardiovascular drug ,Relevance (information retrieval) ,Sequential minimization optimization ,media_common ,Computational model ,business.industry ,Research ,lcsh:R ,Reproducibility of Results ,Cardiovascular Agents ,General Medicine ,Random forest ,Phenotype ,030104 developmental biology ,Databases as Topic ,Drug development ,030220 oncology & carcinogenesis ,Artificial intelligence ,business ,computer ,Algorithms - Abstract
Background Predicting adverse drug reactions (ADRs) has become very important owing to the huge global health burden and failure of drugs. This indicates a need for prior prediction of probable ADRs in preclinical stages which can improve drug failures and reduce the time and cost of development thus providing efficient and safer therapeutic options for patients. Though several approaches have been put forward for in silico ADR prediction, there is still room for improvement. Methods In the present work, we have used machine learning based approach for cardiovascular (CV) ADRs prediction by integrating different features of drugs, biological (drug transporters, targets and enzymes), chemical (substructure fingerprints) and phenotypic (therapeutic indications and other identified ADRs), and their two and three level combinations. To recognize quality and important features, we used minimum redundancy maximum relevance approach while synthetic minority over-sampling technique balancing method was used to introduce a balance in the training sets. Results This is a rigorous and comprehensive study which involved the generation of a total of 504 computational models for 36 CV ADRs using two state-of-the-art machine-learning algorithms: random forest and sequential minimization optimization. All the models had an accuracy of around 90% and the biological and chemical features models were more informative as compared to the models generated using chemical features. Conclusions The results obtained demonstrated that the predictive models generated in the present study were highly accurate, and the phenotypic information of the drugs played the most important role in drug ADRs prediction. Furthermore, the results also showed that using the proposed method, different drugs properties can be combined to build computational predictive models which can effectively predict potential ADRs during early stages of drug development. Electronic supplementary material The online version of this article (10.1186/s12967-019-1918-z) contains supplementary material, which is available to authorized users.
- Published
- 2019
24. HHV-5 epitope: A potential vaccine candidate with high antigenicity and large coverage
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Aditi Singh, Abhinav Grover, Anchala Kumari, Neeraj Kumar, Pawan K. Dhar, Ramesh Chandra, and Sonam Grover
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Models, Molecular ,0301 basic medicine ,Antigenicity ,viruses ,Cytomegalovirus ,Epitopes, T-Lymphocyte ,India ,Herpesvirus Vaccines ,Molecular Dynamics Simulation ,Biology ,Epitope ,03 medical and health sciences ,0302 clinical medicine ,Viral Envelope Proteins ,Structural Biology ,Human herpes ,Humans ,Glycoprotein B ,Antigens, Viral ,Molecular Biology ,Genome, Human ,Human herpes virus ,Outbreak ,T-Lymphocytes, Helper-Inducer ,General Medicine ,biochemical phenomena, metabolism, and nutrition ,Virology ,Toll-Like Receptor 2 ,Molecular Docking Simulation ,030104 developmental biology ,030220 oncology & carcinogenesis ,Epitopes, B-Lymphocyte ,T-Lymphocytes, Cytotoxic - Abstract
Outbreak of Human Herpes virus-5 (HHV-5) infection in emerging countries has raised worldwide health concern owing to prevalence of congenital impairments and life threatening consequences in immunocompromised individuals. Thus, there lies an impending need to develop vaccine against HHV-5. HHV-5 enters into host cells with the help of necessary components glycoprotein B (gB) and H/L. In this study, the conformational linear B-cell and T-cell epitopes for gB of HHV-5 have been predicted using conformational approaches, for their possible collective use as vaccine candidates. We examined epitope's interactions with major histocompatibility complexes using molecular docking and also investigated their stable binding with specific toll like receptor-2 (TLR2), present on host cells during HHV-5 infection. Predicted MHC-I epitope 'LVAIAVVII' with high antigenicity and large coverage of HLA alleles was found to superimpose on MHC-II epitope (Rank 1) and was also identified to be the core sequence of putative B cell epitope 'ILVAIAVVIITYLI'. Resulting epitope was found to have consistent interaction with TLR2 during long term (100 ns) MD run. We also validated this nonamer epitope for its dissimilarity with human genome and high population coverage, suggesting it to be a potential vaccine candidate with higher coverage for both the MHC alleles of Indian population. Communicated by Ramaswamy H. Sarma.
- Published
- 2018
25. Insights into the mutations leading to capreomycin resistance in S-adenosyl-L-methionine binding motif in TlyA from Mycobacterium tuberculosis
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Abhinav Grover, Sonam Grover, Waseem Ali, and Salma Jamal
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Alanine ,Methyltransferase ,Methionine ,Capreomycin ,Mutant ,Wild type ,General Medicine ,Molecular biology ,Ribosome ,chemistry.chemical_compound ,chemistry ,Structural Biology ,Docking (molecular) ,medicine ,Molecular Biology ,medicine.drug - Abstract
Capreomycin is a second line antibiotic used for the treatment of drug resistant Tuberculosis (TB), primary reason of death from a solo infectious organism, Mycobacterium tuberculosis (M.tb). Capreomycin targets the ribosome of bacteria and is known to bind at the interface where the large and small ribosomal subunits interact in M.tb using an S-Adenosyl Methionine (SAM) dependent methyltransferase, TlyA (Rv1794). Besides the methyltransferase activity, TlyA has also been found to show substantial haemolytic activity. The dual activity of TlyA highlights its crucial role in pathogenesis and virulence of M.tb. In the present study, docking and molecular dynamics (MD) simulations were carried out to explore the impact of mutations in a conserved SAM binding motif, 90GASTG94, on the affinity of TlyA enzyme for SAM. Two already reported mutations, A91E and S92L, and the remaining wild type residues, Gly90, Thr93, Gly94 mutated to alanine were taken into consideration resulting in a total of six systems, wild type + SAM, G90A + SAM, A91E + SAM, S92L + SAM, T93A + SAM and G94A + SAM that were subjected to 100 ns MD simulations. Docking scores and MD simulations analyses revealed that in contrast to wild type, mutants reduced the affinity of SAM for TlyA with most prominent effect observed in case of alanine mutants. Mutations also led to the loss of hydrogen bond and hydrophobic interactions and large-scale movement of atoms evident from the principal component analyses indicating their destabilizing impact on TlyA. The present study gives insights into influence of mutations on binding of SAM to TlyA in M.tb and promoting capreomycin resistance. Communicated by Ramaswamy H. Sarma
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- 2021
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26. Cytotoxic T-Lymphocyte Elicited Vaccine against SARS-CoV-2 employing Immunoinformatics Framework
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Neeraj Kumar, Nikita Admane, Anchala Kumari, Damini Sood, Sonam Grover, Vijay Kumar Prajapati, Ramesh Chandra, and Abhinav Grover
- Abstract
Development of effective counteragents against the novel coronavirus disease caused by SARS CoV-2 strains requires clear insights for understanding immune responses associated with it. The succumbing of available therapeutics utterly warrants the development of a potential vaccine to contest the deadly situation. Herein, we report Cytotoxic T-cell Lymphocytes immunomodulator by advanced immunoinformatics avenues for spike-glycoprotein of SARS CoV-2, which can generate robust immune response with convincing immunological parameters (Antigenicity, TAP affinity, MHC-binder) engendering an efficient viral vaccine. Strong binding of the CTL construct with MHC-1 and membrane-specific TLR2 was conferred through molecular docking and molecular dynamics simulation in an explicit system. Steep magnitude RMSD variation and compelling residual fluctuations existed in terminal residues and various loops of the β linker segments of TLR2-epitope (residues 105-156 and 239-254) to about 0.4nm. The reduced Rg value (3.3nm) and stagnant SASA analysis (275nm/S2/N after 8ns and 5ns) for protein surface and its orientation in exposed and buried regions suggests more compactness by strong binding of epitope. The CTL vaccine candidate establishes a high capability to elicit critical immune regulators, like T-cells and memory cells as proven by in silico immunization assays and can be further corroborated through in vitro and in vivo assays.
- Published
- 2020
27. Artificial Intelligence and Machine learning based prediction of resistant and susceptible mutations in Mycobacterium tuberculosis
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Seyed Ehtesham Hasnain, Sonam Grover, Rishabh Gangwar, Abhinav Grover, Salma Jamal, and Mohd Khubaib
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0301 basic medicine ,030106 microbiology ,lcsh:Medicine ,Drug resistance ,Molecular Dynamics Simulation ,Machine learning ,computer.software_genre ,Polymorphism, Single Nucleotide ,Article ,Machine Learning ,Mycobacterium tuberculosis ,03 medical and health sciences ,Bacterial Proteins ,Artificial Intelligence ,Drug Resistance, Multiple, Bacterial ,Tuberculosis, Multidrug-Resistant ,medicine ,Computational models ,Humans ,lcsh:Science ,Author Correction ,Multidisciplinary ,Bacterial disease ,biology ,INHA ,business.industry ,lcsh:R ,Bayes Theorem ,Pyrazinamide ,rpoB ,biology.organism_classification ,Molecular Docking Simulation ,030104 developmental biology ,Genes, Bacterial ,Mutation ,PncA ,lcsh:Q ,Artificial intelligence ,Genes, MDR ,business ,computer ,Algorithms ,Rifampicin ,medicine.drug - Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis (M.tb), causes highest number of deaths globally for any bacterial disease necessitating novel diagnosis and treatment strategies. High-throughput sequencing methods generate a large amount of data which could be exploited in determining multi-drug resistant (MDR-TB) associated mutations. The present work is a computational framework that uses artificial intelligence (AI) based machine learning (ML) approaches for predicting resistance in the genes rpoB, inhA, katG, pncA, gyrA and gyrB for the drugs rifampicin, isoniazid, pyrazinamide and fluoroquinolones. The single nucleotide variations were represented by several sequence and structural features that indicate the influence of mutations on the target protein coded by each gene. We used ML algorithms - naïve bayes, k nearest neighbor, support vector machine, and artificial neural network, to build the prediction models. The classification models had an average accuracy of 85% across all examined genes and were evaluated on an external unseen dataset to demonstrate their application. Further, molecular docking and molecular dynamics simulations were performed for wild type and predicted resistance causing mutant protein and anti-TB drug complexes to study their impact on the conformation of proteins to confirm the observed phenotype.
- Published
- 2020
28. Long-range replica exchange molecular dynamics guided drug repurposing against tyrosine kinase PtkA of Mycobacterium tuberculosis
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Sana Tanweer, Salma Jamal, Rahul Sharma, Hina Singh, Priya Nagpal, Waseem Ali, Abhinav Grover, and Sonam Grover
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Models, Molecular ,Protein Conformation ,Protein domain ,lcsh:Medicine ,Protein tyrosine phosphatase ,Molecular Dynamics Simulation ,Virtual drug screening ,Article ,Protein structure ,Bacterial Proteins ,Protein Domains ,Inosine Pranobex ,Protein phosphorylation ,Phosphorylation ,Tyrosine ,lcsh:Science ,Protein Unfolding ,Multidisciplinary ,Kinase ,Chemistry ,lcsh:R ,Drug Repositioning ,Mycobacterium tuberculosis ,Protein-Tyrosine Kinases ,Esculin ,Computational biology and bioinformatics ,Biochemistry ,lcsh:Q ,Protein Tyrosine Phosphatases ,Tyrosine kinase ,Protein Binding - Abstract
Tuberculosis (TB) is a leading cause of death worldwide and its impact has intensified due to the emergence of multi drug-resistant (MDR) and extensively drug-resistant (XDR) TB strains. Protein phosphorylation plays a vital role in the virulence of Mycobacterium tuberculosis (M.tb) mediated by protein kinases. Protein tyrosine phosphatase A (MptpA) undergoes phosphorylation by a unique tyrosine-specific kinase, protein tyrosine kinase A (PtkA), identified in the M.tb genome. PtkA phosphorylates PtpA on the tyrosine residues at positions 128 and 129, thereby increasing PtpA activity and promoting pathogenicity of MptpA. In the present study, we performed an extensive investigation of the conformational behavior of the intrinsically disordered domain (IDD) of PtkA using replica exchange molecular dynamics simulations. Long-term molecular dynamics (MD) simulations were performed to elucidate the role of IDD on the catalytic activity of kinase core domain (KCD) of PtkA. This was followed by identification of the probable inhibitors of PtkA using drug repurposing to block the PtpA-PtkA interaction. The inhibitory role of IDD on KCD has already been established; however, various analyses conducted in the present study showed that IDDPtkA had a greater inhibitory effect on the catalytic activity of KCDPtkA in the presence of the drugs esculin and inosine pranobex. The binding of drugs to PtkA resulted in formation of stable complexes, indicating that these two drugs are potentially useful as inhibitors of M.tb.
- Published
- 2020
29. Dual inhibition of SARS-CoV-2 spike and main protease through a repurposed drug, rutin
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Anchala Kumari, Priya Nagpal, Himanshi Kukrety, Sonam Grover, Vikrant Singh Rajput, and Abhinav Grover
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Drug ,Polyproteins ,media_common.quotation_subject ,medicine.medical_treatment ,In silico ,Rutin ,030303 biophysics ,Computational biology ,Molecular Dynamics Simulation ,spike protein ,Antiviral Agents ,03 medical and health sciences ,chemistry.chemical_compound ,Structural Biology ,medicine ,Humans ,Protease Inhibitors ,Molecular Biology ,Protein secondary structure ,Coronavirus 3C Proteases ,media_common ,0303 health sciences ,Protease ,drug repurposing ,Drug discovery ,SARS-CoV-2 ,Drug Repositioning ,MD simulation ,General Medicine ,COVID-19 Drug Treatment ,Molecular Docking Simulation ,Drug repositioning ,chemistry ,main protease ,Spike Glycoprotein, Coronavirus ,Research Article - Abstract
The global health emergency caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to alarming numbers of fatalities across the world. So far the researchers worldwide have not been able to discover a breakthrough in the form of a potent drug or an effective vaccine. Therefore, it is imperative to discover drugs to curb the ongoing menace. In silico approaches using FDA approved drugs can expedite the drug discovery process by providing leads that can be pursued. In this report, two drug targets, namely the spike protein and main protease, belonging to structural and non-structural class of proteins respectively, were utilized to carry out drug repurposing based screening. The exposed nature of the spike protein on the viral surface along with its instrumental role in host infection and the involvement of main protease in processing of polyproteins along with no human homologue make these proteins attractive drug targets. Interestingly, the screening identified a common high efficiency binding molecule named rutin. Further, molecular dynamics simulations in explicit solvent affirmed the stable and sturdy binding of rutin with these proteins. The decreased Rg value (4 nm for spike-rutin and 2.23 nm for main protease-rutin) and stagnant SASA analysis (485 nm/S2/N in spike-rutin and 152 nm/S2/N in main protease-rutin) for protein surface and its orientation in the exposed and buried regions suggests a strong binding interaction of the drug. Further, cluster analysis and secondary structure analysis of complex trajectories validated the conformational changes due to binding of rutin., Graphical Abstract Communicated by Ramaswamy H. Sarma
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- 2020
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30. Novel missense mutations in gidB gene associated with streptomycin resistance in Mycobacterium tuberculosis: insights from molecular dynamics
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Abhinav Grover, Sukriti Goyal, Aditi Singh, Salma Jamal, Jagdeep Kaur, Bharati Pandey, and Sonam Grover
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0301 basic medicine ,Methyltransferase ,Protein Conformation ,030106 microbiology ,Mutant ,Mutation, Missense ,Molecular Dynamics Simulation ,Ligands ,Structure-Activity Relationship ,03 medical and health sciences ,Structural Biology ,Drug Resistance, Bacterial ,medicine ,Missense mutation ,Molecular Biology ,Gene ,Genetics ,Binding Sites ,Chemistry ,Point mutation ,Methyltransferases ,Mycobacterium tuberculosis ,General Medicine ,Methylation ,Molecular Docking Simulation ,030104 developmental biology ,Streptomycin ,Thermodynamics ,Threading (protein sequence) ,Hydrophobic and Hydrophilic Interactions ,Algorithms ,Protein Binding ,medicine.drug - Abstract
Streptomycin was the first antibiotic used for the treatment of tuberculosis by inhibiting translational proof reading. Point mutation in gidB gene encoding S-adenosyl methionine (SAM)-dependent 7-methylguanosine (m7G) methyltransferase required for methylation of 16S rRNA confers streptomycin resistance. As there was no structural substantiation experimentally, gidB protein model was built by threading algorithm. In this work, molecular dynamics (MD) simulations coupled with binding free energy calculations were performed to outline the mechanism underlying high-level streptomycin resistance associated with three novel missense mutants including S70R, T146M, and R187M. Results from dynamics analyses suggested that the structure distortion in the binding pocket of gidB mutants modulate SAM binding affinity. At the structural level, these conformational changes bring substantial decrease in the number of residues involved in hydrogen bonding and dramatically reduce thermodynamic stability of mutant gidB-SAM complexes. The outcome of comparative analysis of the MD simulation trajectories revealed lower conformational stability associated with higher flexibility in mutants relative to the wild-type, turns to be major factor driving the emergence of drug resistance toward antibiotic. This study will pave way toward design and development of resistant defiant gidB inhibitors as potent anti-TB agents.
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- 2018
31. Role of pnc A gene mutations W68R and W68G in pyrazinamide resistance
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Abhinav Grover, Sonam Grover, Anchala Kumari, Mansi Aggarwal, Bharati Pandey, and Aditi Singh
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0301 basic medicine ,chemistry.chemical_classification ,030103 biophysics ,Mutant ,Antitubercular Agents ,Cell Biology ,Gene mutation ,Pyrazinamide ,Biochemistry ,Amidohydrolases ,Molecular Docking Simulation ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Pyrazinoic acid ,Enzyme ,chemistry ,Docking (molecular) ,Drug Resistance, Bacterial ,PncA ,Binding site ,Molecular Biology ,Gene - Abstract
Mycobacterium tuberculosis (Mtb) resistance toward anti-tuberculosis drugs is a widespread problem. Pyrazinamide (PZA) is a first line antitubercular drug that kills semi-dormant bacilli when converted into its activated form, that is, pyrazinoic acid (POA) by Pyrazinamidase (PZase) enzyme coded by pncA gene. In this study, we conducted several analyses on native and mutant structures (W68R, W68G) of PZase before and after docking with the PZA drug to explore the molecular mechanism behind PZA resistance caused due to pncA mutations. Structural changes caused by mutations were studied with respect to their effects on functionality of protein. Docking was performed to analyze the protein-drug binding and comparative analysis was done to observe how the mutations affect drug binding affinity and binding site on protein. Native PZase protein was observed to have the maximum binding affinity in terms of docking score as well as shape complementarity in comparison to the mutant forms. Molecular dynamics simulation analyses showed that mutation in the 68th residue of protein results in a structural change at its active site which further affects the biological function of protein, that is, conversion of PZA to POA. Mutations in the protein thereby led to PZA resistance in the bacterium due to the inefficient binding.
- Published
- 2017
32. PGRS Domain of Rv0297 of Mycobacterium tuberculosis Functions in A Calcium Dependent Manner
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P. Manjunath, Jasdeep Singh, Sonam Grover, Firdos Firdos, Seyed E. Hasnain, Tarina Sharma, Anwar Alam, and Nasreen Z. Ehtesham
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QH301-705.5 ,Protein Conformation ,mycobacteria ,Host–pathogen interaction ,Sequence Homology ,Virulence ,Molecular Dynamics Simulation ,host-pathogen interaction ,Intrinsically disordered proteins ,Article ,Catalysis ,Inorganic Chemistry ,Mycobacterium tuberculosis ,Mice ,Bacterial Proteins ,nitric oxide ,Animals ,Humans ,Amino Acid Sequence ,Biology (General) ,Physical and Theoretical Chemistry ,Receptor ,QD1-999 ,Molecular Biology ,Spectroscopy ,Antigens, Bacterial ,Toll-like receptor ,calcium ,biology ,Chemistry ,Macrophages ,Organic Chemistry ,Membrane Proteins ,Gene Expression Regulation, Bacterial ,General Medicine ,biology.organism_classification ,Computer Science Applications ,Cell biology ,tuberculosis ,cytokine release ,TLR4 ,intrinsically disordered proteins ,PE_PGRS ,TLR4 signaling ,Function (biology) - Abstract
Mycobacterium tuberculosis (M.tb), the pathogen causing tuberculosis, is a major threat to human health worldwide. Nearly 10% of M.tb genome encodes for a unique family of PE/PPE/PGRS proteins present exclusively in the genus Mycobacterium. The functions of most of these proteins are yet unexplored. The PGRS domains of these proteins have been hypothesized to consist of Ca2+ binding motifs that help these intrinsically disordered proteins to modulate the host cellular responses. Ca2+ is an important secondary messenger that is involved in the pathogenesis of tuberculosis in diverse ways. This study presents the calcium-dependent function of the PGRS domain of Rv0297 (PE_PGRS5) in M.tb virulence and pathogenesis. Tandem repeat search revealed the presence of repetitive Ca2+ binding motifs in the PGRS domain of the Rv0297 protein (Rv0297PGRS). Molecular Dynamics simulations and fluorescence spectroscopy revealed Ca2+ dependent stabilization of the Rv0297PGRS protein. Calcium stabilized Rv0297PGRS enhances the interaction of Rv0297PGRS with surface localized Toll like receptor 4 (TLR4) of macrophages. The Ca2+ stabilized binding of Rv0297PGRS with the surface receptor of macrophages enhances its downstream consequences in terms of Nitric Oxide (NO) production and cytokine release. Thus, this study points to hitherto unidentified roles of calcium-modulated PE_PGRS proteins in the virulence of M.tb. Understanding the pathogenic potential of Ca2+ dependent PE_PGRS proteins can aid in targeting these proteins for therapeutic interventions.
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- 2021
33. Computational identification of novel natural inhibitors of glucagon receptor for checking type II diabetes mellitus.
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Sonam Grover, Jaspreet Kaur Dhanjal, Sukriti Goyal, Abhinav Grover, and Durai Sundar
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- 2014
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34. Structural insights into mode of actions of novel natural Mycobacterium protein tyrosine phosphatase B inhibitors.
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Jaspreet Kaur Dhanjal, Sonam Grover, Sudhanshu Sharma, Ajeet Singh, and Abhinav Grover
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- 2014
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35. Double Mutants in DNA Gyrase Lead to Ofloxacin Resistance in Mycobacterium tuberculosis
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Salma Jamal, Sonam Grover, Bharati Pandey, Chetna Tyagi, Abhinav Grover, Sukriti Goyal, Jagdeep Kaur, and Aditi Singh
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0301 basic medicine ,Mutation ,030106 microbiology ,Mutant ,Cell Biology ,Drug resistance ,Biology ,biology.organism_classification ,medicine.disease_cause ,Biochemistry ,DNA gyrase ,Microbiology ,Mycobacterium tuberculosis ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Mutant protein ,medicine ,Ofloxacin ,Molecular Biology ,DNA ,medicine.drug - Abstract
Fluoroquinolones are among the most important classes of highly effective antibacterial drugs, exhibiting wide range of activity to cure infectious diseases. Ofloxacin is second generation fluoroquinolone approved by FDA for the treatment of tuberculosis by selectively inhibiting DNA gyrase. However, the emergence of drug resistance owing to mutations in DNA gyrase poses intimidating challenge for the effective therapy of this drug. The double mutants GyrAA90V GyrBD500N and GyrAA90V GyrBT539N are reported to be implicated in conferring higher levels of OFX resistance. The present study was designed to unravel the molecular principles behind development of resistance by the bug against fluoroquinolones. Our results highlighted that polar interactions play critical role in the development of drug resistance and highlight the significant correlation between the free energy calculations predicted by MM-PBSA and stability of the ligand-bound complexes. Modifications at the OFX binding pocket due to amino acid substitution leads to fewer hydrogen bonds in mutants DNA gyrase-OFX complex, which determined the low susceptibility of the ligand in inhibiting the mutant protein. This study provides a structural rationale to the mutation-based resistance to ofloxacin and will pave way for development potent fluoroquinolone-based resistant-defiant drugs. J. Cell. Biochem. 118: 2950-2957, 2017. © 2017 Wiley Periodicals, Inc.
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- 2017
36. Dynamics of fluoroquinolones induced resistance in DNA gyrase of Mycobacterium tuberculosis
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Salma Jamal, Sukriti Goyal, Chetna Tyagi, Abhinav Grover, Aditi Singh, Bharati Pandey, Jagdeep Kaur, and Sonam Grover
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0301 basic medicine ,030103 biophysics ,Protein subunit ,Moxifloxacin ,Mutant ,Microbial Sensitivity Tests ,Biology ,DNA gyrase ,Microbiology ,Mycobacterium tuberculosis ,Structure-Activity Relationship ,03 medical and health sciences ,chemistry.chemical_compound ,Structural Biology ,Drug Resistance, Bacterial ,Humans ,Topoisomerase II Inhibitors ,Tuberculosis ,Molecular Biology ,Molecular Structure ,Wild type ,General Medicine ,biology.organism_classification ,Molecular biology ,Molecular Docking Simulation ,Multiple drug resistance ,030104 developmental biology ,chemistry ,DNA Gyrase ,Docking (molecular) ,Mutation ,DNA ,Fluoroquinolones - Abstract
DNA gyrase is a validated target of fluoroquinolones which are key components of multidrug resistance tuberculosis (TB) treatment. Most frequent occurring mutations associated with high level of resistance to fluoroquinolone in clinical isolates of TB patients are A90V, D94G, and A90V-D94G (double mutant [DM]), present in the larger subunit of DNA Gyrase. In order to explicate the molecular mechanism of drug resistance corresponding to these mutations, molecular dynamics (MD) and mechanics approach was applied. Structure-based molecular docking of complex comprised of DNA bound with Gyrase A (large subunit) and Gyrase C (small subunit) with moxifloxacin (MFX) revealed high binding affinity to wild type with considerably high Glide XP docking score of -7.88 kcal/mol. MFX affinity decreases toward single mutants and was minimum toward the DM with a docking score of -3.82 kcal/mol. Docking studies were also performed against 8-Methyl-moxifloxacin which exhibited higher binding affinity against wild and mutants DNA gyrase when compared to MFX. Molecular Mechanics/Generalized Born Surface Area method predicted the binding free energy of the wild, A90V, D94G, and DM complexes to be -55.81, -25.87, -20.45, and -12.29 kcal/mol, respectively. These complexes were further subjected to 30 ns long MD simulations to examine significant interactions and conformational flexibilities in terms of root mean square deviation, root mean square fluctuation, and strength of hydrogen bond formed. This comparative drug interaction analysis provides systematic insights into the mechanism behind drug resistance and also paves way toward identifying potent lead compounds that could combat drug resistance of DNA gyrase due to mutations.
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- 2017
37. Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis
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Jagdeep Kaur, Sonam Grover, Bharati Pandey, and Abhinav Grover
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0301 basic medicine ,Biochemical Phenomena ,030106 microbiology ,Mutation, Missense ,lcsh:Medicine ,Protein function predictions ,Molecular Dynamics Simulation ,medicine.disease_cause ,Thymidylate synthase ,Cofactor ,Article ,Mycobacterium tuberculosis ,03 medical and health sciences ,Drug Resistance, Bacterial ,medicine ,Missense mutation ,Humans ,Binding site ,lcsh:Science ,chemistry.chemical_classification ,Mutation ,Multidisciplinary ,Binding Sites ,biology ,Diagnostic Tests, Routine ,lcsh:R ,Thymidylate Synthase ,biology.organism_classification ,Aminosalicylic Acid ,030104 developmental biology ,Enzyme ,chemistry ,Biochemistry ,biology.protein ,lcsh:Q ,Molecular modelling ,Mycobacterium - Abstract
Thymidylate synthase A (ThyA) is the key enzyme involved in the folate pathway in Mycobacterium tuberculosis. Mutation of key residues of ThyA enzyme which are involved in interaction with substrate 2′-deoxyuridine-5′-monophosphate (dUMP), cofactor 5,10-methylenetetrahydrofolate (MTHF), and catalytic site have caused para-aminosalicylic acid (PAS) resistance in TB patients. Focusing on R127L, L143P, C146R, L172P, A182P, and V261G mutations, including wild-type, we performed long molecular dynamics (MD) simulations in explicit solvent to investigate the molecular principles underlying PAS resistance due to missense mutations. We found that these mutations lead to (i) extensive changes in the dUMP and MTHF binding sites, (ii) weak interaction of ThyA enzyme with dUMP and MTHF by inducing conformational changes in the structure, (iii) loss of the hydrogen bond and other atomic interactions and (iv) enhanced movement of protein atoms indicated by principal component analysis (PCA). In this study, MD simulations framework has provided considerable insight into mutation induced conformational changes in the ThyA enzyme of Mycobacterium.
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- 2019
38. Peptidyl-prolyl isomerase-B is involved in Mycobacterium tuberculosis biofilm formation and a generic target for drug repurposing-based intervention
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Ashutosh Kumar, Sonam Grover, Monika Kumari, Seyed E. Hasnain, Deeksha Tripathi, Mamta Rani, Nasreen Z. Ehtesham, Saurabh Pandey, Anwar Alam, Aditi Singh, and Yusuf Akhter
- Subjects
Tuberculosis ,biology ,medicine.drug_class ,Mycobacterium smegmatis ,Isoniazid ,Antibiotics ,Biofilm ,biology.organism_classification ,medicine.disease ,Applied Microbiology and Biotechnology ,Microbiology ,lcsh:Microbial ecology ,Mycobacterium tuberculosis ,PPIB ,medicine ,lcsh:QR100-130 ,Ethambutol ,Biotechnology ,medicine.drug - Abstract
Tuberculosis (TB), a disease caused by Mycobacterium tuberculosis (M.tb), takes one human life every 15 s globally. Disease relapse occurs due to incomplete clearance of the pathogen and reactivation of the antibiotic tolerant bacilli. M.tb, like other bacterial pathogens, creates an ecosystem of biofilm formed by several proteins including the cyclophilins. We show that the M.tb cyclophilin peptidyl-prolyl isomerase (PpiB), an essential gene, is involved in biofilm formation and tolerance to anti-mycobacterial drugs. We predicted interaction between PpiB and US FDA approved drugs (cyclosporine-A and acarbose) by in-silico docking studies and this was confirmed by surface plasmon resonance (SPR) spectroscopy. While all these drugs inhibited growth of Mycobacterium smegmatis (M.smegmatis) when cultured in vitro, acarbose and cyclosporine-A showed bacteriostatic effect while gallium nanoparticle (GaNP) exhibited bactericidal effect. Cyclosporine-A and GaNP additionally disrupted M.tb H37Rv biofilm formation. Co-culturing M.tb in their presence resulted in significant (2–4 fold) decrease in dosage of anti-tubercular drugs- isoniazid and ethambutol. Comparison of the cyclosporine-A and acarbose binding sites in PpiB homologues of other biofilm forming infectious pathogens revealed that these have largely remained unaltered across bacterial species. Targeting bacterial biofilms could be a generic strategy for intervention against bacterial pathogens. Tuberculosis, caused by Mycobacterium tuberculosis, is the leading cause of death due to a single infectious agent. New therapeutic options are needed, and repurposing clinically approved drugs to destroy biofilms is an attractive approach, as these microbial communities are often less susceptible to antibiotics. A team lead by Seyed Hasnain at the Indian Institute of Technology Delhi identified an enzyme, PpiB, from M. tuberculosis that promoted biofilm formation and showed that PpiB interacts with several drugs that are currently used to treat diabetes, immunological diseases and cancer. These drugs destabilise M. tuberculosis biofilms in culture and enhanced the potency of two current anti-tuberculosis antibiotics. Future work is needed to test these medications against tuberculosis in humans, but given PpiB is found in different bacteria, there may be broader promise of using these repurposed drugs to combat other infections.
- Published
- 2019
39. Endoplasmic Reticulum Stress: Importance in Pathogenesis of Mycobacterium tuberculosis
- Author
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Tarina Sharma, Sonam Grover, Seyed E. Hasnain, and Nasreen Z. Ehtesham
- Subjects
Mycobacterium tuberculosis ,Pathogenesis ,Tuberculosis ,Antigen ,ATF6 ,Endoplasmic reticulum ,Immunology ,Unfolded protein response ,medicine ,Biology ,medicine.disease ,biology.organism_classification ,Pathogen - Abstract
Mycobacterium tuberculosis (M.tb), the cause of deadly disease tuberculosis, is an opportunistic pathogen that primarily infects host alveolar macrophages. M.tb has developed several mechanisms to persist in infected host cells and to disseminate the disease. Its pathogenesis mainly depends on its competence to modulate the host machinery for its own benefit. One of the cellular responses triggered by M.tb is endoplasmic reticulum stress in infected macrophages, which eventually disturbs the physiological functioning of the ER. Uncontrolled ER stress activates IRE1, PERK, and ATF6 pathway to induce apoptosis of infected cells. Although apoptosis is known to control and clear the infection in primary stages of infection, in case of M.tb-infected ER stressed macrophages, apoptosis is able to disseminate the pathogen during its advanced stages. M.tb-infected lung granulomas are the preferential site of accumulation of apoptotic macrophages, thereby increasing the risk of disease dissemination. The present chapter will describe the mechanism for ER stress response generated by known M.tb virulence factors such as ESAT-6, HBHA, 38-kDa antigen, and PE_PGRS5. Future insights to describe M.tb infection in respect of eliciting ER stress response-mediated apoptosis and host interacting partners has the potential in identifying novel targets for vaccination and drugs to combat the disease.
- Published
- 2019
40. Mycobacterial Methyltransferases: Significance in Pathogenesis and Virulence
- Author
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Salma Jamal, Sonam Grover, Nasreen Z. Ehtesham, Rishabh Gangwar, Seyed E. Hasnain, Sabeeha Ali, and Khairun Nisaa
- Subjects
chemistry.chemical_classification ,Methyltransferase ,chemistry ,Mechanism (biology) ,Virulence ,RNA ,Methylation ,Computational biology ,Epigenetics ,Biology ,Genome ,Mycolic acid - Abstract
Mycobacterium tuberculosis (M.tb) is a pathogen of incredible international prominence owing to its persistence for long duration inside human host in both active and latent form, complex eradication methods and imposing long-term treatment procedures. The mechanisms employed by M.tb to adjust and survive inside extreme host environment and to evade the immune system of host need to be explored in greater depth in order to enable the rational design of novel treatment strategies. Methylation of biomolecules plays a significant role in almost every kingdom of life but has not been extensively addressed in the case of M.tb. The genome of M.tb codes for 121 methyltransferases (MTases) in spite of the reductive evolution of its genome. In the present chapter, we will discuss in detail about various MTases modifying DNA, RNA, protein, mycolic acid and other biomolecules of M.tb along with the host. This will also shed light on how methylation is implicated in virulence and influences the mechanism of pathogenesis of M.tb.
- Published
- 2019
41. Mycobacterium Tuberculosis: Molecular Infection Biology, Pathogenesis, Diagnostics and New Interventions
- Author
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Seyed Ehtesham Hasnain, Nasreen Z. Ehtesham, Sonam Grover, Seyed Ehtesham Hasnain, Nasreen Z. Ehtesham, and Sonam Grover
- Subjects
- Parasitology, Diseases, Post-translational modification, Immunology, Pharmacology
- Abstract
This book reviews recent advances in the molecular and infection biology, pathology, and molecular epidemiology of Mycobacterium tuberculosis, as well as the identification and validation of novel molecular drug targets for the treatment of this mycobacterial disease.Despite being completely curable, tuberculosis is still one of the leading global causes of death. M. tuberculosis, the causative organism – one of the smartest pathogens known – adopts highly intelligent strategies for survival and pathogenesis. Presenting a wealth of information on the molecular infection biology of M. tuberculosis, as well as nontuberculous mycobacteria (NTM), the book provides an overview of the functional role of the PE/PPE group of proteins, which is exclusive to the genus Mycobacteria, of host-pathogen interactions, and virulence. It also explores the pathogenesis of the infection, pathology, epidemiology, and diagnosis of NTM. Finally it discusses current and novel approaches in vaccine development against tuberculosis, including the role of nanotechnology. With state-of-the-art contributions from experts in the respective domains, this book is an informative resource for practitioners as well as medical postgraduate students and researchers.
- Published
- 2019
42. Cheminformatics Based Machine Learning Approaches for Assessing Glycolytic Pathway Antagonists of Mycobacterium tuberculosis
- Author
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Sonam Grover, Salma Jamal, Kanupriya Tiwari, Sukriti Goyal, Abhinav Grover, and Aditi Singh
- Subjects
0301 basic medicine ,Tuberculosis ,In silico ,Overfitting ,Biology ,Machine learning ,computer.software_genre ,Machine Learning ,Mycobacterium tuberculosis ,03 medical and health sciences ,Naive Bayes classifier ,Fructose-Bisphosphate Aldolase ,Drug Discovery ,medicine ,Humans ,Enzyme Inhibitors ,business.industry ,Organic Chemistry ,Computational Biology ,General Medicine ,medicine.disease ,biology.organism_classification ,High-Throughput Screening Assays ,Computer Science Applications ,030104 developmental biology ,Drug development ,Infectious disease (medical specialty) ,Cheminformatics ,Drug Design ,Artificial intelligence ,business ,Glycolysis ,computer ,Algorithms - Abstract
Background: Tuberculosis is the second leading cause of death from an infectious disease worldwide after HIV, thus reasoning the expeditions in antituberculosis research. The rising number of cases of infection by resistant forms of M. tuberculosis has given impetus to the development of novel drugs that have different targets and mechanisms of action against the bacterium. Methods: In this study, we have used machine learning algorithms on the available high throughput screening data of inhibitors of fructose bisphosphate aldolase, an enzyme central to the glycolysis pathway in M. tuberculosis, to build predictive classification models to identify actives against Mycobacterium tuberculosis, the causative organism of tuberculosis. We used Naive Bayes, Random Forest and C4.5 J48 algorithms available from Weka were used for building predictive classification models. Additionally, a set of most relevant attributes was selected using genetic search algorithm which offered improved model performance by avoiding over fitting and generating faster and cost effective models. Results: The model built using machine learning methods in this study provided good accuracy of classification of test compounds which suggests that in silico methods can be successfully used for screening of large datasets to identify potential drug leads. The substructure fragment analysis serves to further potentiate the M. tuberculosis drug development process as it would facilitate identification of structural fragments that are responsible for biological activity against this crucial glycolysis pathway target.
- Published
- 2016
43. Molecular principles behind pyrazinamide resistance due to mutations in panD gene in Mycobacterium tuberculosis
- Author
-
Sukriti Goyal, Salma Jamal, Jagdeep Kaur, Bharati Pandey, Chetna Tyagi, Abhinav Grover, Sonam Grover, and Aditi Singh
- Subjects
0301 basic medicine ,Protein Conformation ,Antitubercular Agents ,Drug resistance ,Molecular Dynamics Simulation ,Ligands ,Mycobacterium tuberculosis ,03 medical and health sciences ,0302 clinical medicine ,Protein structure ,Bacterial Proteins ,Mutant protein ,Drug Resistance, Bacterial ,Genetics ,medicine ,Gene ,Histidine ,Principal Component Analysis ,biology ,General Medicine ,Pyrazinamide ,biology.organism_classification ,030104 developmental biology ,Genes, Bacterial ,Docking (molecular) ,030220 oncology & carcinogenesis ,Mutation ,medicine.drug - Abstract
The latest resurrection of drug resistance poses serious threat to the treatment and control of the disease. Mutations have been detected in panD gene in the Mycobacterium tuberculosis (Mtb) strains. Mutation of histidine to arginine at residue 21 (H21R) and isoleucine to valine at residue 29 (I49V) in the non-active site of panD gene has led to PZA resistance. This study will help in reconnoitering the mechanism of pyrazinamide (PZA) resistance caused due to double mutation identified in the panD gene of M. tuberculosis clinical isolates. It is known that panD gene encodes aspartate decarboxylase essential for β-alanine synthesis that makes it a potential therapeutic drug target for tuberculosis treatment. The knowledge about the molecular mechanism conferring drug resistance in M. tuberculosis is scarce, which is a significant challenge in designing successful therapeutic drug. In this study, structural and dynamic repercussions of H21R-I49V double mutation in panD complexed with PZA have been corroborated through docking and molecular dynamics based simulation. The double mutant (DM) shows low docking score and thus, low binding affinity for PZA as compared to the native protein. It was observed that the mutant protein exhibits more structural fluctuation at the ligand binding site in comparison to the native type. Furthermore, the flexibility and compactness analyses indicate that the double mutation influence interaction of PZA with the protein. The hydrogen-bond interaction patterns further supported our results. The covariance and PCA analysis elucidated that the double mutation affects the collective motion of residues in phase space. The results have been presented with an explanation for the induced drug resistance conferred by the H21R-I49V double mutation in panD gene and gain valuable insight to facilitate the advent of efficient therapeutics for combating resistance against PZA.
- Published
- 2016
44. Analyses of methyltransferases across the pathogenicity spectrum of different mycobacterial species point to an extremophile connection
- Author
-
Sonam Grover, Kuldeep Dalal, Seyed E. Hasnain, Paras Gupta, Nasreen Z. Ehtesham, Abhinav Grover, Parvinderdeep S. Kahlon, Sukriti Goyal, and Sabeeha
- Subjects
Proteomics ,0301 basic medicine ,Methyltransferase ,Gene Transfer, Horizontal ,Virulence Factors ,030106 microbiology ,Virulence ,Mycobacterium ,03 medical and health sciences ,Species Specificity ,Molecular Biology ,Genetics ,Antigens, Bacterial ,Genes, Essential ,Phylogenetic tree ,biology ,Point mutation ,DNA ,Methyltransferases ,biology.organism_classification ,Genes, Bacterial ,Proteome ,Niche adaptation ,Function (biology) ,Biotechnology - Abstract
Tuberculosis is a devastating disease, taking one human life every 20 seconds globally. We hypothesize that professional pathogens such as M.tb have acquired specific features that might assist in causing infection, persistence and transmissible pathology in their host. We have identified 121 methyltransferases (MTases) in the M.tb proteome, which use a variety of substrates - DNA, RNA, protein, intermediates of mycolic acid biosynthesis and other fatty acids - that are involved in cellular maintenance within the host. A comparative analysis of the proteome of the virulent strain H37Rv and the avirulent strain H37Ra identified 3 MTases, which displayed significant variations in terms of N-terminal extension/deletion and point mutations, possibly impacting various physicochemical properties. The cross-proteomic comparison of MTases of M.tb H37Rv with 15 different Mycobacterium species revealed the acquisition of novel MTases in a MTB complex as a function of evolution. Phylogenetic analysis revealed that these newly acquired MTases showed common roots with certain extremophiles such as halophilic and acidophilic organisms. Our results establish an evolutionary relationship of M.tb with halotolerant organisms and also the role of MTases of M.tb in withstanding the host osmotic stress, thereby pointing to their likely role in pathogenesis, virulence and niche adaptation.
- Published
- 2016
45. Structural basis for isoniazid resistance in KatG double mutants of Mycobacterium tuberculosis
- Author
-
Bharati Pandey, Aditi Singh, Abhinav Grover, Anchala Kumari, Sonam Grover, and Aneesh Rabha
- Subjects
0301 basic medicine ,Protein Conformation ,030106 microbiology ,Mutant ,Antitubercular Agents ,Drug resistance ,Molecular Dynamics Simulation ,Microbiology ,Mycobacterium tuberculosis ,03 medical and health sciences ,Bacterial Proteins ,Drug Resistance, Bacterial ,medicine ,Isoniazid ,Catalase-peroxidase ,biology ,Chemistry ,Active site ,biology.organism_classification ,Catalase ,Molecular biology ,030104 developmental biology ,Infectious Diseases ,Docking (molecular) ,Mutation ,biology.protein ,Mutant Proteins ,Mycobacterium ,medicine.drug ,Protein Binding - Abstract
The failure of drugs for effective treatment against infectious diseases can be attributed to resistant forms of causative agents. The evasive nature of Mycobacterium tuberculosis is partly associated to its physical features, such as having a thick cell wall and incorporation of beneficial mutations leading to drug resistance. The pro drug Isoniazid (INH) interacts with an enzyme catalase peroxidase to get converted into its active form and upon activation stops the cell wall synthesis thus killing the Mycobacterium. The most common mutation i.e. S315T leads to high degree of drug resistance by virtue of its position in the active site. Here, we have characterized the prominent attributes of two double mutant isolates S315 T/D194G and S315T/M624V which are multi drug resistant and extremely drug resistant, respectively. Protein models were generated using the crystal structure which were then subjected to energy minimization and long term molecular dynamics simulations. Further, computational analysis showed decreasing ability of INH binding to the mutants in order of: Native > S315T/D194G > S315T/M624V. Also, a trend was observed that as the docking score and binding area decreased, there was a significant increase in the distortion of the 3D geometry of the mutants as observed by PCA analysis.
- Published
- 2018
46. Whole genome sequencing: A new paradigm in the surveillance and control of human tuberculosis
- Author
-
Nasreen Z. Ehtesham, Sonam Grover, Seyed E. Hasnain, and Ronan F. O’Toole
- Subjects
Microbiology (medical) ,Tuberculosis ,Immunology ,Computational biology ,Bacterial genome size ,Microbiology ,DNA sequencing ,Disease Outbreaks ,Mycobacterium tuberculosis ,Drug Resistance, Bacterial ,medicine ,Humans ,Whole genome sequencing ,biology ,business.industry ,biology.organism_classification ,medicine.disease ,Bacterial Typing Techniques ,Biotechnology ,Molecular Typing ,Infectious Diseases ,Population Surveillance ,business ,Genome, Bacterial - Abstract
Whole Genome Sequencing (WGS) is emerging as a very powerful tool for the management, outbreak analyses, surveillance and determining drug resistance of human infectious pathogens including Mycobacterium tuberculosis and MRSA. WGS can also discriminate relapse TB from re-infection and the resolution provided by WGS has no comparison to conventional technologies. With current cost coming down to
- Published
- 2015
47. Wild-type catalase peroxidase vs G279D mutant type: Molecular basis of Isoniazid drug resistance in Mycobacterium tuberculosis
- Author
-
Anchala Kumari, Aditi Singh, Bharati Pandey, Abhinav Grover, Aishwarya Singh, and Sonam Grover
- Subjects
0301 basic medicine ,030103 biophysics ,Mutant ,Glycine ,Biology ,Molecular Dynamics Simulation ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,Mutant protein ,Drug Resistance, Bacterial ,Genetics ,medicine ,Isoniazid ,Heme ,Catalase-peroxidase ,Peroxidase ,chemistry.chemical_classification ,Aspartic Acid ,Wild type ,General Medicine ,Mycobacterium tuberculosis ,biochemical phenomena, metabolism, and nutrition ,bacterial infections and mycoses ,Catalase ,Molecular biology ,030104 developmental biology ,Enzyme ,Biochemistry ,chemistry ,Genes, Bacterial ,Mutation ,Mutant Proteins ,medicine.drug - Abstract
Mycobacterium tuberculosis katG gene is responsible for production of an enzyme catalase peroxidase that peroxidises and activates the prodrug Isoniazid (INH), a first-line antitubercular agent. INH interacts with catalase peroxidase enzyme within its heme pocket and gets converted to an active form. Mutations occurring in katG gene are often linked to reduced conversion rates for INH. This study is focussed on one such mutation occurring at residue 279, where glycine often mutates to aspartic acid (G279D). In the present study, several structural analyses were performed to study the effect of this mutation on functionality of KatG protein. On comparison, mutant protein exhibited a lower docking score, smaller binding cavity and reduced affinity towards INH. Molecular dynamics analysis revealed the mutant to be more rigid and less compact than the native protein. Essential dynamics analysis determined correlated motions of residues within the protein structure. G279D mutant was found to have many residues that showed related motions and an undesirable effect on the functionality of protein.
- Published
- 2017
48. Mechanistic Principles Behind Molecular Mechanism of Rifampicin Resistance in Mutant RNA Polymerase Beta Subunit of Mycobacterium tuberculosis
- Author
-
Pallavi Somvanshi, Aditi Singh, Siddharth Sinha, Sonam Grover, Abhinav Grover, and Mriganko Das
- Subjects
0301 basic medicine ,030106 microbiology ,Mutant ,Biology ,Molecular Dynamics Simulation ,Biochemistry ,Mycobacterium tuberculosis ,03 medical and health sciences ,Bacterial Proteins ,Mutant protein ,Drug Resistance, Bacterial ,polycyclic compounds ,medicine ,Binding site ,Molecular Biology ,Genetics ,Binding Sites ,Wild type ,Cell Biology ,DNA-Directed RNA Polymerases ,bacterial infections and mycoses ,rpoB ,biology.organism_classification ,Molecular biology ,030104 developmental biology ,Mutation ,Rifampin ,Rifampicin ,medicine.drug ,Mycobacterium - Abstract
Evolution of drug-resistant Mycobacterium strains threatens the TB treatment and control programs globally. Rifampicin (RIF) is an important first line antitubercular drug. Resistance to Rifampicin is caused mainly by mutations in its target RNA polymerase beta subunit protein (RpoB). RpoB contains a Rifampicin resistance determining region (RRDR) and has several potent sites for mutations. In this study, we have investigated mutations of a single site (H451) to eight different amino acids, involved in RIF resistance. Long-term molecular dynamics simulations were performed on wild type (WT) and mutant protein structures and various structural analysis were carried out to elucidate the dynamic behavior of WT and mutant forms. Essential dynamics uncovered the difference in conformational flexibility and collective modes of motions between WT and mutants. MMPBSA calculations and interaction pattern analysis revealed the binding site relocation in some mutants. This study presents an exhaustive analysis of RIF binding to the WT and mutant RpoB and clearly highlights structural mechanism for differences in stable binding of Rifampicin with WT than the mutant targets. J. Cell. Biochem. 118: 4594-4606, 2017. © 2017 Wiley Periodicals, Inc.
- Published
- 2017
49. Group-based QSAR and molecular dynamics mechanistic analysis revealing the mode of action of novel piperidinone derived protein–protein inhibitors of p53-MDM2
- Author
-
Sonam Grover, Chetna Tyagi, Abhinav Grover, Manisha Goyal, Sukriti Goyal, and Jaspreet Kaur Dhanjal
- Subjects
Quantitative structure–activity relationship ,Stereochemistry ,DNA repair ,Regulator ,Quantitative Structure-Activity Relationship ,Antineoplastic Agents ,Molecular Dynamics Simulation ,P53 mdm2 ,Molecular dynamics ,Piperidines ,Materials Chemistry ,Humans ,Molecule ,Protein Interaction Domains and Motifs ,Physical and Theoretical Chemistry ,Spectroscopy ,Binding Sites ,biology ,Chemistry ,Robustness (evolution) ,Hydrogen Bonding ,Proto-Oncogene Proteins c-mdm2 ,Computer Graphics and Computer-Aided Design ,Molecular Docking Simulation ,biology.protein ,Mdm2 ,Tumor Suppressor Protein p53 ,Hydrophobic and Hydrophilic Interactions ,Protein Binding - Abstract
Tumour suppressor p53 is known to play a central role in prevention of tumour development, DNA repair, senescence and apoptosis which is in normal cells maintained by negative feedback regulator MDM2 (Murine Double Minute 2). In case of dysfunctioning of this regulatory loop, tumour development starts thus resulting in cancerous condition. Inhibition of p53-MDM2 binding would result in activation of the tumour suppressor. In this study, a novel robust fragment-based QSAR model has been developed for piperidinone derived compounds experimentally known to inhibit p53-MDM2 interaction. The QSAR model developed showed satisfactory statistical parameters for the experimentally reported dataset (r2 = 0.9415, q2 = 0.8958, pred_r2 = 0.8894 and F-test = 112.7314), thus judging the robustness of the model. Low standard error values (r2_se = 0.3003, q2_se = 0.4009 and pred_r2_se = 0.3315) confirmed the accuracy of the developed model. The regression equation obtained constituted three descriptors (R2-DeltaEpsilonA, R1-RotatableBondCount and R2-SssOCount), two of which had positive contribution while third showed negative correlation. Based on the developed QSAR model, a combinatorial library was generated and activities of the compounds were predicted. These compounds were docked with MDM2 and two top scoring compounds with binding affinities of −10.13 and −9.80 kcal/mol were selected. The binding modes of actions of these complexes were analyzed using molecular dynamics simulations. Analysis of the developed fragment-based QSAR model revealed that addition of unsaturated electronegative groups at R2 site and groups with more rotatable bonds at R1 improved the inhibitory activity of these potent lead compounds. The detailed analysis carried out in this study provides a considerable basis for the design and development of novel piperidinone-based lead molecules against cancer and also provides mechanistic insights into their mode of actions.
- Published
- 2014
50. Double Mutants in DNA Gyrase Lead to Ofloxacin Resistance in Mycobacterium tuberculosis
- Author
-
Bharati, Pandey, Sonam, Grover, Chetna, Tyagi, Sukriti, Goyal, Salma, Jamal, Aditi, Singh, Jagdeep, Kaur, and Abhinav, Grover
- Subjects
Ofloxacin ,Amino Acid Substitution ,Bacterial Proteins ,DNA Gyrase ,Drug Resistance, Bacterial ,Mutation, Missense ,Mycobacterium tuberculosis - Abstract
Fluoroquinolones are among the most important classes of highly effective antibacterial drugs, exhibiting wide range of activity to cure infectious diseases. Ofloxacin is second generation fluoroquinolone approved by FDA for the treatment of tuberculosis by selectively inhibiting DNA gyrase. However, the emergence of drug resistance owing to mutations in DNA gyrase poses intimidating challenge for the effective therapy of this drug. The double mutants GyrA
- Published
- 2016
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