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Article ; Online: Antimicrobial resistance: new insights and therapeutic implications.

Sheikh, Bashir Ahmad / Bhat, Basharat Ahmad / Mir, Manzoor Ahmad

2022 Volume 106, Issue 19-20, Page(s) 6427–6440

Abstract: Antimicrobial resistance has not been a new phenomenon. Still, the number of resistant organisms, the geographic areas affected by emerging drug resistance, and the magnitude of resistance in a single organism are enormous and mounting. Disease and ... ...

Abstract	Antimicrobial resistance has not been a new phenomenon. Still, the number of resistant organisms, the geographic areas affected by emerging drug resistance, and the magnitude of resistance in a single organism are enormous and mounting. Disease and disease-causing agents formerly thought to be contained by antibiotics are now returning in new forms resistant to existing therapies. Antimicrobial resistance is one of the most severe and complicated health issues globally, driven by interrelated dynamics in humans, animals, and environmental health sectors. Coupled with various epidemiological factors and a limited pipeline for new antimicrobials, all these misappropriations allow the transmission of drug-resistant organisms. The problem is likely to worsen soon. Antimicrobial resistance in general and antibiotic resistance in particular is a shared global problem. Actions taken by any single country can adversely or positively affect the other country. Targeted coordination and prevention strategies are critical in stopping the spread of antibiotic-resistant organisms and hence its overall management. This article has provided in-depth knowledge about various methods that can help mitigate the emergence and spread of antimicrobial resistance globally. KEY POINTS: • Overview of antimicrobial resistance as a global challenge and explain various reasons for its rapid progression. • Brief about the intrinsic and acquired resistance to antimicrobials and development of antibiotic resistance in bacteria. • Systematically organized information is provided on different strategies for tackling antimicrobial resistance for the welfare of human health.
MeSH term(s)	Animals ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Bacteria ; Drug Resistance, Bacterial ; Humans
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2022-09-19
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-022-12175-8
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Article ; Online: Exploration of comprehensive marine natural products database against dengue viral non-structural protein 1 using high-throughput computational studies.

Bhat, Basharat Ahmad / Algaissi, Abdullah / Khamjan, Nizar A / Dar, Tanvir Ul Hassan / Dar, Sajad Ahmad / Varadharajan, Venkatramanan / Qasir, Naif A / Lohani, Mohtashim

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–10

Abstract: Dengue virus (DENV) non-structural protein 1 (NS1) is a versatile quasi-protein essential for the multiplication of the virus. This study applied high-throughput virtual screening (HTVS) and molecular dynamics (MD) simulation to detect the potential ... ...

Abstract	Dengue virus (DENV) non-structural protein 1 (NS1) is a versatile quasi-protein essential for the multiplication of the virus. This study applied high-throughput virtual screening (HTVS) and molecular dynamics (MD) simulation to detect the potential marine natural compounds against the NS1 of DENV. The structure of the NS1 protein was retrieved from Protein Data Bank with (PDB ID: 4O6B). Missing residues were added using modeler software. Molecular operating environment (MOE) programme was used to prepare the protein before docking. Virtual screening was performed on PyRx software to identify natural compounds retrieved from Comprehensive Marine Natural Products Database (CMNPD) against the NS1 protein, and best-docked compounds were examined by molecular docking and molecular dynamic (MD) simulation. Out of 31,561 marine compounds, the top 10 compounds showed docking scores lesser than -8.0 kcal/mol. One of the best hit compounds, CMNPD6802, was further analyzed using MD simulation study at 100 nanoseconds and Molecular Mechanics with Generalized Born and Surface Area Solvation (MM/GBSA). Based on its total binding energy, determined using the MM/GBSA approach, CMNPD6802 was ranked first. Its pharmacokinetic properties concerning the target protein NS1 were also evaluated. The results of the MD simulation showed that CMNPD6802 remained in close contact with the protein throughout the activation period, mapped using principal component analysis. These findings suggest that CMNPD6802 could serve as an NS1 inhibitor and may be a potential candidate for treating DENV infections.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2297006
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Article: Editorial: Omics technologies in livestock improvement: From selection to breeding decisions.

Ahmad, Syed Mudasir / De Donato, Marcos / Bhat, Basharat Ahmad / Diallo, Abdoulaye Banire / Peters, Sunday O

Frontiers in genetics

2023 Volume 13, Page(s) 1113417

Language	English
Publishing date	2023-01-04
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.1113417
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Article ; Online: Network pharmacology and experimental validation for deciphering the action mechanism of

Bhat, Basharat Ahmad / Rashid Mir, Wajahat / Alkhanani, Mustfa / Almilaibary, Abdullah / Mir, Manzoor Ahmad

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–21

Abstract: Fritillaria ... ...

Abstract	Fritillaria cirrhosa
Language	English
Publishing date	2023-11-10
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2274966
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Article ; Online: Metabolite fingerprinting of phytoconstituents from Fritillaria cirrhosa D. Don and molecular docking analysis of bioactive peonidin with microbial drug target proteins.

Bhat, Basharat Ahmad / Mir, Wajahat Rashid / Sheikh, Bashir Ahmad / Alkanani, Mustafa / Mir, Manzoor Ahmad

Scientific reports

2022 Volume 12, Issue 1, Page(s) 7296

Abstract: Fritillaria cirrhosa D. Don (Liliaceae), a valuable and critically endangered medicinal herb of northwest India, including Jammu and Kashmir, grows in temperate to alpine regions of the Himalaya. It is known as the traditional herb for cardiovascular ... ...

Abstract	Fritillaria cirrhosa D. Don (Liliaceae), a valuable and critically endangered medicinal herb of northwest India, including Jammu and Kashmir, grows in temperate to alpine regions of the Himalaya. It is known as the traditional herb for cardiovascular diseases, respiratory diseases, and metabolic disorders. The plant bulbs are precious and are used to cure many other health complications. The current study analysed the phytoconstituents by liquid chromatography-mass spectrometry (LC-MS) of different crude extracts (methanolic, petroleum ether, and ethyl acetate) of F. cirrhosa. The LC-MS analysis from the bulbs of F. cirrhosa yielded 88 bioactive compounds, with the vast majority having therapeutic applications. Further, determination of minimum inhibitory concentrations (MICs) by broth microdilution method of F. cirrhosa against tested bacterial and fungal pathogens showed remarkable results with MICs ranging between 6.25-200 µg/mL and 50-400 µg/mL, respectively. Subsequently, these 88 identified phytocompounds were tested for their bioactivity through ADMET prediction by SwissADME and in silico molecular docking studies. Results revealed that Peonidin might have maximum antibacterial and antifungal activity against various microbial protein drug targets among the phytochemical compounds identified. Furthermore, the highest binding affinity complex was subjected to molecular dynamic simulation (MDS) analysis using Desmond Schrodinger v3.8. The root-mean-square deviation (RMSD) graphs obtained through the molecular dynamic simulations indicated the true bonding interactions, further validated using the root-mean-square fluctuation (RMSF) graphs which provided a better understanding of the amino acids present in the proteins responsible for the molecular motions and fluctuations. To our best knowledge, this is the first description of the phytochemical constituents of the bulbs of F.cirrhosa analyzed through LC-MS, which show pharmacological significance. The in silico molecular docking and molecular dynamics study of peonidin was also performed to confirm its broad-spectrum activities based on the binding interactions with the antibacterial and antifungal target proteins. The present study results will create a way for the invention of herbal medicines for several ailments by using F. cirrhosa plants, which may lead to the development of novel drugs.
MeSH term(s)	Anthocyanins ; Anti-Bacterial Agents/pharmacology ; Antifungal Agents ; Fritillaria/chemistry ; Molecular Docking Simulation ; Phytochemicals/pharmacology ; Plant Extracts/pharmacology ; Plants, Medicinal/chemistry
Chemical Substances	Anthocyanins ; Anti-Bacterial Agents ; Antifungal Agents ; Phytochemicals ; Plant Extracts ; peonidin (D0O766G47B)
Language	English
Publishing date	2022-05-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-10796-7
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Article ; Online: Evaluation of the

Mir, Wajahat Rashid / Bhat, Basharat Ahmad / Almilaibary, Abdullah / Asdaq, Syed Mohammed Basheeruddin / Mir, Manzoor Ahmad

Medicinal chemistry (Shariqah (United Arab Emirates))

2022 Volume 18, Issue 10, Page(s) 1109–1121

Abstract: Ethnopharmacological relevance: The burden of antimicrobial resistance demands a continued search for new antimicrobial drugs. The synthetic drugs used clinically have serious side effects. Natural products or compounds derived from natural sources show ...

Abstract	Ethnopharmacological relevance: The burden of antimicrobial resistance demands a continued search for new antimicrobial drugs. The synthetic drugs used clinically have serious side effects. Natural products or compounds derived from natural sources show diversity in structure and play an essential role in drug discovery and development. Objective: Delphinium roylei is an important medicinal herb of Kashmir Himalaya, India. Traditionally this medicinal plant treats liver infections, skin problems, and chronic lower back pain. The current study evaluates the antimicrobial potential of various extracts by in -vitro and in -silico studies. Methods: Three extracts and 168 bioactive compounds analysed through LC-MS data, with the vast majority of them having therapeutic applications. D. roylei have been screened for the antimicrobial activity against bacteria (Escherichai coli, Streptococcus pneumonia, Haemophilus influenzae, Neisseria mucosa) and fungi (Candida albicans, Candida glabrata, Candida paropsilosis) species through molecular docking using autodock Vina, MD simulation and a broth microdilution method for minimum inhibitory concentration (MIC) evaluation. Results: The extracts and the compounds analyzed through the LC-MS technique of Delphinium roylie showed significant antimicrobial activity. Conclusion: Our study established that the leaf extracts of Delphinium roylei exhibit antimicrobial activity and thus confirm its importance in traditional medicine.
MeSH term(s)	Anti-Bacterial Agents ; Anti-Infective Agents ; Candida albicans ; Delphinium ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Plant Extracts ; Plants, Medicinal
Chemical Substances	Anti-Bacterial Agents ; Anti-Infective Agents ; Plant Extracts
Language	English
Publishing date	2022-05-04
Publishing country	Netherlands
Document type	Journal Article
ISSN	1875-6638
ISSN (online)	1875-6638
DOI	10.2174/1573406418666220429093956
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Article: Integrons in the development of antimicrobial resistance: critical review and perspectives.

Bhat, Basharat Ahmad / Mir, Rakeeb Ahmad / Qadri, Hafsa / Dhiman, Rohan / Almilaibary, Abdullah / Alkhanani, Mustfa / Mir, Manzoor Ahmad

Frontiers in microbiology

2023 Volume 14, Page(s) 1231938

Abstract: Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, ...

Abstract	Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, the key players capable of transferring genes from bacterial chromosomes to plasmids and their integration by integrase to the target pathogenic host. Moreover, integrons play a central role in disseminating and assembling genes connected with antibiotic resistance in pathogenic and commensal bacterial species. They exhibit a large and concealed diversity in the natural environment, raising concerns about their potential for comprehensive application in bacterial adaptation. They should be viewed as a dangerous pool of resistance determinants from the "One Health approach." Among the three documented classes of integrons reported viz., class-1, 2, and 3, class 1 has been found frequently associated with AMRs in humans and is a critical genetic element to serve as a target for therapeutics to AMRs through gene silencing or combinatorial therapies. The direct method of screening gene cassettes linked to pathogenesis and resistance harbored by integrons is a novel way to assess human health. In the last decade, they have witnessed surveying the integron-associated gene cassettes associated with increased drug tolerance and rising pathogenicity of human pathogenic microbes. Consequently, we aimed to unravel the structure and functions of integrons and their integration mechanism by understanding horizontal gene transfer from one trophic group to another. Many updates for the gene cassettes harbored by integrons related to resistance and pathogenicity are extensively explored. Additionally, an updated account of the assessment of AMRs and prevailing antibiotic resistance by integrons in humans is grossly detailed-lastly, the estimation of AMR dissemination by employing integrons as potential biomarkers are also highlighted. The current review on integrons will pave the way to clinical understanding for devising a roadmap solution to AMR and pathogenicity. Graphical AbstractThe graphical abstract displays how integron-aided AMRs to humans: Transposons capture integron gene cassettes to yield high mobility integrons that target res sites of plasmids. These plasmids, in turn, promote the mobility of acquired integrons into diverse bacterial species. The acquisitions of resistant genes are transferred to humans through horizontal gene transfer.
Language	English
Publishing date	2023-08-31
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1231938
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Article ; Online: Unravelling diversity, drivers, and indicators of soil microbiome of Trillium govanianum, an endangered plant species of the Himalaya.

Islam, Shahid Ul / Mangral, Zahid Ahmed / Hussain, Khalid / Tariq, Lubna / Bhat, Basharat Ahmad / Khuroo, Anzar Ahmad / Hassan Dar, Tanvir Ul

Environmental research

2023 Volume 227, Page(s) 115819

Abstract: In an era of global environmental change, conservation of threatened biodiversity and ecosystem restoration are formidable ecological challenges. The forest understory strata and the belowground soil environment including rhizospheric microbial ... ...

Abstract	In an era of global environmental change, conservation of threatened biodiversity and ecosystem restoration are formidable ecological challenges. The forest understory strata and the belowground soil environment including rhizospheric microbial communities, which are crucial for ecosystem functioning and overall forest biodiversity maintenance, have remained understudied. Here, we investigate the soil microbiome of Trillium govanianum - an endangered Himalayan Forest herb, to unravel the underground diversity, drivers, and potential indicators of the microbial community. We collected rhizospheric and bulk soil samples for microbiome and physicochemical analysis at three sites along an elevation gradient (2500-3300 m) in Kashmir Himalaya. Amplicon sequencing of 16 S rRNA and ITS was used to identify the bacterial and fungal soil microorganisms. We found significant differences in the structure and diversity of microbial community (bacterial and fungal) between the rhizosphere and bulk soil along the altitudinal gradient, and noticeable shifts in the nutrient level in dominant microbial phyla associated with T. govanianum. A significant difference between soil physicochemical parameters and increasing altitude suggests that microbial community structure is determined by altitude and soil type. Similarly, the microbial communities showed a significant (P < 0.05) correlation with soil physicochemical variables along the altitudinal gradient. The moisture content in bacterial and total organic carbon in fungal communities showed the most substantial impact on the physiochemical drivers. We also identify potential bacterial and fungal plant growth promoter indicator species in the soil microbiome of T. govanianum. Overall, our findings provide novel research insights that can be pivotal in designing integrated species recovery programs and long-term restoration plans for T. govanianum, with learnings for biodiversity conservation elsewhere.
MeSH term(s)	Animals ; Soil/chemistry ; Endangered Species ; Trillium ; Biodiversity ; Plants ; Bacteria/genetics ; Microbiota ; Soil Microbiology ; Fungi/genetics
Chemical Substances	Soil
Language	English
Publishing date	2023-04-01
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205699-9
ISSN	1096-0953 ; 0013-9351
ISSN (online)	1096-0953
ISSN	0013-9351
DOI	10.1016/j.envres.2023.115819
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Article ; Online: Anti-lung Cancer Activity of Synthesized Substituted 1,4-Benzothiazines: An Insight from Molecular Docking and Experimental Studies.

Amin, Andleeb / Khazir, Zubaid-Ul- / Ji, Arfa / Bhat, Basharat Ahmad / Murtaza, Dar / Hurrah, Aaqib A / Bhat, Imtiyaz A / Parveen, Shaheena / Nisar, Syed / Sharma, Praveen Kumar

Anti-cancer agents in medicinal chemistry

2024 Volume 24, Issue 5, Page(s) 358–371

Abstract: Background: Thiazine, a 6-membered distinctive heterocyclic motif with sulfur and nitrogen atoms, is one of the heterocyclic compounds that functions as a core scaffold in a number of medicinally significant molecules. Small thiazine-based compounds may ...

Abstract	Background: Thiazine, a 6-membered distinctive heterocyclic motif with sulfur and nitrogen atoms, is one of the heterocyclic compounds that functions as a core scaffold in a number of medicinally significant molecules. Small thiazine-based compounds may operate simultaneously on numerous therapeutic targets and by employing a variety of methods to halt the development, proliferation, and vasculature of cancer cells. We have, herein, reported a series of substituted 1,4 benzothiazines as potential anticancer agents for the treatment of lung cancer. Methods: In order to synthesize 2,3-disubstituted-1,4 benzothiazines in good yield, a facile green approach for the oxidative cycloaddition of 2-amino benzenethiol and 1,3-dicarbonyls employing a catalytic amount of ceric ammonium nitrate has been devised. All the molecules have been characterized by spectral analysis and tested for anticancer activity against the A-549 lung cancer cell line using various functional assays. Further in silico screening of compound 3c against six crucial inflammatory molecular targets, such as Il1-α (PDB ID: 5UC6), Il1- β (PDB ID: 6Y8I), Il6 (PDB ID: 1P9M), vimentin (PDB ID: 3TRT), COX-2 (PDB ID: 5KIR), Il8 (PDB ID: 5D14), and TNF-α (PDB ID: 2AZ5), was done using AutoDock tool. Results: Among the synthesized compounds, propyl 3-methyl-3,4-dihydro-2H-benzo[b][1,4]thiazine-2- carboxylate (3c) was found to be most active based on cell viability assays using A-549 lung cancer cell line and was found to effectively downregulate various pro-inflammatory genes, like Il1-α, Il1-β, Il6, vimentin, COX-2, Il8, and TNF-α Conclusion: A green unconventional route for the synthesis of 2,3-disubstituted-1,4 benzothiazines has been developed. All the molecules were screened for their activity against lung cancer and the data suggested that the presence of an additional unbranched alkyl group attached to the thiazine ring increased their activity. Also,
MeSH term(s)	Humans ; Molecular Docking Simulation ; Vimentin ; Structure-Activity Relationship ; Cell Line, Tumor ; Cyclooxygenase 2 ; Interleukin-6 ; Interleukin-8/pharmacology ; Tumor Necrosis Factor-alpha ; Antineoplastic Agents/chemistry ; Thiazines/pharmacology ; Lung Neoplasms/drug therapy ; Cell Proliferation ; Drug Screening Assays, Antitumor
Chemical Substances	1,4-benzothiazine ; Vimentin ; Cyclooxygenase 2 (EC 1.14.99.1) ; Interleukin-6 ; Interleukin-8 ; Tumor Necrosis Factor-alpha ; Antineoplastic Agents ; Thiazines
Language	English
Publishing date	2024-02-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2217610-X
ISSN	1875-5992 ; 1871-5206
ISSN (online)	1875-5992
ISSN	1871-5206
DOI	10.2174/0118715206276737231103114924
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Article ; Online: Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity.

Raza, Ali / Salehi, Hajar / Bashir, Shanza / Tabassum, Javaria / Jamla, Monica / Charagh, Sidra / Barmukh, Rutwik / Mir, Rakeeb Ahmad / Bhat, Basharat Ahmad / Javed, Muhammad Arshad / Guan, Dong-Xing / Mir, Reyazul Rouf / Siddique, Kadambot H M / Varshney, Rajeev K

Plant cell reports

2024 Volume 43, Issue 3, Page(s) 80

Abstract: The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop ... ...

Abstract	The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.
MeSH term(s)	Proteomics ; Ecosystem ; Artificial Intelligence ; Gene Expression Profiling ; Metals/toxicity ; Soil
Chemical Substances	Metals ; Soil
Language	English
Publishing date	2024-02-27
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	8397-5
ISSN	1432-203X ; 0721-085X ; 0721-7714
ISSN (online)	1432-203X
ISSN	0721-085X ; 0721-7714
DOI	10.1007/s00299-024-03153-7
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