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Article ; Online: In-silico

Khan, Shama / Madhi, Shabir A / Olwagen, Courtney

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 3, Page(s) 1506–1517

Abstract: The development of new antimicrobial drugs is needed to combat multi-drug resistant and novel hypervirulent strains ... ...

Abstract	The development of new antimicrobial drugs is needed to combat multi-drug resistant and novel hypervirulent strains of
MeSH term(s)	Klebsiella pneumoniae ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents ; Drug Discovery
Chemical Substances	Anti-Bacterial Agents ; Anti-Infective Agents
Language	English
Publishing date	2023-04-27
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2200571
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Article ; Online: Integrated In-Silico and In Vitro analysis to Decipher the contribution of bisphenol-A in cervical cancer.

Khan, Nadeem Ghani / Adiga, Divya / Rai, Padmalatha Satwadi / Kabekkodu, Shama Prasada

Toxicology

2024 Volume 504, Page(s) 153791

Abstract: Bisphenol A (BPA) is a synthetic chemical widely used as a monomer for producing polycarbonate plastics. The present investigation employed an in-silico approach to identify BPA-responsive genes and comprehend the biological functions affected using in ... ...

Abstract	Bisphenol A (BPA) is a synthetic chemical widely used as a monomer for producing polycarbonate plastics. The present investigation employed an in-silico approach to identify BPA-responsive genes and comprehend the biological functions affected using in vitro studies. A Comparative Toxicogenomics Database search identified 29 BPA-responsive genes in cervical cancer (CC). Twenty-nine genes were screened using published datasets, and thirteen of those showed differential expression between normal and CC samples. Protein-Protein Interaction Networks (PPIN) analysis identified BIRC5, CASP8, CCND1, EGFR, FGFR3, MTOR, VEGFA, DOC2B, WNT5A, and YY1 as hub genes. KM-based survival analysis identified that CCND, EGFR, VEGFA, FGFR3, DOC2B, and YY1 might affect CC patient survival. SiHa and CaSki cell proliferation, migration, and invasion were all considerably accelerated by BPA exposure. Changes in cell morphology, remodeling of the actin cytoskeleton, increased number and length of filopodia, elevated intracellular reactive oxygen species and calcium, and lipid droplet accumulation were noted upon BPA exposure. BPA treatment upregulated the expression of epithelial to mesenchymal transition pathway members and enhanced the nuclear translocation of CTNNB1. We showed that the enhanced migration and nuclear translocation of CTNNB1 upon BPA exposure is a calcium-dependent process. The present study identified potential BPA-responsive genes and provided novel insights into the biological effects and mechanisms affected by BPA in CC. Our study raises concern over the use of BPA.
Language	English
Publishing date	2024-03-29
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	184557-3
ISSN	1879-3185 ; 0300-483X
ISSN (online)	1879-3185
ISSN	0300-483X
DOI	10.1016/j.tox.2024.153791
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Article: The Role of 4-Phenylbutyric Acid in Gut Microbial Dysbiosis in a Mouse Model of Simulated Microgravity.

Shama, Shama / Qaisar, Rizwan / Khan, Naveed Ahmed / Tauseef, Isfahan / Siddiqui, Ruqaiyyah

Life (Basel, Switzerland)

2022 Volume 12, Issue 9

Abstract: The altered gut microbes of astronauts during space travel may contribute to health issues after their return to Earth. Previously, an association between the elevated endoplasmic reticulum (ER) stress and gut microbial dysbiosis has been described. ... ...

Abstract	The altered gut microbes of astronauts during space travel may contribute to health issues after their return to Earth. Previously, an association between the elevated endoplasmic reticulum (ER) stress and gut microbial dysbiosis has been described. Herein, we induced gut microbial changes in mice under a simulated microgravity environment in an established model of hindlimb unloaded (HU) mice. The intestinal metabolomic profiles under microgravity conditions using the HU model were examined, along with the potential role of 4-phenylbutyric acid (4-PBA), a potent ER stress inhibitor. For a microgravity environment, the mice were suspended in special cages individually for three weeks. Mice were sacrificed, and gut dissections were performed, followed by amplicon sequencing analysis of bacterial species via DNA extraction and 16S rRNA analysis. The results indicate that the gut bacterial communities of mice differed under gravity and microgravity conditions. Principal component analyses revealed differences in the bacterial community structure in all groups. Around 434 operational taxonomic units (OTUs) were specific to mice seen in controls, while 620 OTUs were specific to HU mice. Additionally, 321 bacterial OTUs were specific to HU mice treated with 4-PBA. When the relative abundance of taxa was analyzed, Bacteroidetes dominated the gut of control and HU mice treated with 4-PBA.. In contrast, the untreated HU mice were dominated by Firmicutes. At the genus level, a reduction in beneficial species of
Language	English
Publishing date	2022-08-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life12091301
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Article ; Online: Structure-based identification of novel inhibitors targeting the enoyl-ACP reductase enzyme of Acinetobacter baumannii

Shama Khan / Shabir A. Madhi / Courtney Olwagen

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 12

Abstract: Abstract Acinetobacter baumannii is a Gram-negative multidrug-resistant bacterial pathogen primarily associated with nosocomial infections resulting in increased morbidity and mortality in adults and infants, especially in sub-Saharan Africa where the ... ...

Abstract	Abstract Acinetobacter baumannii is a Gram-negative multidrug-resistant bacterial pathogen primarily associated with nosocomial infections resulting in increased morbidity and mortality in adults and infants, especially in sub-Saharan Africa where the clinical burden is high. New therapeutics are needed to treat multidrug-resistant Acinetobacter baumannii infections and reduce transmission. The study used computer-integrated drug discovery approaches including pharmacophore modelling, molecular docking, and molecular dynamics simulation to screen potential inhibitors against the enoyl-acyl carrier protein reductase—FabI protein of Acinetobacter baumannii. The top three potential inhibitors: 21272541 > 89795992 > 89792657 showed favourable binding free energies including coulombic energy, van der Waals energy, and polar and non-polar energies. Furthermore, all three complexes were extremely stable and compact with reduced fluctuations during the simulations period. Inhibitor 21272541 exhibited the highest binding affinity against the Acinetobacter baumannii FabI protein. This is similar to our recent report, which also identified 21272541 as the lead inhibitor against Klebsiella pneumoniae infections. Future clinical studies evaluating drug effectiveness should prioritise inhibitor 21272541 which could be effective in treating infections caused by Gram-negative organisms.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Enhancing microbial diversity as well as multi-organ health in hind-limb unloaded mice.

Shama, Shama / Ranade, Anu V / Qaisar, Rizwan / Khan, Naveed Ahmed / Tauseef, Isfahan / Elmoselhi, Adel / Siddiqui, Ruqaiyyah

Life sciences in space research

2023 Volume 40, Page(s) 62–71

Abstract: During space travel, the gut microbiota is changed which can lead to health-related issues. Previously, we utilized the hind-limb unloaded (HU) mouse, which is an established ground-based in-vivo model of microgravity and observed altered gut microbiota. ...

Abstract	During space travel, the gut microbiota is changed which can lead to health-related issues. Previously, we utilized the hind-limb unloaded (HU) mouse, which is an established ground-based in-vivo model of microgravity and observed altered gut microbiota. In this study, we evaluated the beneficial effects of novel bacterial conditioned media in HU mice to understand if they can offset the effects of unloading in the HU mouse model. We aimed to explore the influence of bacterial conditioned media on diversity and quantity of intestinal microbes in HU mice, and investigated the microarchitecture of mice retinas and kidneys to evaluate the potential systemic effects of bacterial conditioned media in HU mice. Four-month-old, male C57/Bl6 mice were separated into groups: including the ground-based control group, the HU group mice fed with vehicle as placebo (HU-placebo mice), and the HU group fed with bacterial conditioned media (HU-CP mice) and kept under controlled environmental conditions for three weeks. Next, mice were sacrificed; gut dissections were conducted, and metagenomic analysis of bacterial species was performed via DNA extraction and 16S rRNA analysis. The results revealed an HU-induced reduction in intestinal microbial diversity, and an increase in pathogenic bacteria dominated by Firmicutes (45%). In contrast, supplementation with bacterial conditioned media for three weeks led to a significant increase in gut microbial diversity with noticeable changes in the OTUs abundance in the HU mice. Additionally, HU-induced muscle weakness and structural abnormalities in the retina and kidney were partially prevented with bacterial conditioned media. Moreover, a greater diversity of several bacteria in the HU-CP was observed including, Bacteriodota, Firmicutes, Proteobacteria, Actionobacteriota, Verrucomicorbiota, Cyanobacteria, Gemmatimonadota, Acidobacteriota, Chloroflexi, Myxococcota, and others. Prospective research involving molecular mechanistic studies are needed to comprehend the systemic effects of bacterial metabolites conditioned media on experimental animal models under chronic stress.
MeSH term(s)	Mice ; Male ; Animals ; RNA, Ribosomal, 16S/genetics ; Culture Media, Conditioned ; Prospective Studies ; Gastrointestinal Microbiome/genetics ; Cyanobacteria
Chemical Substances	RNA, Ribosomal, 16S ; Culture Media, Conditioned
Language	English
Publishing date	2023-09-01
Publishing country	Netherlands
Document type	Journal Article
ISSN	2214-5532
ISSN (online)	2214-5532
DOI	10.1016/j.lssr.2023.08.006
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Article ; Online: Structure-based identification of novel inhibitors targeting the enoyl-ACP reductase enzyme of Acinetobacter baumannii.

Khan, Shama / Madhi, Shabir A / Olwagen, Courtney

Scientific reports

2023 Volume 13, Issue 1, Page(s) 21331

Abstract: Acinetobacter baumannii is a Gram-negative multidrug-resistant bacterial pathogen primarily associated with nosocomial infections resulting in increased morbidity and mortality in adults and infants, especially in sub-Saharan Africa where the clinical ... ...

Abstract	Acinetobacter baumannii is a Gram-negative multidrug-resistant bacterial pathogen primarily associated with nosocomial infections resulting in increased morbidity and mortality in adults and infants, especially in sub-Saharan Africa where the clinical burden is high. New therapeutics are needed to treat multidrug-resistant Acinetobacter baumannii infections and reduce transmission. The study used computer-integrated drug discovery approaches including pharmacophore modelling, molecular docking, and molecular dynamics simulation to screen potential inhibitors against the enoyl-acyl carrier protein reductase-FabI protein of Acinetobacter baumannii. The top three potential inhibitors: 21272541 > 89795992 > 89792657 showed favourable binding free energies including coulombic energy, van der Waals energy, and polar and non-polar energies. Furthermore, all three complexes were extremely stable and compact with reduced fluctuations during the simulations period. Inhibitor 21272541 exhibited the highest binding affinity against the Acinetobacter baumannii FabI protein. This is similar to our recent report, which also identified 21272541 as the lead inhibitor against Klebsiella pneumoniae infections. Future clinical studies evaluating drug effectiveness should prioritise inhibitor 21272541 which could be effective in treating infections caused by Gram-negative organisms.
MeSH term(s)	Humans ; Oxidoreductases/metabolism ; Acinetobacter baumannii ; Molecular Docking Simulation ; Anti-Bacterial Agents/chemistry ; Drug Discovery/methods ; Enzyme Inhibitors/chemistry
Chemical Substances	Oxidoreductases (EC 1.-) ; Anti-Bacterial Agents ; Enzyme Inhibitors
Language	English
Publishing date	2023-12-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-48696-z
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Article ; Online: Noncoding RNAs in Alzheimer's Disease: Overview of Functional and Therapeutic Significance.

Adiga, Divya / Eswaran, Sangavi / Sriharikrishnaa, S / Khan, Nadeem G / Kumar, Dileep / Kabekkodu, Shama Prasada

Current topics in medicinal chemistry

2024

Abstract: Alzheimer's disease (AD) is a multifactorial disorder resulting from the complex interaction between genetic, epigenetic, and environmental factors. It represents an impending epidemic and lacks effective pharmacological interventions. The emergence of ... ...

Abstract	Alzheimer's disease (AD) is a multifactorial disorder resulting from the complex interaction between genetic, epigenetic, and environmental factors. It represents an impending epidemic and lacks effective pharmacological interventions. The emergence of high throughput sequencing techniques and comprehensive genome evaluation has uncovered a diverse spectrum of non-- coding RNA (ncRNA) families. ncRNAs are the critical modulators of an eclectic array of biological processes and are now transpiring as imperative players in diagnosing and treating various diseases, including neurodegenerative disorders. Several ncRNAs are explicitly augmented in the brain, wherein they potentially regulate cognitive abilities and other functions of the central nervous system. Growing evidence suggests the substantial role of ncRNAs as modulators of tau phosphorylation, Aβ production, neuroinflammation, and neuronal survival. It indicates their therapeutic relevance as a biomarker and druggable targets against AD. The current review summarizes the existing literature on the functional significance of ncRNAs in AD pathogenesis and its imminent implications in clinics.
Language	English
Publishing date	2024-04-09
Publishing country	United Arab Emirates
Document type	Journal Article
ZDB-ID	2064823-6
ISSN	1873-4294 ; 1568-0266
ISSN (online)	1873-4294
ISSN	1568-0266
DOI	10.2174/0115680266293212240405042540
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Article ; Online: Investigating the role of thymol as a promising inhibitor of pyruvate dehydrogenase kinase 3 for targeted cancer therapy.

Jairajpuri, Deeba Shamim / Khan, Shama / Anwar, Saleha / Hussain, Afzal / Alajmi, Mohamed F / Hassan, Imtaiyaz

International journal of biological macromolecules

2024 Volume 259, Issue Pt 2, Page(s) 129314

Abstract: Protein kinases have emerged as major contributors to various diseases. They are currently exploited as a potential target in drug discovery because they play crucial roles in cell signaling, growth, and regulation. Their dysregulation is associated with ...

Abstract	Protein kinases have emerged as major contributors to various diseases. They are currently exploited as a potential target in drug discovery because they play crucial roles in cell signaling, growth, and regulation. Their dysregulation is associated with inflammatory disorders, cancer, and neurodegenerative diseases. Pyruvate dehydrogenase kinase 3 (PDK3) has become an attractive drug target in cancer therapeutics. In the present study, we investigated the effective role of thymol in PDK3 inhibition due to the high affinity predicted through molecular docking studies. Hence, to better understand this inhibition mechanism, we carried out a 100 ns molecular dynamics (MD) simulation to analyse the dynamics and stability of the PDK3-thymol complex. The PDK3-thymol complex was stable and energetically favourable, with many intramolecular hydrogen bond interactions in the PDK3-thymol complex. Enzyme inhibition assay showed significant inhibition of PDK3 by thymol, revealing potential inhibitory action of thymol towards PDK3 (IC
MeSH term(s)	Humans ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase/chemistry ; Thymol/pharmacology ; Molecular Docking Simulation ; Protein Kinases/metabolism ; Neoplasms/drug therapy
Chemical Substances	Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; Thymol (3J50XA376E) ; Protein Kinases (EC 2.7.-)
Language	English
Publishing date	2024-01-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.129314
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Article ; Online: Exploring therapeutic potential of Rutin by investigating its cyclin-dependent kinase 6 inhibitory activity and binding affinity.

Yousuf, Mohd / Khan, Shama / Hussain, Afzal / Alajmi, Mohamed F / Shamsi, Anas / Haque, Qazi Mohd Rizwanul / Islam, Asimul / Hassan, Md Imtaiyaz

International journal of biological macromolecules

2024 Volume 264, Issue Pt 2, Page(s) 130624

Abstract: Cyclin-dependent kinase 6 (CDK6) participates in numerous signalling pathways and regulates various physiological processes. Due to its unique structural features and promising therapeutic potential, CDK6 has emerged as a drug target for designing and ... ...

Abstract	Cyclin-dependent kinase 6 (CDK6) participates in numerous signalling pathways and regulates various physiological processes. Due to its unique structural features and promising therapeutic potential, CDK6 has emerged as a drug target for designing and developing small-molecule inhibitors for anti-cancer therapeutics and other CDK6-associated diseases. The current study evaluates binding affinity and the inhibitory potential of rutin for CDK6 to develop a proof of concept for rutin as a potent CDK6 inhibitor. Molecular docking and 200 ns all-atom simulations reveal that rutin binds to the active site pocket of CDK6, forming interactions with key residues of the binding pocket. In addition, the CDK6-rutin complex remains stable throughout the simulation trajectory. A high binding constant (Ka = 7.6 × 10
MeSH term(s)	Humans ; Cyclin-Dependent Kinase 6 ; Rutin/pharmacology ; Molecular Docking Simulation ; Phosphorylation ; Protein Processing, Post-Translational ; Neoplasms
Chemical Substances	Cyclin-Dependent Kinase 6 (EC 2.7.11.22) ; Rutin (5G06TVY3R7)
Language	English
Publishing date	2024-03-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.130624
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Article ; Online: Ganoderma lucidum

Ahmad, Md Faruque / Ahmad, Fakhruddin Ali / Zeyaullah, Md / Alsayegh, Abdulrahman A / Mahmood, Syed Esam / AlShahrani, Abdullah M / Khan, Mohammad Suhail / Shama, Eman / Hamouda, Alshaimaa / Elbendary, Ehab Y / Attia, Kandil Abdel Hai Ali

Nutrients

2023 Volume 15, Issue 8

Abstract: Ganoderma ... ...

Abstract	Ganoderma lucidum
MeSH term(s)	Humans ; Reishi ; Triterpenes/pharmacology ; Polysaccharides ; Non-alcoholic Fatty Liver Disease/drug therapy
Chemical Substances	Triterpenes ; Polysaccharides
Language	English
Publishing date	2023-04-13
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2518386-2
ISSN	2072-6643 ; 2072-6643
ISSN (online)	2072-6643
ISSN	2072-6643
DOI	10.3390/nu15081874
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