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Article ; Online: Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae)

Waqar Ahmad / Sajjad Asaf / Ahmed Al-Rawahi / Ahmed Al-Harrasi / Abdul Latif Khan

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

2023 Volume 18

Abstract: Abstract The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least ... ...

Abstract	Abstract The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp—typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16–24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mangrove tree (Avicennia marina)

Sajjad Asaf / Abdul Latif Khan / Muhammad Numan / Ahmed Al-Harrasi

Scientific Reports, Vol 11, Iss 1, Pp 1-

insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

2021 Volume 15

Abstract: Abstract Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic ... ...

Abstract	Abstract Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Rational Design of Novel Inhibitors of α-Glucosidase

Sobia Ahsan Halim / Sumaira Jabeen / Ajmal Khan / Ahmed Al-Harrasi

Pharmaceuticals, Vol 14, Iss 482, p

An Application of Quantitative Structure Activity Relationship and Structure-Based Virtual Screening

2021 Volume 482

Abstract: α-Glucosidase is considered a prime drug target for Diabetes Mellitus and its inhibitors are used to delay carbohydrate digestion for the treatment of diabetes mellitus. With the aim to design α-glucosidase inhibitors with novel chemical scaffolds, three ...

Abstract	α-Glucosidase is considered a prime drug target for Diabetes Mellitus and its inhibitors are used to delay carbohydrate digestion for the treatment of diabetes mellitus. With the aim to design α-glucosidase inhibitors with novel chemical scaffolds, three folds ligand and structure based virtual screening was applied. Initially linear quantitative structure activity relationship (QSAR) model was developed by a molecular operating environment (MOE) using a training set of thirty-two known inhibitors, which showed good correlation coefficient (r 2 = 0.88), low root mean square error (RMSE = 0.23), and cross-validated correlation coefficient r 2 (q 2 = 0.71 and RMSE = 0.31). The model was validated by predicting the biological activities of the test set which depicted r 2 value of 0.82, indicating the robustness of the model. For virtual screening, compounds were retrieved from zinc is not commercial (ZINC) database and screened by molecular docking. The best docked compounds were chosen to assess their pharmacokinetic behavior. Later, the α-glucosidase inhibitory potential of the selected compounds was predicted by their mode of binding interactions. The predicted pharmacokinetic profile, docking scores and protein-ligand interactions revealed that eight compounds preferentially target the catalytic site of α-glucosidase thus exhibit potential α-glucosidase inhibition in silico . The α-glucosidase inhibitory activities of those Hits were predicted by QSAR model, which reflect good inhibitory activities of these compounds. These results serve as a guidelines for the rational drug design and development of potential novel anti-diabetic agents.
Keywords	α-Glucosidase ; QSAR modeling ; homology modeling ; molecular docking ; ADMET profiling ; Medicine ; R ; Pharmacy and materia medica ; RS1-441
Subject code	540
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: In Silico Prediction of Novel Inhibitors of SARS-CoV-2 Main Protease through Structure-Based Virtual Screening and Molecular Dynamic Simulation

Sobia Ahsan Halim / Muhammad Waqas / Ajmal Khan / Ahmed Al-Harrasi

Pharmaceuticals, Vol 14, Iss 896, p

2021 Volume 896

Abstract: The unprecedented pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is threatening global health. SARS-CoV-2 has caused severe disease with significant mortality since December 2019. The enzyme chymotrypsin-like protease (3CLpro) ... ...

Abstract	The unprecedented pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is threatening global health. SARS-CoV-2 has caused severe disease with significant mortality since December 2019. The enzyme chymotrypsin-like protease (3CLpro) or main protease (M pro ) of the virus is considered to be a promising drug target due to its crucial role in viral replication and its genomic dissimilarity to human proteases. In this study, we implemented a structure-based virtual screening (VS) protocol in search of compounds that could inhibit the viral M pro . A library of >eight hundred compounds was screened by molecular docking into multiple structures of M pro , and the result was analyzed by consensus strategy. Those compounds that were ranked mutually in the ‘Top-100’ position in at least 50% of the structures were selected and their analogous binding modes predicted simultaneously in all the structures were considered as bioactive poses. Subsequently, based on the predicted physiological and pharmacokinetic behavior and interaction analysis, eleven compounds were identified as ‘Hits’ against SARS-CoV-2 M pro . Those eleven compounds, along with the apo form of M pro and one reference inhibitor ( X77 ), were subjected to molecular dynamic simulation to explore the ligand-induced structural and dynamic behavior of M pro . The MM-GBSA calculations reflect that eight out of eleven compounds specifically possess high to good binding affinities for M pro . This study provides valuable insights to design more potent and selective inhibitors of SARS-CoV-2 M pro .
Keywords	SARS coronavirus ; SARS-CoV-2 main protease ; structure-based virtual screening ; molecular dynamic simulation ; hit identification ; Medicine ; R ; Pharmacy and materia medica ; RS1-441
Subject code	333 ; 540
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The 3D Genome

Tapan Kumar Mohanta / Awdhesh Kumar Mishra / Ahmed Al-Harrasi

International Journal of Molecular Sciences, Vol 22, Iss 11585, p

From Structure to Function

2021 Volume 11585

Abstract: The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and ...

Abstract	The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding factor domains, cohesin, and chromatin structures are the prominent identified components that encode the 3D structure of the genome. Although TADs are the major contributors to 3D genome organization, they are absent in Arabidopsis . However, a few research groups have reported the presence of TAD-like structures in the plant kingdom.
Keywords	3D ; genome ; topologically associated domain ; cohesin ; lamin ; chromosome capture ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	572
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Validated Capillary Zone Electrophoresis Method for Impurity Profiling and Determination of Ni II (3-OMe-Salophene)

Sami El Deeb / Adel Ehab Ibrahim / Ahmed Al-Harrasi / Gerhard Wolber / Ronald Gust

Separations, Vol 9, Iss 25, p

2022 Volume 25

Abstract: A capillary zone electrophoresis method was developed for the determination of Ni II (3-OMe-salophene), a substance with anticancer activity in vitro. A fused silica capillary (56 cm × 100 µm) was used for this purpose. The method was optimized in terms ... ...

Abstract	A capillary zone electrophoresis method was developed for the determination of Ni II (3-OMe-salophene), a substance with anticancer activity in vitro. A fused silica capillary (56 cm × 100 µm) was used for this purpose. The method was optimized in terms of parameters affecting the electrophoretic conditions in order to optimize separation efficiency and total time of migration. The analysis was best performed using an operating buffer of 50 mM borate, adjusted to pH 9.3, mixed with acetonitrile (50%, v / v ) as organic modifier. Injections were performed hydrodynamically by applying a pressure of 50 mbar for 8 s, and a 30 kV separation voltage was selected at 25 °C. Detection was carried out at 250 nm using diode array detector (DAD). The method allowed the separation of Ni II (3-OMe-salophene) from four other structurally related impurities in a total migration time (t m ) of 8 min. Peak identification was achieved using the standard reference of individual impurities. The purity of the migrated Ni II (3-OMe-salophene) was confirmed by Ultra-violet (UV) scan overlay depending on DAD. The linear ranges for the determination of Ni II (3-OMe-salophene) was 400–20,000 ng mL −1 with limit of detection (LOD) of 120 ng mL −1 . Acceptable intra-day and inter-day precisions were achieved (%relative standard deviation (RSD) results were less than 0.76% and 0.30%, respectively). The proposed method was assessed for greenness and compared to reported methodologies to prove superiority.
Keywords	impurity profiling ; anticancer ; capillary zone electrophoresis ; Ni II (3-OMe-salophene) ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	333
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Synthesis of new bis(dimethylamino)benzophenone hydrazone for diabetic management

Momin Khan / Ghulam Ahad / Aftab Alam / Saeed Ullah / Ajmal Khan / Kanwal / Uzma Salar / Abdul Wadood / Amar Ajmal / Khalid Mohammed Khan / Shahnaz Perveen / Jalal Uddin / Ahmed Al-Harrasi

Heliyon, Vol 10, Iss 1, Pp e23323- (2024)

In-vitro and in-silico approach

1481

Abstract: Inhibiting α-glucosidase is a reliable method for reducing blood sugar levels in diabetic individuals. Bis(dimethylamino)benzophenone derivatives 1–27 were synthesized from bis(dimethylamino)benzophenone via two-step reaction. Different spectroscopic ... ...

Abstract	Inhibiting α-glucosidase is a reliable method for reducing blood sugar levels in diabetic individuals. Bis(dimethylamino)benzophenone derivatives 1–27 were synthesized from bis(dimethylamino)benzophenone via two-step reaction. Different spectroscopic techniques, including EI-MS and 1H NMR, were employed to characterize all synthetic derivatives. The elemental composition of synthetic compounds was confirmed by elemental analysis and results were found in agreement with the calculated values. The synthetic compounds 1–27 were evaluated for α-glucosidase inhibitory activity, except five compounds all derivatives showed good to moderate inhibitory potential in the range of IC50 = 0.28 ± 2.65 - 0.94 ± 2.20 μM. Among them, the most active compounds were 5, 8, 9, and 12 with IC50 values of 0.29 ± 4.63, 0.29 ± 0.93, 0.28 ± 3.65, and 0.28 ± 2.65, respectively. Furthermore, all these compounds were found to be non-toxic on human fibroblast cell lines (BJ cell lines). Kinetics study of compounds 8 and 9 revealed competitive type of inhibition with Ki values 2.79 ± 0.011 and 3.64 ± 0.012 μM, respectively. The binding interactions of synthetic compounds were also confirmed through molecular docking studies that indicated that compounds fit well in the active site of enzyme. Furthermore, a total of 30ns MD simulation was carried out for the most potent complexes of the series. The molecular dynamics study revealed that compound-8 and compound-12 were stable during the MD simulation.
Keywords	4,4-Bis(dimethylamino)benzophenone ; Schiff bases ; α-glucosidase inhibitors ; Structure-activity relationship ; Molecular docking ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	540 ; 500
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Phytoimmunomodulators

Partibha Hooda / Rohit Malik / Saurabh Bhatia / Ahmed Al-Harrasi / Asim Najmi / Khalid Zoghebi / Maryam A. Halawi / Hafiz A. Makeen / Syam Mohan

Heliyon, Vol 10, Iss 1, Pp e23790- (2024)

A review of natural modulators for complex immune system

1481

Abstract: In the past few decades, the medicinal properties of plants and their effects on the human immune system are being studied extensively. Plants are an incredible source of traditional medicines that help cure various diseases, including altered immune ... ...

Abstract	In the past few decades, the medicinal properties of plants and their effects on the human immune system are being studied extensively. Plants are an incredible source of traditional medicines that help cure various diseases, including altered immune mechanisms and are economical and benign compared to allopathic medicines. Reported data in written documents such as Traditional Chinese medicine, Indian Ayurvedic medicine support the supplementation of botanicals for immune defense reactions in the body and can lead to safe and effective immunity responses. Additionally, some botanicals are well-identified as magical herbal remedies because they act upon the pathogen directly and help boost the immunity of the host. Chemical compounds, also known as phytochemicals, obtained from these botanicals looked promising due to their effects on the human immune system by modulating the lymphocytes which subsequently reduce the chances of getting infected. This paper summarises most documented phytochemicals and how they act on the immune system, their properties and possible mechanisms, screening conventions, formulation guidelines, comparison with synthetic immunity-enhancers, marketed immunity-boosting products, and immune-booster role in the ongoing ghastly corona virus wave. However, it focuses mainly on plant metabolites as immunomodulators. In addition, it also sheds light on the current advancements and future possibilities in this field. From this thorough study, it can be stated that the plant-based secondary metabolites contribute significantly to immunity building and could prove to be valuable medicaments for the design and development of novel immunomodulators even for a pandemic like COVID-19.
Keywords	Phytoimmunomodulators ; Secondary metabolites ; Ayurveda ; Traditional Chinese medicine ; COVID-19 ; Immunomodulators ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	006
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assessment of ubiquitin specific Peptidase-18 gene in peripheral blood of chronic hepatitis C patients treated with direct-acting antiviral drugs

Sami Ullah / Mariam Naveed / Amjad Ali / Sadia Bibi / Wafa Idrees / Shazia Rafique / Muhammad Idrees / Muhammad Waqas / Jalal Uddin / Afnan Jan / Ajmal Khan / Ahmed Al-Harrasi

Heliyon, Vol 10, Iss 2, Pp e24581- (2024)

2024

Abstract: Hepatitis C virus (HCV) infection remains one of the leading causes of liver complications globally. Ubiquitin Specific Peptidase-18 (USP18) is a ubiquitin-specific protease that cleaves interferon-stimulated gene 15 (ISG15) from ISGylated protein ... ...

Abstract	Hepatitis C virus (HCV) infection remains one of the leading causes of liver complications globally. Ubiquitin Specific Peptidase-18 (USP18) is a ubiquitin-specific protease that cleaves interferon-stimulated gene 15 (ISG15) from ISGylated protein complexes and is involved in regulating interferon responsiveness. To study the effect of direct-acting antivirals (DAAs) on the USP18 gene using qPCR, 132 participants were recruited and classified into different groups based on treatment duration. USP18 expression was raised compared to rapid virologic response (RVR) and early virologic response (EVR) groups with P = 0.0026 and P = 0.0016, respectively. USP18 was found to be 7.36 folds higher in naïve patients than those with RVR and sustained viral response (SVR). In RVR and SVR groups where patients had cleared HCV RNA after treatment with direct-acting antiviral agents (DAA) therapy, the expression of USP18 was found to be low, with a fold change of 1.3 and 1.4 folds, respectively. Expression of USP18 was significantly higher in the non-RVR group than in the RVR group. In the No EVR group, gene expression was significantly higher than in the EVR group. It is concluded that targeting HCV proteins using DAAs can cause USP18 expression to be normalized more effectively. Moreover, USP18 is a vital marker indicating treatment resistance and distinguishing responders from non-responders during DAA therapy.
Keywords	HCV ; DAAs ; USP18 ; Expression ; Chronic ; Patients ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	570 ; 610
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship

Sajjad Asaf / Abdul Latif Khan / Arif Khan / Ahmed Al-Harrasi

International Journal of Molecular Sciences, Vol 21, Iss 3280, p

2020 Volume 3280

Abstract: Genus Prosopis (family Fabaceae) are shrubby trees, native to arid and semi-arid regions of Asia, Africa, and America and known for nitrogen fixation. Here, we have sequenced the complete chloroplast (cp) genomes of two Prosopis species ( P . juliflora ... ...

Abstract	Genus Prosopis (family Fabaceae) are shrubby trees, native to arid and semi-arid regions of Asia, Africa, and America and known for nitrogen fixation. Here, we have sequenced the complete chloroplast (cp) genomes of two Prosopis species ( P . juliflora and P . cineraria ) and compared them with previously sequenced P. glandulosa , Adenanthera microsperma , and Parkia javanica belonging to the same family. The complete genome sequences of Prosopis species and related species ranged from 159,389 bp ( A . microsperma ) to 163,677 bp ( P . cineraria ). The overall GC contents of the genomes were almost the similar (35.9–36.6%). The P. juliflora and P. cineraria genomes encoded 132 and 131 genes, respectively, whereas both the species comprised of 85 protein-coding genes higher than other compared species. About 140, 134, and 129 repeats were identified in P . juliflora , P . cineraria and P . glandulosa cp genomes, respectively. Similarly, the maximum number of simple sequence repeats were determined in P . juliflora (88), P . cineraria (84), and P. glandulosa (78). Moreover, complete cp genome comparison determined a high degree of sequence similarity among P . juliflora , P. cineraria, and P. glandulosa, however some divergence in the intergenic spacers of A. microsperma and Parkia javanica were observed. The phylogenetic analysis showed that P . juliflora is closer to P . cineraria than P. glandulosa .
Keywords	plastid genome ; Fabaceae ; phylogenetic position ; comparative analysis ; inverted repeats ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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