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Article ; Online: Molecular Dissection of Herpes Simplex Virus Type 1 to Elucidate Molecular Mechanisms Behind Latency and Comparison of Its Codon Usage Patterns with Genes Modulated During Alzheimer's Disease as a Part of Host-Pathogen Interaction.

Gurjar, Pankaj / Khan, Azmat Ali / Alanazi, Amer M / Vasil'ev, Vasilii G / Zouganelis, George / Alexiou, Athanasios

2024 Volume 97, Issue 3, Page(s) 1111–1123

Abstract: Background: Herpes simplex virus type 1 (HSV-1) is associated with Alzheimer's disease, which goes into a cycle of latency and reactivation. The present study was envisaged to understand the reasons for latency and specific molecular patterns present in ...

Abstract	Background: Herpes simplex virus type 1 (HSV-1) is associated with Alzheimer's disease, which goes into a cycle of latency and reactivation. The present study was envisaged to understand the reasons for latency and specific molecular patterns present in the HSV-1. Objective: The objective is the molecular dissection of Herpes simplex virus type 1 to elucidate molecular mechanisms behind latency and compare its codon usage patterns with genes modulated during Alzheimer's disease as a part of host-pathogen interaction. Methods: In the present study, we tried to investigate the potential reasons for the latency of HSV-1 virus bioinformatically by determining the CpG patterns. Also, we investigated the codon usage pattern, the presence of rare codons, codon context, and protein properties. Results: The top 222 codon pairs graded based on their frequency in the HSV-1 genome revealed that with only one exception (CUG-UUU), all other codon pairs have codons ending with G/C. Considering it an extension of host-pathogen interaction, we compared HSV-1 codon usage with that of codon usage of genes modulated during Alzheimer's disease, and we found that CGT and TTT are only two codons that exhibited similar codon usage patterns and other codons showed statistically highly significant different codon preferences. Dinucleotide CpG tends to mutate to TpG, suggesting the presence of mutational forces and the imperative role of CpG methylation in HSV-1 latency. Conclusions: Upon comparison of codon usage between HSV-1 and Alzheimer's disease genes, no similarities in codon usage were found as a part of host-pathogen interaction. CpG methylation plays an imperative role in latency HSV-1.
MeSH term(s)	Humans ; Herpesvirus 1, Human/genetics ; Codon Usage ; Alzheimer Disease/genetics ; Host-Pathogen Interactions/genetics ; Herpes Simplex/metabolism
Language	English
Publishing date	2024-01-31
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1440127-7
ISSN	1875-8908 ; 1387-2877
ISSN (online)	1875-8908
ISSN	1387-2877
DOI	10.3233/JAD-231083
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Zs.A 6084: Show issues

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Article ; Online: Identification of the myxobacterial secondary metabolites Aurachin A and Soraphinol A as promising inhibitors of thymidylate kinase of the Monkeypox virus.

Ali, Yasir / Khan, Azmat Ali / Alanazi, Amer M / Abdikakharovich, Sidikov Akmal / Shah, Junaid Ali / Ren, Zhi-Guang / Khattak, Saadullah

Molecular diversity

2024

Abstract: Thymidylate kinase (TMPK) of monkeypox virus (MPXV) has emerged as a promising target for potential therapeutics due to its significant role in pyrimidine metabolism. While smallpox drugs are advised for treating monkeypox, the European Medicine Agency ... ...

Abstract	Thymidylate kinase (TMPK) of monkeypox virus (MPXV) has emerged as a promising target for potential therapeutics due to its significant role in pyrimidine metabolism. While smallpox drugs are advised for treating monkeypox, the European Medicine Agency has sanctioned Tecovirimat due to its potent nanomolar activity. Nonetheless, there is a need for monkeypox-specific therapeutic options. In this work, we employed docking-based virtual screening and molecular dynamics (MD) simulations to identify myxobacterial secondary metabolites as promising anti-viral natural compounds capable of inhibiting thymidylate kinase. The computational pharmacokinetics and manual curation of top-scoring compounds identified six lead compounds that were compared in terms of protein-ligand contacts and protein-essential dynamics. The study shows that among the six candidates, Aurachin A and the Soraphinol analogues such as Soraphinol A and Soraphinol C remain very stable compared to other compounds, enabling the active site integrity via a stable dynamics pattern. We also show that other compounds such as Phenoxan, Phenylnannolone C, and 8E-Aurafuron B remain unstable and have a negative impact on the active site integrity and may not be suitable binders for TMPK protein. Analyzing the Aurachin A and Soraphinol A binding, the established hydrogen bonds with Arg93 and the conserved hydrophobic interaction with Tyr101 are consistent with previous experimental interactions. Additionally, a deeper insight into the indole and the aromatic ring interaction through π-π stacking and π-cation interactions, as well as the background of Aurachin A and Soraphinol A as a bioactive compound, has significant implications not only for its potential as a promising drug but also for directing future drug discovery efforts targeting the TMPK protein.
Language	English
Publishing date	2024-01-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10764-x
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Zs.A 4946: Show issues

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Article ; Online: Unveiling the antiviral potential of Plant compounds from the Meliaceae family against the Zika virus through QSAR modeling and MD simulation analysis.

Shukla, Divyanshi / Alanazi, Amer M / Panda, Siva Prasad / Dwivedi, Vivek Dhar / Kamal, Mohammad Amjad

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–16

Abstract: Zika virus (ZIKV) is a flavivirus transmitted by mosquitoes, causing neurological disorders and congenital malformations. RNA-dependent RNA polymerase (RdRp) is one of its essential enzymes and a promising drug target for antiviral therapy due to its ... ...

Abstract	Zika virus (ZIKV) is a flavivirus transmitted by mosquitoes, causing neurological disorders and congenital malformations. RNA-dependent RNA polymerase (RdRp) is one of its essential enzymes and a promising drug target for antiviral therapy due to its involvement in the growth and multiplication of the virus. In this study, we conducted a QSAR-based chemical library screening from the Meliaceae family to identify potential RdRp inhibitors. The QSAR model was built using the known inhibitors of RdRp NS5 of ZIKV and their biological activity (EC50), along with the structural and chemical characteristics of the compounds. The top two hit compounds were selected from QSAR screening for further analysis using molecular docking to evaluate their binding energies and intermolecular interactions with RdRp, including the critical residue Trp
Language	English
Publishing date	2023-09-20
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2259498
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Article ; Online: The effect of ascorbic acid and cranberry on the bond strength, surface roughness, and surface hardness of bleached enamel with hydrogen peroxide and zinc phthalocyanine activated by photodynamic therapy.

Alanazi, Amer M / Khan, Azmat Ali / Mahmood, Amer / Tahir, Araib / Kamal, Mohammad Amjad

Photodiagnosis and photodynamic therapy

2023 Volume 43, Page(s) 103685

Abstract: Aim: To evaluate the effect of different bleaching methods 40% (hydrogen peroxide) HP and Zinc Phthalocyanine (ZP) activated by photodynamic therapy (PDT) with the utilization of diverse procedures of reversal (10% ascorbic acid and 6% cranberry ... ...

Abstract	Aim: To evaluate the effect of different bleaching methods 40% (hydrogen peroxide) HP and Zinc Phthalocyanine (ZP) activated by photodynamic therapy (PDT) with the utilization of diverse procedures of reversal (10% ascorbic acid and 6% cranberry solution) on bond values, surface microhardness and surface roughness of bleached enamel surface. Material and methods: An aggregate of 60 extracted human mandibular molars was gathered and the buccal surface of each specimen was exposed to 2 mm of enamel surface for bleaching with chemical and photoactivated agents with the use of reversal solutions. Specimens were divided into six groups (n = 10) at random- Group 1: samples bleached with 40% HP with 10% ascorbic acid (reversal agent), group 2: ZP activated by PDT with 10% ascorbic acid (reversal agent), group 3: 40% HP with 6% cranberry solution as a reversal agent, group 4: ZP activated by PDT with 6% cranberry solution, group 5: 40% HP and group 6: ZP activated by PDT with no reversal agents. Resin cement restoration was performed via etch and rinse technique and SBS was estimated by using the universal testing machine, SMH by using Vickers hardness tester, and Ra by stylus profilometer. Statistical analysis was executed using the ANOVA test and the Tukey multiple tests (p<0.05). Results: Enamel surface bleached with 40% HP reversed with 10% ascorbic acid displayed the highest SBS while 40% HP with no reversal agent use showed the least SBS. For SMH, ZP activated by PDT when applied on the enamel surface and reversed with 10% ascorbic acid showed the highest SMH while when bleached with 40% HP and reversed with 6% cranberry solution showed the least SMH value. For Ra, Group 3: samples bleached with 40% HP with 6% cranberry solution as reversal agent showed the highest Ra value while bleaching of enamel surface with ZP activated by PDT with 6% cranberry displayed the least Ra value. Conclusion: Bleached enamel surface with Zinc Phthalocyanine activated by PDT with the application of 10% ascorbic acid as reversal solution has demonstrated the highest SBS and SMH with acceptable surface roughness for bonding adhesive resin to the enamel surface.
MeSH term(s)	Humans ; Hydrogen Peroxide/pharmacology ; Ascorbic Acid/pharmacology ; Ascorbic Acid/chemistry ; Vaccinium macrocarpon ; Tooth Bleaching/methods ; Hardness ; Composite Resins/chemistry ; Photochemotherapy/methods ; Photosensitizing Agents/pharmacology ; Hypochlorous Acid
Chemical Substances	Hydrogen Peroxide (BBX060AN9V) ; Ascorbic Acid (PQ6CK8PD0R) ; Zn(II)-phthalocyanine (14320-04-8) ; Composite Resins ; Photosensitizing Agents ; Hypochlorous Acid (712K4CDC10)
Language	English
Publishing date	2023-06-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2149918-4
ISSN	1873-1597 ; 1572-1000
ISSN (online)	1873-1597
ISSN	1572-1000
DOI	10.1016/j.pdpdt.2023.103685
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Article: Synthetic biology approach revealed enhancement in haeme oxygenase-1 gene expression by codon pair optimization while reduction by codon deoptimization.

Khandia, Rekha / Pandey, Megha Katare / Khan, Azmat Ali / Baklanov, Igor / Alanazi, Amer M / Nepali, Prakash / Gurjar, Pankaj / Choudhary, Om Prakash

Annals of medicine and surgery (2012)

2024 Volume 86, Issue 3, Page(s) 1359–1369

Abstract: Haem oxygenase-1 (HO-1) is a ubiquitously expressed gene involved in cellular homoeostasis, and its imbalance in expression results in various disorders. To alleviate such disorders, HO-1 gene expression needs to be modulated. Codon usage bias results ... ...

Abstract	Haem oxygenase-1 (HO-1) is a ubiquitously expressed gene involved in cellular homoeostasis, and its imbalance in expression results in various disorders. To alleviate such disorders, HO-1 gene expression needs to be modulated. Codon usage bias results from evolutionary forces acting on any nucleotide sequence and determines the gene expression. Like codon usage bias, codon pair bias also exists, playing a role in gene expression. In the present study, HO-1 gene was recoded by manipulating codon and codon pair bias, and four such constructs were made through codon/codon pair deoptimization and codon/codon pair optimization to reduce and enhance the HO-1 gene expression. Codon usage analysis was done for these constructs for four tissues brain, heart, pancreas and liver. Based on codon usage in different tissues, gene expression of these tissues was determined in terms of the codon adaptation index. Based on the codon adaptation index, minimum free energy, and translation efficiency, constructs were evaluated for enhanced or decreased HO-1 expression. The analysis revealed that for enhancing gene expression, codon pair optimization, while for reducing gene expression, codon deoptimization is efficacious. The recoded constructs developed in the study could be used in gene therapy regimens to cure HO-1 over or underexpression-associated disorders.
Language	English
Publishing date	2024-01-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2745440-X
ISSN	2049-0801
ISSN	2049-0801
DOI	10.1097/MS9.0000000000001465
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Article: Molecular insights into codon usage analysis of mitochondrial fission and fusion gene: relevance to neurodegenerative diseases.

Khandia, Rekha / Pandey, Megha Katare / Garg, Rajkumar / Khan, Azmat Ali / Baklanov, Igor / Alanazi, Amer M / Nepali, Prakash / Gurjar, Pankaj / Choudhary, Om Prakash

Annals of medicine and surgery (2012)

2024 Volume 86, Issue 3, Page(s) 1416–1425

Abstract: Mitochondrial dysfunction is the leading cause of neurodegenerative disorders like Alzheimer's disease and Parkinson's disease. Mitochondria is a highly dynamic organelle continuously undergoing the process of fission and fusion for even distribution of ... ...

Abstract	Mitochondrial dysfunction is the leading cause of neurodegenerative disorders like Alzheimer's disease and Parkinson's disease. Mitochondria is a highly dynamic organelle continuously undergoing the process of fission and fusion for even distribution of components and maintaining proper shape, number, and bioenergetic functionality. A set of genes governs the process of fission and fusion.
Language	English
Publishing date	2024-01-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2745440-X
ISSN	2049-0801
ISSN	2049-0801
DOI	10.1097/MS9.0000000000001725
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Article ; Online: Optimization of photosynthetically active radiation, temperature, and urea deprivation for increasing neutral lipids and fatty acids in Scenedesmus obliquus and Chlorella vulgaris as biodiesels

Govindarajan, Rasiravathanahalli Kaveriyappan / Thiruvengadam, Rekha / Alanazi, Amer M. / Pandiaraj, Saravanan / Mathivanan, Krishnamurthy / Thiruvengadam, Muthu / Kim, Jin Hee

Biomass and Bioenergy. 2023 July, v. 174 p.106854-

2023

Abstract: The present study investigated the impact of photosynthetically active radiation (PAR), culture temperature, and urea addition on the biomass, total lipid, lipidomic profile, and fatty acid productivity in Scenedesmus obliquus (S. obliquus) and Chlorella ...

Abstract	The present study investigated the impact of photosynthetically active radiation (PAR), culture temperature, and urea addition on the biomass, total lipid, lipidomic profile, and fatty acid productivity in Scenedesmus obliquus (S. obliquus) and Chlorella vulgaris (C. vulgaris) for sustainable biodiesels. In this study, S. obliquus and C. vulgaris, respectively, showed generally high cell densities with 1.23 g/L and 1.22 g/L of dried cell weights and 18.2% and 17.65% of lipids. Of the various PARs tested (10, 20, 40, and 60 μmol/m²/sec), 60 μmol/m²/sec showed maximal biomass yields for both species (1.78 g/L of dried cell weight and 25.7% of lipids for S. obliquus; and 1.74 g/L of dried cell weight and 24.6% of lipids for C. vulgaris). Of the various temperatures (27 °C, 37 °C, and 47 °C), 27 °C showed maximal dried cell weights (1.22 g/L for S. obliquus and 1.23 g/L for C. vulgaris), whereas 47 °C accumulated high levels of lipids (23.5% for S. obliquus and 21.6% for C. vulgaris). On the other hands, urea deprivation in the medium increased lipid levels in both species compared to no deprivation (10% increase for S. obliquus and 8% increase for C. vulgaris). The fatty acid profile showed that palmitic acid with 16 carbons and double bonds was dominant among major fatty acids, accounting for 30.55% for S. obliquus and 26.6% for C. vulgaris. Furthermore, urea deprivation and 60 μmol/m²/sec of PAR showed the highest proportions of unsaturated fatty acids in both species (27.55% for urea deprivation and 30.55% for PAR in S. obliquus; and 28.33% for urea deprivation and 26.6% for PAR in C. vulgaris).
Keywords	Chlorella vulgaris ; Scenedesmus obliquus ; biodiesel ; biomass ; fatty acid composition ; lipidomics ; palmitic acid ; photosynthetically active radiation ; temperature ; urea ; Microalgae ; Lipids ; Fatty acids
Language	English
Dates of publication	2023-07
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	1090121-8
ISSN	0961-9534
ISSN	0961-9534
DOI	10.1016/j.biombioe.2023.106854
Database	NAL-Catalogue (AGRICOLA)

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Z 5470: Show issues

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Article ; Online: Spectroscopic, molecular docking and dynamic simulation studies of binding between the new anticancer agent olmutinib and human serum albumin.

Alanazi, Amer M / Bakheit, Ahmed H / Attwa, Mohamed W / Abdelhameed, Ali Saber

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 24, Page(s) 14236–14246

Abstract: In this study, the interaction between human serum albumin (HSA), which is the key bio-distributor of exogenous and endogenous compounds in the human bloodstream, and HM61713 (Olmutinib; OMB), which is used as an anticancer drug, is examined by multiple ... ...

Abstract	In this study, the interaction between human serum albumin (HSA), which is the key bio-distributor of exogenous and endogenous compounds in the human bloodstream, and HM61713 (Olmutinib; OMB), which is used as an anticancer drug, is examined by multiple spectroscopic techniques (steady-state fluorescence, UV spectrophotometry, synchronous, and 3 D fluorescence) combined with molecular docking and molecular dynamic simulation investigations. The fluorescence results clearly demonstrated quenching in HSA fluorescence in the existence of OMB indicating the formation of complex and have also shown that the interaction is static. Fluorescence spectroscopy was used to obtain the binding constant values that revealed a strong interaction between the HSA and OMB at 298 K with a binding constant of 7.39x10
MeSH term(s)	Humans ; Serum Albumin, Human/chemistry ; Molecular Docking Simulation ; Protein Binding ; Binding Sites ; Antineoplastic Agents ; Spectrometry, Fluorescence/methods ; Thermodynamics ; Circular Dichroism
Chemical Substances	Serum Albumin, Human (ZIF514RVZR) ; olmutinib (CHL9B67L95) ; Antineoplastic Agents
Language	English
Publishing date	2021-11-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.2001380
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Zs.A 2093: Show issues

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Article: Evaluation of the Efficacy, Biocompatibility, and Permeation of Bupivacaine-Loaded Poly(epsilon-caprolactone) Nano-Capsules as an Anesthetic.

Zhao, Wangcheng / Du, Yan / Ashfaq, Shameen / Ali, Shafaqat / Alanazi, Amer M / Santi, Moreno

Journal of biomedical nanotechnology

2022 Volume 18, Issue 1, Page(s) 268–276

Abstract: In this study bupivacaine (BVC) was encapsulated in Nano-capsules of poly- ...

Abstract	In this study bupivacaine (BVC) was encapsulated in Nano-capsules of poly-
MeSH term(s)	Anesthetics, Local/chemistry ; Animals ; Bupivacaine/chemistry ; Caproates ; Lactones ; Polyesters ; Rats ; Swine
Chemical Substances	Anesthetics, Local ; Caproates ; Lactones ; Polyesters ; polycaprolactone (24980-41-4) ; caprolactone (56RE988L1R) ; Bupivacaine (Y8335394RO)
Language	English
Publishing date	2022-02-18
Publishing country	United States
Document type	Journal Article
ISSN	1550-7033
ISSN	1550-7033
DOI	10.1166/jbn.2022.3223
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Article: Molecular Diagnostic of Ochratoxin A With Specific Aptamers in Corn and Groundnut via Fabrication of a Microfluidic Device.

Shahdeo, Deepshikha / Khan, Azmat Ali / Alanazi, Amer M / Bajpai, Vivek K / Shukla, Shruti / Gandhi, Sonu

Frontiers in nutrition

2022 Volume 9, Page(s) 851787

Abstract: Ochratoxin A (OTA) is one of the predominant mycotoxins that contaminate a wide range of food commodities. In the present study, a 36-mer aptamer was used as a molecular recognition element coupled with gold nanoparticles (AuNPs) for colorimetric ... ...

Abstract	Ochratoxin A (OTA) is one of the predominant mycotoxins that contaminate a wide range of food commodities. In the present study, a 36-mer aptamer was used as a molecular recognition element coupled with gold nanoparticles (AuNPs) for colorimetric detection of OTA in a microfluidic paper-based analytical device (μPADs). The μPADs consisted of three zones: control, detection, and sample, interconnected by channels. UV-vis spectroscopy (UV-vis), Dynamic Light Scattering (DLS), and Transmission Electron Microscopy (TEM) were used for characterization of AuNPs and AuNPs/Aptamer. According to the colorimetric assay, limit of detection (LOD) was found to be 242, 545.45, and 95.69 ng/mL in water, corn, and groundnut, respectively. The HPLC detection method achieved acceptable coefficient in standard curves (
Language	English
Publishing date	2022-03-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2776676-7
ISSN	2296-861X
ISSN	2296-861X
DOI	10.3389/fnut.2022.851787
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