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Article ; Online: Subtractive proteomics-guided vaccine targets identification and designing of multi-epitopes vaccine for immune response instigation against Burkholderia pseudomallei.

Alshabrmi, Fahad M / Alatawi, Eid A

International journal of biological macromolecules

2024 Volume 270, Issue Pt 1, Page(s) 132105

Abstract: In this study, a methodical workflow using subtractive proteomics, vaccine designing, molecular simulation, and agent-based modeling approaches were used to annotate the whole proteome of Burkholderia pseudomallei (strain K96243) for vaccine designing. ... ...

Abstract	In this study, a methodical workflow using subtractive proteomics, vaccine designing, molecular simulation, and agent-based modeling approaches were used to annotate the whole proteome of Burkholderia pseudomallei (strain K96243) for vaccine designing. Among the total 5717 proteins in the whole proteome, 505 were observed to be essential for the pathogen's survival and pathogenesis predicted by the Database of Essential Genes. Among these, 23 vaccine targets were identified, of which fimbrial assembly chaperone (Q63UH5), Outer membrane protein (Q63UH1), and Hemolysin-like protein (Q63UE4) were selected for the subsequent analysis based on the systematic approaches. Using immunoinformatic approaches CTL (cytotoxic T lymphocytes), HTL (helper T lymphocytes), IFN-positive, and B cell epitopes were predicted for these targets. A total of 9 CTL epitopes were added using the GSS linker, 6 HTL epitopes using the GPGPG linker, and 6 B cell epitopes using the KK linker. An adjuvant was added for enhanced antigenicity, an HIV-TAT peptide for improved delivery, and a PADRE sequence was added to form a 466 amino acids long vaccine construct. The construct was classified as non-allergenic, highly antigenic, and experimentally feasible. Molecular docking results validated the robust interaction of MEVC with immune receptors such as TLR2/4. Furthermore, molecular simulation revealed stable dynamics and compact nature of the complexes. The binding free energy results further validated the robust binding. In silico cloning, results revealed GC contents of 50.73 % and a CIA value of 0.978 which shows proper downstream processing. Immune simulation results reported that after the three injections of the vaccine a robust secondary immune response, improved antigen clearance, and effective immune memory generation were observed highlighting its potential for effective and sustained immunity. Future directions should encompass experimental validations, animal model studies, and clinical trials to substantiate the vaccine's efficacy, safety, and immunogenicity.
Language	English
Publishing date	2024-05-06
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.2024.132105
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Zs.B 2374: Show issues

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Article ; Online: Deciphering the mechanism of resistance by novel double mutations in pncA in Mycobacterium tuberculosis using protein structural graphs (PSG) and structural bioinformatic approaches.

Alshabrmi, Fahad M / Alatawi, Eid A

Computers in biology and medicine

2023 Volume 154, Page(s) 106599

Abstract: The evolution of MDR and XDR-TB is a growing concern and public health safety threat around the world. Gene mutations are the prime cause of drug resistance in tuberculosis, however the reports of double mutations further aggravated the situation. ... ...

Abstract	The evolution of MDR and XDR-TB is a growing concern and public health safety threat around the world. Gene mutations are the prime cause of drug resistance in tuberculosis, however the reports of double mutations further aggravated the situation. Despite the large-scale genomic sequencing and identification of novel mutations, structure investigation of the protein is still required to structurally and functionally characterize these novel mutations to design novel drugs for improved clinical outcome. Hence, we used structural bioinformatics approaches i.e. molecular modeling, residues communication and molecular simulation to understand the impact of novel double S59Y-L85P, D86G-V180F and S104G-V130 M mutation on the structure, function of pncA encoded Pyrazinamidase (PZase) and resistance of Pyrazinamide (PZA). Our results revealed that these mutations alter the binding paradigm and destabilize the protein to release the drug. Protein commination network (PCN) revealed variations in the hub residues and sub-networks which consequently alter the internal communication and signaling. The region 1-75 demonstrated higher flexibility in the mutant structures and minimal by the wild type which destabilize of the internally arranged beta-sheets which consequently reduce the binding of PZA and potentially Fe ion in the mutants. Hydrogen bonding analysis further validated the findings. The total binding free energy (ΔG) for each complex i.e. wild type -7.46 kcal/mol, S59Y-L85P -5.21 kcal/mol, S104G-V130 M -5.33 kcal/mol while for the D86G-V180F mutant the TBE was calculated to be -6.26 kcal/mol. This further confirms that these mutations reduce the binding energy of PZA for PZase and causes resistance in the effective therapy for TB. The trajectories motion was also observed to be affected by these mutations. In conclusion, these mutations use destabilizing approach to reduce the binding of PZA and causes resistance. These features can be used to design novel structure-based drugs against Tuberculosis.
MeSH term(s)	Humans ; Mycobacterium tuberculosis/genetics ; Antitubercular Agents/pharmacology ; Pyrazinamide/pharmacology ; Tuberculosis/drug therapy ; Tuberculosis/genetics ; Mutation ; Computational Biology ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial/genetics
Chemical Substances	Antitubercular Agents ; Pyrazinamide (2KNI5N06TI)
Language	English
Publishing date	2023-01-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2023.106599
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Article ; Online: Efficiency of magnesium oxide nanoparticle in contaminants removal from environmental water samples: Optimization through central composite design.

Guo, Yuntian / Zhou, Zhenyu / Alshabrmi, Fahad M

Chemosphere

2024 , Page(s) 141734

Abstract: This experimental study was conducted to synthesize magnesium oxide (MgO) nanoparticles and investigate their efficiency in removing arsenic, brilliant cresyl blue, and neutral red from aqueous solutions. The MgO nanoparticles were characterized using X- ... ...

Abstract	This experimental study was conducted to synthesize magnesium oxide (MgO) nanoparticles and investigate their efficiency in removing arsenic, brilliant cresyl blue, and neutral red from aqueous solutions. The MgO nanoparticles were characterized using X-ray diffraction (XRD), energy dispersive X-ray (EDS), Fourier-transform infrared spectroscopy (FTIR), and field emission scanning electron microscopy (FESEM) analyses. The results revealed that the synthesized MgO nanoparticles had a spherical structure with an estimated average size of approximately 30 nm. The influence of solution pH, concentration, adsorbent amount, type of eluent, and interference of interfering ions was examined and optimized for removing arsenic, brilliant cresyl blue, and neutral red. The optimal conditions for the removal process were determined as pH of 7, MgO amount of 0.037 g, ultrasonication time of 16 min, and concentration of 25 mg L
Language	English
Publishing date	2024-04-05
Publishing country	England
Document type	Journal Article
ZDB-ID	120089-6
ISSN	1879-1298 ; 0045-6535 ; 0366-7111
ISSN (online)	1879-1298
ISSN	0045-6535 ; 0366-7111
DOI	10.1016/j.chemosphere.2024.141734
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Article ; Online: Structural and Dynamic Insights into the W68L, L85P, and T87A Mutations of

Alatawi, Eid A / Alshabrmi, Fahad M

International journal of environmental research and public health

2022 Volume 19, Issue 3

Abstract: Tuberculosis (TB), the most frequent bacterium-mediated infectious disease caused ... ...

Abstract	Tuberculosis (TB), the most frequent bacterium-mediated infectious disease caused by
MeSH term(s)	Amidohydrolases/chemistry ; Amidohydrolases/genetics ; Antitubercular Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Mutation ; Mycobacterium tuberculosis/genetics ; Pyrazinamide/chemistry ; Pyrazinamide/pharmacology
Chemical Substances	Antitubercular Agents ; Pyrazinamide (2KNI5N06TI) ; Amidohydrolases (EC 3.5.-)
Language	English
Publishing date	2022-01-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2175195-X
ISSN	1660-4601 ; 1661-7827
ISSN (online)	1660-4601
ISSN	1661-7827
DOI	10.3390/ijerph19031615
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Article ; Online: Exploring therapeutic targets and drug candidates for obesity: a combined network pharmacology, bioinformatics approach.

Aloufi, Bandar / Alshabrmi, Fahad M / Sreeharsha, Nagaraja / Rehman, Abdur

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–22

Abstract: The remarkably high prevalence of obesity in Saudi Arabia reflects a global epidemic demanding urgent attention due to its associated health risks. The integration of traditional medicine, a vital cultural aspect, involves the use of medicinal plants to ... ...

Abstract	The remarkably high prevalence of obesity in Saudi Arabia reflects a global epidemic demanding urgent attention due to its associated health risks. The integration of traditional medicine, a vital cultural aspect, involves the use of medicinal plants to address various diseases, including obesity. This research merges network pharmacology (NP) and bioinformatics to innovate obesity treatment by identifying effective phytochemicals from native plants in the Taif valley. Focusing on six indigenous plants-
Language	English
Publishing date	2023-10-09
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2265491
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Article: Exploring potent aldose reductase inhibitors for anti-diabetic (anti-hyperglycemic) therapy: integrating structure-based drug design, and MMGBSA approaches.

Shahab, Muhammad / Zheng, Guojun / Alshabrmi, Fahad M / Bourhia, Mohammed / Wondmie, Gezahign Fentahun / Mohammad Salamatullah, Ahmad

Frontiers in molecular biosciences

2023 Volume 10, Page(s) 1271569

Abstract: Aldose reductase (AR) is an important target in the development of therapeutics against hyper-glycemia-induced health complications such as retinopathy, etc. In this study, we employed a combination of structure-based drug design, molecular simulation, ... ...

Abstract	Aldose reductase (AR) is an important target in the development of therapeutics against hyper-glycemia-induced health complications such as retinopathy, etc. In this study, we employed a combination of structure-based drug design, molecular simulation, and free energy calculation approaches to identify potential hit molecules against anti-diabetic (anti-hyperglycemic)-induced health complications. The 3D structure of aldoreductase was screened for multiple compound libraries (1,00,000 compounds) and identified as ZINC35671852, ZINC78774792 from the ZINC database, Diamino-di nitro-methyl dioctyl phthalate, and Penta-o-galloyl-glucose from the South African natural compounds database, and Bisindolylmethane thiosemi-carbazides and Bisindolylme-thane-hydrazone from the Inhouse database for this study. The mode of binding interactions of the selected compounds later predicted their aldose reductase inhibitory potential. These com-pounds interact with the key active site residues through hydrogen bonds, salt bridges, and π-π interactions. The structural dynamics and binding free energy results further revealed that these compounds possess stable dynamics with excellent binding free energy scores. The structures of the lead inhibitors can serve as templates for developing novel inhibitors, and
Language	English
Publishing date	2023-11-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1271569
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Article ; Online: Exploring bi-carbazole-linked triazoles as inhibitors of prolyl endo peptidase via integrated in vitro and in silico study.

Ullah, Saeed / Mansoor, Farheen / Khan, Salman Ali / Jabeen, Uzma / Almars, Amany I / Almohaimeed, Hailah M / Basri, Ahmed M / Alshabrmi, Fahad M

Scientific reports

2024 Volume 14, Issue 1, Page(s) 7675

Abstract: A serine protease called prolyl endopeptidase (PEP) hydrolyses the peptide bonds on the carboxy side of the proline ring. The excessive PEP expression in brain results in neurodegenerative illnesses like dementia, Alzheimer's disease, and Parkinson's ... ...

Abstract	A serine protease called prolyl endopeptidase (PEP) hydrolyses the peptide bonds on the carboxy side of the proline ring. The excessive PEP expression in brain results in neurodegenerative illnesses like dementia, Alzheimer's disease, and Parkinson's disease. Results of the prior studies on antioxidant activity, and the non-cytotoxic effect of bi-carbazole-linked triazoles, encouraged us to extend our studies towards its anti-diabetic potential. Hence, for this purpose all compounds 1-9 were evaluated to reveal their anti-prolyl endo peptidase activity. Fortunately, seven compounds resulted into significant inhibitory capability ranging from 26 to 63 µM. Among them six compounds 4-9 exhibited more potent inhibitory activity with IC
MeSH term(s)	Peptide Hydrolases ; Triazoles/pharmacology ; Triazoles/chemistry ; Prolyl Oligopeptidases ; Serine Endopeptidases ; Carbazoles ; Structure-Activity Relationship ; Molecular Docking Simulation
Chemical Substances	Peptide Hydrolases (EC 3.4.-) ; Triazoles ; Prolyl Oligopeptidases (EC 3.4.21.26) ; Serine Endopeptidases (EC 3.4.21.-) ; Carbazoles
Language	English
Publishing date	2024-04-01
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/s41598-024-58428-6
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Article ; Online: Structure-based design of promising natural products to inhibit thymidylate kinase from Monkeypox virus and validation using free energy calculations.

Khan, Abbas / Adil, Shoaib / Qudsia, Hafiza Ayesha / Waheed, Yasir / Alshabrmi, Fahad M / Wei, Dong-Qing

Computers in biology and medicine

2023 Volume 158, Page(s) 106797

Abstract: Monkeypox (MPXV) is a globally growing public health concern with 80,328 active cases and 53 deaths have been reported. No specific vaccine or drug is available for the treatment of MPXV. Hence, the current study also employed structure-based drug ... ...

Abstract	Monkeypox (MPXV) is a globally growing public health concern with 80,328 active cases and 53 deaths have been reported. No specific vaccine or drug is available for the treatment of MPXV. Hence, the current study also employed structure-based drug designing, molecular simulation, and free energy calculation methods to identify potential hit molecules against the TMPK of MPXV, which is a replicatory protein that helps the virus to replicate its DNA and increase the number of DNAs in the host cell. The 3D structure of TMPK was modeled with AlphaFold and screening of multiple natural products libraries (4,71,470 compounds) identified TCM26463, TCM2079, and TCM29893 from traditional Chinese medicines database (TCM), SANC00240, SANC00984, and SANC00986 South African natural compounds database (SANCDB), NPC474409, NPC278434 and NPC158847 from NPASS (natural product activity and species source database) while CNP0404204, CNP0262936, and CNP0289137 were shortlisted from coconut database (collection of open natural products) as the best hits. These compounds interact with the key active site residues through hydrogen bonds, salt bridges, and pie-pie interactions. The structural dynamics and binding free energy results further revealed that these compounds possess stable dynamics with excellent binding free energy scores. Moreover, the dissociation constant (K
MeSH term(s)	Humans ; Monkeypox virus/genetics ; Biological Products/pharmacology ; Mpox (monkeypox)
Chemical Substances	dTMP kinase (EC 2.7.4.9) ; Biological Products
Language	English
Publishing date	2023-03-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2023.106797
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Article ; Online: Immunoinformatics-driven In silico vaccine design for Nipah virus (NPV): Integrating machine learning and computational epitope prediction.

Shahab, Muhammad / Iqbal, Muhammad Waleed / Ahmad, Abbas / Alshabrmi, Fahad M / Wei, Dong-Qing / Khan, Abbas / Zheng, Guojun

Computers in biology and medicine

2024 Volume 170, Page(s) 108056

Abstract: The Nipah virus (NPV) is a highly lethal virus, known for its significant fatality rate. The virus initially originated in Malaysia in 1998 and later led to outbreaks in nearby countries such as Bangladesh, Singapore, and India. Currently, there are no ... ...

Abstract	The Nipah virus (NPV) is a highly lethal virus, known for its significant fatality rate. The virus initially originated in Malaysia in 1998 and later led to outbreaks in nearby countries such as Bangladesh, Singapore, and India. Currently, there are no specific vaccines available for this virus. The current work employed the reverse vaccinology method to conduct a comprehensive analysis of the entire proteome of the NPV virus. The aim was to identify and choose the most promising antigenic proteins that could serve as potential candidates for vaccine development. We have also designed B and T cell epitopes-based vaccine candidate using immunoinformatics approach. We have identified a total of 5 novel Cytotoxic T Lymphocytes (CTL), 5 Helper T Lymphocytes (HTL), and 6 linear B-cell potential antigenic epitopes which are novel and can be used for further vaccine development against Nipah virus. Then we performed the physicochemical properties, antigenic, immunogenic and allergenicity prediction of the designed vaccine candidate against NPV. Further, Computational analysis indicated that these epitopes possessed highly antigenic properties and were capable of interacting with immune receptors. The designed vaccine were then docked with the human immune receptors, namely TLR-2 and TLR-4 showed robust interaction with the immune receptor. Molecular dynamics simulations demonstrated robust binding and good dynamics. After numerous dosages at varied intervals, computational immune response modeling showed that the immunogenic construct might elicit a significant immune response. In conclusion, the immunogenic construct shows promise in providing protection against NPV, However, further experimental validation is required before moving to clinical trials.
MeSH term(s)	Humans ; Nipah Virus ; Immunoinformatics ; Vaccines, Subunit/chemistry ; Epitopes, B-Lymphocyte/chemistry ; Molecular Dynamics Simulation ; Vaccine Development ; Computational Biology/methods ; Molecular Docking Simulation
Chemical Substances	Vaccines, Subunit ; Epitopes, B-Lymphocyte
Language	English
Publishing date	2024-01-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2024.108056
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Article ; Online: Toxicological Profile of Polyethylene Terephthalate (PET) Microplastic in Ingested

Kauts, Simran / Mishra, Yachana / Yousuf, Sumaira / Bhardwaj, Rima / Singh, Sandeep K / Alshabrmi, Fahad M / Abdurahman, Mahmoud / Vamanu, Emanuel / Singh, Mahendra P

Toxics

2023 Volume 11, Issue 9

Abstract: Microplastics are readily available in the natural environment. Due to the pervasiveness of microplastic pollution, its effects on living organisms necessitate further investigation. The size, time of exposure, and amount of microplastic particles appear ...

Abstract	Microplastics are readily available in the natural environment. Due to the pervasiveness of microplastic pollution, its effects on living organisms necessitate further investigation. The size, time of exposure, and amount of microplastic particles appear to be the most essential factor in determining their toxicological effects, either organismal or sub-organismal. For our research work, we preferred to work on a terrestrial model organism
Language	English
Publishing date	2023-09-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2733883-6
ISSN	2305-6304 ; 2305-6304
ISSN (online)	2305-6304
ISSN	2305-6304
DOI	10.3390/toxics11090782
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