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Saleem T, Jamal SB, Alzahrani B, Basheer A, Wajid Abbasi S, Ali M, Rehman AU, Faheem M. In-silico drug design for the novel Karachi-NF001 strain of brain-eating amoeba: Naegleria fowleri. Front Mol Biosci 2023; 10:1098217. [PMID: 36845543 PMCID: PMC9948250 DOI: 10.3389/fmolb.2023.1098217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Naegleria fowleri (N. fowleri) is a free-living thermophilic amoeba of fresh water and soil. The amoeba primarily feeds on bacteria but can be transmitted to humans upon contact with freshwater sources. Furthermore, this brain-eating amoeba enters the human body through the nose and travels to the brain to cause primary amebic meningoencephalitis (PAM). N. fowleri has been reported globally since its discovery in 1961. Recently a new strain of N. fowleri named Karachi-NF001 was found in a patient who had traveled from Riyadh, Saudi Arabia to Karachi in 2019. There were 15 unique genes identified in the genome of the Karachi-NF001 strain compared to all the previously reported strains of N. fowleri worldwide. Six of these genes encode well-known proteins. In this study, we performed in-silico analysis on 5 of these 6 proteins, namely, Rab family small GTPase, NADH dehydrogenase subunit 11, two Glutamine-rich protein 2 proteins (locus tags: 12086 and 12110), and Tigger transposable element-derived protein 1. We conducted homology modeling of these 5 proteins followed by their active site identification. These proteins were subjected to molecular docking against 105 anti-bacterial ligand compounds as potential drugs. Subsequently, the 10 best-docked compounds were determined for each protein and ranked according to the number of interactions and their binding energies. The highest binding energy was recorded for the two Glutamine-rich protein 2 proteins with different locus tags, and results have shown that the protein-inhibitor complex was stable throughout the simulation run. Moreover, future in-vitro studies could validate the findings of our in-silico analysis and identify potential therapeutic drugs against N. fowleri infections.
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Affiliation(s)
- Tayyab Saleem
- Department of Life Technologies, Faculty of Technology, University of Turku, Turku, Finland
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Badr Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Amina Basheer
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Mahwish Ali
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Ashfaq Ur Rehman
- Department of Biochemistry and Molecular Biology, University of California, Irvine, Irvine, CA, United States
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan,*Correspondence: Muhammad Faheem,
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Ghaffar A, Sehgal SA, Fatima R, Batool R, Aimen U, Awan S, Batool S, Ahmad F, Nurulain SM. Molecular docking analyses of CYP450 monooxygenases of Tribolium castaneum (Herbst) reveal synergism of quercetin with paraoxon and tetraethyl pyrophosphate: in vivo and in silico studies. Toxicol Res (Camb) 2020; 9:212-221. [PMID: 32670552 PMCID: PMC7329183 DOI: 10.1093/toxres/tfaa023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/17/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
Pest management in stored grain industry is a global issue due to the development of insecticide resistance in stored grain insect pests. Excessive use of insecticides at higher doses poses a serious threat of food contamination and residual toxicity for grain consumers. Since the development of new pesticide incurs heavy costs, identifying an effective synergist can provide a ready and economical tool for controlling resistant pest populations. Therefore, the synergistic property of quercetin with paraoxon and tetraethyl pyrophosphate has been evaluated against the larvae and adults of Tribolium castaneum (Herbst). Comparative molecular docking analyses were carried out to further identify the possible mechanism of synergism. It was observed that quercetin has no insecticidal when applied at the rate of 1.5 and 3.0 mg/g; however, a considerable synergism was observed when applied in combination with paraoxon. The comparative molecular docking analyses of CYP450 monooxygenase (CYP15A1, CYP6BR1, CYP6BK2, CYP6BK3) family were performed with quercetin, paraoxon and tetraethyl pyrophosphate which revealed considerable molecular interactions, predicting the inhibition of CYP450 isoenzyme by all three ligands. The study concludes that quercetin may be an effective synergist for organophosphate pesticides depending upon the dose and type of the compound. In addition, in silico analyses of the structurally diversified organophosphates can effectively differentiate the organophosphates which are synergistic with quercetin.
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Affiliation(s)
- Ammarah Ghaffar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad 45550, Pakistan
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Kotwali Rd, Gurunanakpura, Faisalabad 38000, Pakistan
| | - Rida Fatima
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad 45550, Pakistan
| | - Roya Batool
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad 45550, Pakistan
| | - Ume Aimen
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad 45550, Pakistan
| | - Sliha Awan
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad 45550, Pakistan
| | - Sajida Batool
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad 45550, Pakistan
| | - Faheem Ahmad
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad 45550, Pakistan
| | - Syed M Nurulain
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad 45550, Pakistan
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Tahir RA, Bashir A, Yousaf MN, Ahmed A, Dali Y, Khan S, Sehgal SA. In Silico identification of angiotensin-converting enzyme inhibitory peptides from MRJP1. PLoS One 2020; 15:e0228265. [PMID: 32012183 PMCID: PMC6996805 DOI: 10.1371/journal.pone.0228265] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 01/12/2020] [Indexed: 01/14/2023] Open
Abstract
Hypertension is considered as one of the most common diseases that affect human beings (both male and female) due to its high prevalence and also extending widely to both industrialize and developing countries. Angiotensin-converting enzyme (ACE) has a significant role in the regulation of blood pressure and ACE inhibition with inhibitory peptides is considered as a major target to prevent hypertension. In the current study, a blood pressure regulating honey protein (MRJP1) was examined to identify the ACE inhibitory peptides. The 3D structure of MRJP1 was predicted by utilizing the threading approach and further optimized by performing molecular dynamics simulation for 30 nanoseconds (ns) to improve the quality factor up to 92.43%. Root mean square deviation and root mean square fluctuations were calculated to evaluate the structural features and observed the fluctuations in the timescale of 30 ns. AHTpin server based on scoring vector machine of regression models, proteolysis and structural characterization approaches were implemented to identify the potential inhibitory peptides. The anti-hypertensive peptides were scrutinized based on the QSAR models of anti-hypertensive activity and the molecular docking analyses were performed to explore the binding affinities and potential interacting residues. The peptide "EALPHVPIFDR" showed the strong binding affinity and higher anti-hypertensive activity along with the global energy of -58.29 and docking score of 9590. The aromatic amino acids especially Tyr was observed as the key residue to design the dietary peptides and drugs like ACE inhibitors.
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Affiliation(s)
- Rana Adnan Tahir
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, China
- Department of Biosciences, COMSATS University Islamabad Sahiwal Campus, Sahiwal, Pakistan
| | - Afsheen Bashir
- Khyber Girls Medical College, Hayatabad, Peshawar, Pakistan
| | | | - Azka Ahmed
- Department of Biosciences, COMSATS University Islamabad Sahiwal Campus, Sahiwal, Pakistan
| | - Yasmine Dali
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences; Beijing, China
| | - Sanaullah Khan
- Department of Zoology, University of Peshawar, Peshawar, Pakistan
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
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Sehgal SA, Hammad MA, Tahir RA, Akram HN, Ahmad F. Current Therapeutic Molecules and Targets in Neurodegenerative Diseases Based on in silico Drug Design. Curr Neuropharmacol 2018; 16:649-663. [PMID: 29542412 PMCID: PMC6080102 DOI: 10.2174/1570159x16666180315142137] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 01/01/2018] [Accepted: 03/02/2018] [Indexed: 12/20/2022] Open
Abstract
Abstract: Background As the number of elderly persons increases, neurodegenerative diseases are becoming ubiquitous. There is currently a great need for knowledge concerning management of old-age neurodegenerative diseases; the most important of which are: Alzheimer’s disease, Parkinson’s disease, Amyotrophic Lateral Sclerosis, and Huntington’s disease. Objective To summarize the potential of computationally predicted molecules and targets against neurodegenerative diseases. Method Review of literature published since 1997 against neurodegenerative diseases, utilizing as keywords: in silico, Alzheimer’s disease, Parkinson’s disease, Amyotrophic Lateral Sclerosis ALS, and Huntington’s disease was conducted. Results and Conclusion Due to the costs associated with experimentation and current ethical law, performing experiments directly on living organisms has become much more difficult. In this scenario, in silico techniques have been successful and have become powerful tools in the search to cure disease. Researchers use the Computer Aided Drug Design pipeline which: 1) generates 3-dimensional structures of target proteins through homology modeling 2) achieves stabilization through molecular dynamics simulation, and 3) exploits molecular docking through large compound libraries. Next generation sequencing is continually producing enormous amounts of raw sequence data while neuroimaging is producing a multitude of raw image data. To solve such pressing problems, these new tools and algorithms are required. This review elaborates precise in silico tools and techniques for drug targets, active molecules, and molecular docking studies, together with future prospects and challenges concerning possible breakthroughs in Alzheimer’s, Parkinson’s, Amyotrophic Lateral Sclerosis, and Huntington’s disease.
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Affiliation(s)
- Sheikh Arslan Sehgal
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences; Beijing, China.,Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan.,University of Chinese Academy of Sciences, Beijing, China
| | - Mirza A Hammad
- University of Chinese Academy of Sciences, Beijing, China.,National Laboratory of Biomacromolecules, Institute of Biophysics; Chinese Academy of Sciences; Beijing, China
| | - Rana Adnan Tahir
- Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan.,Beijing Key Laboratory of Separation and Analysis in Biomedical and Pharmaceuticals, Department of Biomedical Engineering, School of Life Sciences, Beijing Institute of Technology, China
| | - Hafiza Nisha Akram
- Department of Environmental Sciences, Quaid-e-Azam University Islamabad, Pakistan
| | - Faheem Ahmad
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
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Pollegioni L, Piubelli L, Molla G, Rosini E. D-Amino Acid Oxidase-pLG72 Interaction and D-Serine Modulation. Front Mol Biosci 2018; 5:3. [PMID: 29417050 PMCID: PMC5787542 DOI: 10.3389/fmolb.2018.00003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 01/08/2018] [Indexed: 12/30/2022] Open
Abstract
pLG72 is a small, primate-specific protein of 153 amino acids. It is the product of the G72 gene, expressed in testis, spinal cord, and brain. The presence of G72 transcript and pLG72 has recurrently been called into question, however G72 mRNA and pLG72 protein levels were higher in blood and brain of patients with schizophrenia than in healthy controls. On the one hand, the SNP rs2391191 corresponding to the R30K substitution in pLG72 was genetically linked to schizophrenia, reduced thickness of the brain cortex in schizophrenia-affected individuals, and altered memory function. Various lines of evidence indicated that pLG72 is a mitochondrial protein, specifically an extrinsic protein bound on the outer membrane. Over the years, pLG72 was proposed to be involved in different functions: (a) overexpression induces mitochondria fragmentation, increasing the numbers of shorter and more mobile ones which could be delivered faster to regions of intense growth and facilitating the dendritic complexity; (b) it might induce oxidative stress by interacting with methionine-R-sulfoxide reductase B2; and (c) it binds and modulates the activity of FMN-containing oxidoreductase of the respiratory complex I. The main role of this protein, however, is related to its binding to the human flavoenzyme D-amino acid oxidase (hDAAO), i.e., the main catabolic enzyme for D-enantiomer of serine. This D-amino acid is a main endogenous coagonist of the N-methyl-D-aspartate type glutamate receptor (NMDAR) involved in main functions such as synaptic plasticity, learning, memory, and excitotoxicity. For this work, we reviewed the recent literature concerning the hDAAO-pLG72 interaction, focusing on the molecular details of the interaction, the effect of hDAAO function and stability, and the cellular effects, especially on D-serine concentration. The main effects related to the pathological R30K substitution are also reported. We have highlighted the gaps in our knowledge of this human protein as well as the relevance of clarifying the molecular details of hDAAO-pLG72 interaction in order to design molecules to modulate hDAAO activity/stability and thus NMDAR function acting at the D-serine cellular level.
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Affiliation(s)
- Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy.,The Protein Factory, Politecnico di Milano and Università degli studi dell'Insubria, Milan, Italy
| | - Luciano Piubelli
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy.,The Protein Factory, Politecnico di Milano and Università degli studi dell'Insubria, Milan, Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy.,The Protein Factory, Politecnico di Milano and Università degli studi dell'Insubria, Milan, Italy
| | - Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy.,The Protein Factory, Politecnico di Milano and Università degli studi dell'Insubria, Milan, Italy
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Pharmacoinformatics, Adaptive Evolution, and Elucidation of Six Novel Compounds for Schizophrenia Treatment by Targeting DAOA (G72) Isoforms. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5925714. [PMID: 28197415 PMCID: PMC5288522 DOI: 10.1155/2017/5925714] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/22/2016] [Indexed: 12/16/2022]
Abstract
Studies on Schizophrenia so far reveal a complex picture of neurological malfunctioning reported to be strongly associated with DAOA. Detailed sequence analyses proved DAOA as a primate specific gene having conserved gene desert region on both upstream and downstream region. The analyses of 10 MB chromosomal region of primates, birds, rodents, and reptiles having DAOA evidenced the conserved part in primates and in the rest of species, while DAOA is only present in primates. DAOA has four isoforms having one interaction partner DAO. Protein-protein analyses of four DAOA isoforms with DAO were performed individually and find potential interacting residues computationally. It was observed that molecular docking of approved FDA drugs revealed efficient results but there was no common drug with effective binding to all DAOA isoforms. Library of compounds was constructed by virtual screening of 2D similarity search against recommended SZ drugs in conjunction with their physiochemical properties. Molecular docking resulted in six novel compounds exhibiting maximum binding affinity with selected four DAOA isoforms. However not the entire schizophrenic population responds to the single drug and interestingly in this study six novel compounds having promising results and same binding site to that DAOA that may be used to interact with DAO against four DAOA isoforms were observed.
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Sehgal SA, Mannan S, Ali S. Pharmacoinformatic and molecular docking studies reveal potential novel antidepressants against neurodegenerative disorders by targeting HSPB8. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:1605-18. [PMID: 27226709 PMCID: PMC4866741 DOI: 10.2147/dddt.s101929] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Charcot-Marie-Tooth (CMT) disease is an inherited peripheral neuromuscular disorder characterized by length-dependent and progressive degeneration of peripheral nerves, leading to muscular weakness. Research has shown that mutated HSPB8 may be responsible for depression, neurodegenerative disorders, and improper functioning of peripheral nerves, resulting in neuromuscular disorders like CMT. In the current work, a hybrid approach of virtual screening and molecular docking studies was followed by homology modeling and pharmacophore identification. Detailed screening analyses were carried out by 2-D similarity search against prescribed antidepressant drugs with physicochemical properties. LigandScout was employed to ascertain novel molecules and pharmacophore properties. In this study, we report three novel compounds that showed maximum binding affinity with HSPB8. Docking analysis elucidated that Met37, Ser57, Ser58, Trp60, Thr63, Thr114, Lys115, Asp116, Gly117, Val152, Val154, Leu186, Asp189, Ser190, Gln191, and Glu192 are critical residues for ligand-receptor interactions. Our analyses suggested paroxetine as a potent compound for targeting HSPB8. Selected compounds have more effective energy scores than the selected drug analogs. Additionally, site-directed mutagenesis could be significant for further analysis of the binding pocket. The novel findings based on an in silico approach may be momentous for potent drug design against depression and CMT.
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Affiliation(s)
- Sheikh Arslan Sehgal
- Department of Bioscience, COMSATS Institute of Information Technology, Sahiwal, Pakistan; State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China; University of Chinese Academy of Sciences, Beijing, People's Republic of China; Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Shazia Mannan
- Department of Bioscience, COMSATS Institute of Information Technology, Sahiwal, Pakistan
| | - Sannia Ali
- Department of Bioscience, COMSATS Institute of Information Technology, Sahiwal, Pakistan
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