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Abdel-Naim AB, Kumar P, Bazuhair MA, Rizg WY, Niyazi HA, Alkuwaity K, Niyazi HA, Alharthy SA, Harakeh S, Haque S, Prakash A, Kumar V. Computational insights into dynamics and conformational stability of N-acetylmannosamine kinase mutations. J Biomol Struct Dyn 2024:1-11. [PMID: 38502682 DOI: 10.1080/07391102.2024.2323702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
The activity of UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) is essential for the biosynthesis of sialic acid, which is involved in cellular processes in health and diseases. GNE contains an N-terminal epimerase domain and a C-terminal kinase domain (N-acetylmannosamine kinase, MNK). Mutations of the GNE protein led to hypoactivity of the enzyme and cause sialurea or autosomal recessive inclusion body myopathy/Nonaka myopathy. Here, we used all-atom molecular dynamics (MD) simulations to comprehend the folding, dynamics and conformational stability of MNK variants, including the wild type (WT) and three mutants (H677R, V696M and H677R/V696M). The deleterious and destabilizing nature of MNK mutants were predicted using different prediction tools. Results predicted that mutations modulate the stability, flexibility and function of MNK. The effect of mutations on the conformational stability and dynamics of MNK was next studied through the free-energy landscape (FEL), hydrogen-bonds and secondary structure changes. The FEL results show that the mutations interfere with various conformational transitions in both WT and mutants, exposing the structural underpinnings of protein destabilization and unfolding brought on by mutation. We discover that, when compared to the other two mutations, V696M and H677R/V696M, H677R has the most harmful effects. These findings have a strong correlation with published experimental studies that demonstrate how these mutations disrupt MNK activity. Hence, this computational study describes the structural details to unravel the mutant effects at the atomistic resolution and has implications for understanding the GNE's physiological and pathological role.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashraf B Abdel-Naim
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Mohamed Saeed Tamer Chair for Pharmaceutical Industries, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pawan Kumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohammed A Bazuhair
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Clinical Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Waleed Y Rizg
- Mohamed Saeed Tamer Chair for Pharmaceutical Industries, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hatoon A Niyazi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalil Alkuwaity
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hanouf A Niyazi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saif A Alharthy
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Toxicology and Forensic Sciences Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Yousef Abdul Latif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, India
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Singh P, Kanhed A, Khatik GL, Datusalia AK. Identifying potential neuroprotective polyphenols targeting endoplasmic reticulum stress through an in silico approach. J Biomol Struct Dyn 2024; 42:834-847. [PMID: 37021457 DOI: 10.1080/07391102.2023.2196354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023]
Abstract
The endoplasmic reticulum (ER) is essential in many cellular processes, including protein processing, lipid metabolism, and calcium storage. Dysregulation of ER function has been linked with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, etc. The primary pathological alteration explicated in the diseases is the accumulation of misfolded proteins in the neuronal cells. ER stress-associated activation of PERK-mediated pro-apoptotic cell death leads to neurodegeneration. In this study, we have primarily screened the potential polyphenols evidenced for neuroprotective activity. The 24 polyphenols were selected to explore their binding affinity towards various proteins of ER cascade such as pPERK (phospho-PERK), EIF2 (Eukaryotic Initiation Factor 2), and ATF4 (Activating Transcription Factor 4). On the basis of binding affinity, four phytopolyphenols were further selected for in-silico ADMET and molecular dynamic simulation. Among them curcumin found to be the most promising and serve as a potential hit against all three targets of ER cascade. The selected proteins' active site has demonstrated high stability of curcumin binding according to molecular dynamics findings. Though curcumin exhibited a significant hit in interaction with targets but needs to be further improved in drug-ability criteria. Thus, seventy derivatives of curcumin scaffold (from the published literature) were also screened with improve in druggability criteria, which showed good interaction with unfolded protein response related targets. The new scaffolds serve considerable potential to be developed as novel polyphenolic lead for neurodegenerative disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pooja Singh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, India
| | - Ashish Kanhed
- Shobhaben Pratapbhai Patel - School of Pharmacy & Technology Management, SVKM's NMIMS University, Mumbai, India
| | - Gopal Lal Khatik
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, India
| | - Ashok Kumar Datusalia
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, India
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, India
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3
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Haque S, Kumar P, Mathkor DM, Bantun F, Jalal NA, Mufti AH, Prakash A, Kumar V. In silico evaluation of the inhibitory potential of nucleocapsid inhibitors of SARS-CoV-2: a binding and energetic perspective. J Biomol Struct Dyn 2023; 41:9797-9807. [PMID: 36379684 DOI: 10.1080/07391102.2022.2146752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/07/2022] [Indexed: 11/17/2022]
Abstract
The COVID-19 outbreak brought on by the SARS-CoV-2 virus continued to infect a sizable population worldwide. The SARS-CoV-2 nucleocapsid (N) protein is the most conserved RNA-binding structural protein and is a desirable target because of its involvement in viral transcription and replication. Based on this aspect, this study focused to repurpose antiviral compounds approved or in development for treating COVID-19. The inhibitors chosen are either FDA-approved or are currently being studied in clinical trials against COVID-19. Initially, they were designed to target stress granules and other RNA biology. We have utilized structure-based molecular docking and all-atom molecular dynamics (MD) simulation approach to investigate in detail the binding energy and binding modes of the different anti-N inhibitors to N protein. The result showed that five drugs including Silmitasterib, Ninetanidinb, Ternatin, Luteolin, Fedratinib, PJ34, and Zotatafin were found interacting with RNA binding sites as well as to predicted protein interface with higher binding energy. Overall, drug binding increases the stability of the complex with maximum stability found in the order, Silmitasertib > PJ34 > Zotatatafin. In addition, the frustration changes due to drug binding brings a decrease in local frustration and this decrease is mainly observed in α-helix, β3, β5, and β6 strands and are important for drug binding. Our in-silico data suggest that an effective interaction occurs for some of the tested drugs and prompt their further validation to reduce the rapid outspreading of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Pawan Kumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ahmad Hasan Mufti
- Medical Genetics Department, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, Uttar Pradesh, India
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4
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Patel A, Tiwari K, Asrani P, Alothaid H, Alahmari AFA, Mirdad R, Ajmal MR, Tarique M. Glutaredoxin proteins from E. coli isoforms were compared in terms of energy frustration. BRAZ J BIOL 2023; 83:e273091. [PMID: 37729314 DOI: 10.1590/1519-6984.273091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/05/2023] [Indexed: 09/22/2023] Open
Abstract
Glutaredoxin (GRXs) protein plays a vital role inside the cell, including redox control of transcription to the cell's antioxidant defense, apoptosis, and cellular differentiation regulation. In this study, we have investigated the energy landscape and characterized the pattern of local frustration in different forms and states of the GRX protein ofE. coli.Analysis was done on the conformational alterations, significant changes in the frustration pattern, and different GRXs such as GRX-II, GRX-III, GRX-II-GSH, and GRX-III-GSH complex. We have found the practice of frustration, and structure was quite similar in the same isoform having different states of protein; however, a significant difference was observed between different isoforms. Moreover, oxidation of GRX-I introduced an extra α-helix increasing the destabilizing interactions within the protein. The study of frustrated contacts on oxidized and reduced GRX and with bound and unbound Glutathione indicates its potential application in activating and regulating the behavior of GRXs.
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Affiliation(s)
- A Patel
- King Khalid University, College of Medicine, Department of Clinical Biochemistry, Abha, Kingdom of Saudi Arabia
| | - K Tiwari
- King Khalid University, College of Medicine, Department of Clinical Biochemistry, Abha, Kingdom of Saudi Arabia
- Amity University, Amity Institute of Microbial Biotechnology, Noida, UP, India
| | - P Asrani
- Amity University, Amity Institute of Microbial Biotechnology, Noida, UP, India
| | - H Alothaid
- Al Baha University, Faculty of Applied Medical Sciences, Department of Basic Medical Sciences, Al Baha, Al Baha Province, Saudi Arabia
| | - A F A Alahmari
- King Khalid University, College of Medicine, Department of Clinical Biochemistry, Abha, Saudi Arabia
| | - R Mirdad
- King Khalid University, Department of Surgery, Abha, Saudi Arabia
| | - M R Ajmal
- University of Tabuk, Faculty of Science, Biochemistry Department, Physical Biochemistry Research Laboratory, Tabuk, Saudi Arabia
| | - M Tarique
- Almanac Life Science India Private Limited, New Delhi, India
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5
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Haque S, Khatoon F, Ashgar SS, Faidah H, Bantun F, Jalal NA, Qashqari FSI, Kumar V. Energetic and frustration analysis of SARS-CoV-2 nucleocapsid protein mutations. Biotechnol Genet Eng Rev 2023:1-21. [PMID: 36708355 DOI: 10.1080/02648725.2023.2170031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 01/11/2023] [Indexed: 01/29/2023]
Abstract
The ongoing COVID-19 spreads worldwide with the ability to evolve in diverse human populations. The nucleocapsid (N) protein is one of the mutational hotspots in the SARS-CoV-2 genome. The N protein is an abundant RNA-binding protein critical for viral genome packaging. It comprises two large domains including the N-terminal domain (NTD) and the C-terminal domain (CTD) linked by the centrally located linker region. Mutations in N protein have been reported to increase the severity of disease by modulating viral transmissibility, replication efficiency as well as virulence properties of the virus in different parts of the world. To study the effect of N protein missense mutations on protein stability, function, and pathogenicity, we analyzed 228 mutations from each domain of N protein. Further, we have studied the effect of mutations on local residual frustration changes in N protein. Out of 228 mutations, 11 mutations were predicted to be deleterious and destabilized. Among these mutations, R32C, R191C, and R203 M mutations fall into disordered regions and show significant change in frustration state. Overall, this work reveals that by altering the energetics and residual frustration, N protein mutations might affect the stability, function, and pathogenicity of the SARS-CoV-2.
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Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Fatima Khatoon
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, India
| | - Sami S Ashgar
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Fadi S I Qashqari
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, India
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6
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Khatoon F, Kumar V, Anjum F, Shafie A, Adnan M, Hassan MI. Frustration analysis of TBK1 missense mutations reported in ALS/FTD and cancer patients. 3 Biotech 2022; 12:174. [PMID: 35845111 PMCID: PMC9283588 DOI: 10.1007/s13205-022-03240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Tank-binding kinase 1 (TBK1) is a multifunctional kinase having essential roles in cellular processes, autophagy/mitophagy, and selective clearance of damaged proteins. More than 90 mutations in the TBK1 gene are linked with multiple cancer types, amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). Some of these missense mutations disrupt the abilities of TBK1 to dimerize, associate with the mitophagy receptor optineurin (OPTN), autoactivate, or catalyze phosphorylation. Some mutations may cause severe dysregulation of the pathway, while others induce a limited disruption. Here, we have studied those mutations reported in cancer, ALS and FTD, and subsequently investigated the effect of missense mutations on the structure and function of TBK1 for localized residual frustration change. Out of 33 ALS/FTD causing mutations and 28 oncogenic mutations, 10 mutations and 12 oncogenic mutations showed significant change in the residual frustration. The local frustration plays an important role in the conformation of protein structure in active and inactive kinases. Our analysis reports the change in residual frustration state, conformational change and effect on active and inactive TBK1 function due to ALS/FTD causing and oncogenic missense mutations. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03240-0.
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7
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Yousuf M, Alam M, Shamsi A, Khan P, Hasan GM, Rizwanul Haque QM, Hassan MI. Structure-guided design and development of cyclin-dependent kinase 4/6 inhibitors: A review on therapeutic implications. Int J Biol Macromol 2022; 218:394-408. [PMID: 35878668 DOI: 10.1016/j.ijbiomac.2022.07.156] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022]
Abstract
Cyclin-dependent kinase 6 (EC 2.7.11.22) play significant roles in numerous biological processes and triggers cell cycle events. CDK6 controlled the transcriptional regulation. A dysregulated function of CDK6 is linked with the development of progression of multiple tumor types. Thus, it is considered as an effective drug target for cancer therapy. Based on the direct roles of CDK4/6 in tumor development, numerous inhibitors developed as promising anti-cancer agents. CDK4/6 inhibitors regulate the G1 to S transition by preventing Rb phosphorylation and E2F liberation, showing potent anti-cancer activity in several tumors, including HR+/HER2- breast cancer. CDK4/6 inhibitors such as abemaciclib, palbociclib, and ribociclib, control cell cycle, provoke cell senescence, and induces tumor cell disturbance in pre-clinical studies. Here, we discuss the roles of CDK6 in cancer along with the present status of CDK4/6 inhibitors in cancer therapy. We further discussed, how structural features of CDK4/6 could be implicated in the design and development of potential anti-cancer agents. In addition, the therapeutic potential and limitations of available CDK4/6 inhibitors are described in detail. Recent pre-clinical and clinical information for CDK4/6 inhibitors are highlighted. In addition, combination of CDK4/6 inhibitors with other drugs for the therapeutic management of cancer are discussed.
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Affiliation(s)
- Mohd Yousuf
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | | | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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8
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Wahiduzzaman, Kumar V, Anjum F, Shafie A, Elasbali AM, Islam A, Ahmad F, Hassan MI. Delineating the Aggregation-Prone Hotspot Regions (Peptides) in the Human Cu/Zn Superoxide Dismutase 1. ACS OMEGA 2021; 6:33985-33994. [PMID: 34926946 PMCID: PMC8675042 DOI: 10.1021/acsomega.1c05321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 11/19/2021] [Indexed: 02/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, incurable neurodegenerative disease described by progressive degeneration of motor neurons. The most common familial form of ALS (fALS) has been associated with mutations in the Cu/Zn superoxide dismutase (SOD1) gene. Mutation-induced misfolding and aggregation of SOD1 is often found in ALS patients. In this work, we probe the aggregation properties of peptides derived from the SOD1. To examine the source of SOD1 aggregation, we have employed a computational algorithm to identify four peptides from the SOD1 protein sequence that aggregates into a fibril. Aided by computational algorithms, we identified four peptides likely involved in SOD1 fibrillization. These four aggregation-prone peptides were 14VQGIINFE21, 30KVWGSIKGL38, 101DSVISLS107, and 147GVIGIAQ153. In addition, the formation of fibril propensities from the identified peptides was investigated through different biophysical techniques. The atomic structures of two fibril-forming peptides from the C-terminal SOD1 showed that the steric zippers formed by 101DSVISLS107 and 147GVIGIAQ153 vary in their arrangement. We also discovered that fALS mutations in the peptide 147GVIGIAQ153 increased the fibril-forming propensity and altered the steric zipper's packing. Thus, our results suggested that the C-terminal peptides of SOD1 have a central role in amyloid formation and might be involved in forming the structural core of SOD1 aggregation observed in vivo.
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Affiliation(s)
- Wahiduzzaman
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Vijay Kumar
- Amity
Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP 201303, India
| | - Farah Anjum
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Alaa Shafie
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Abdelbaset Mohamed Elasbali
- Clinical
Laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Sakaka 72388, Saudi Arabia
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faizan Ahmad
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Md. Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
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9
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Kumar V. Molecular interactions between C9ORF72 and SMCR8: A local energetic frustration perspective. Biochem Biophys Res Commun 2021; 570:1-7. [PMID: 34256240 DOI: 10.1016/j.bbrc.2021.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/06/2021] [Indexed: 11/19/2022]
Abstract
The hexanucleotide repeat expansion in C9orf72 represents a major cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). C9orf72, together with SMCR8 and WDR41, can form a stable complex that regulates autophagy and membrane trafficking. Very recently, the cryo-EM structure of C9orf72-SMCR8-WDR41 helps in understanding the structure-function relationship of C9orf72. This protein complex is indispensable to several cellular processes and is strongly linked to familial ALS and FTD. Understanding the molecular basis of the C9orf72-SMCR8 protein-protein interaction is thus important to comprehend their function. To establish a basis for understanding the relationships between sequence, structure, and function of the C9orf72, this study reports a local frustration analysis on the C9orf72-SMCR8 complex structure. An analysis of local frustration profiles indicated that (1) the structural domains in C9orf72 are minimally-frustrated and relatively conserved, (2) high frustration patches on the protein-protein interface (3) increased frustration in the C-terminal helices involved in the dimerization of C9orf72 structures.
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Affiliation(s)
- Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, UP, 201303, India.
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10
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Alam M, Hasan GM, Hassan MI. A review on the role of TANK-binding kinase 1 signaling in cancer. Int J Biol Macromol 2021; 183:2364-2375. [PMID: 34111484 DOI: 10.1016/j.ijbiomac.2021.06.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/19/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
TANK-binding kinase 1 (TBK1) regulates various biological processes including, NF-κB signaling, immune response, autophagy, cell division, Ras-mediated oncogenesis, and AKT pro-survival signaling. Enhanced TBK1 activity is associated with autoimmune diseases and cancer, suggesting its role in therapeutic targeting of interferonopathies. In addition, dysregulation of TBK1 activity promotes several inflammatory disorders and oncogenesis. Structural and biochemical study reports provide the molecular process of TBK1 activation and recap the substrate selection about TBK1. This review summarizes recent findings on the molecular mechanisms by which TBK1 is involved in cancer signaling. The IKK-ε and TBK1 are together associated with inflammatory diseases by inducing type I IFNs. Furthermore, TBK1 signaling regulates radiation-induced epithelial-mesenchymal transition by controlling phosphorylation of GSK-3β and expression of Zinc finger E-box-binding homeobox 1, suggesting, TBK1 could be targeted for radiotherapy-induced metastasis therapy. Despite a considerable increase in the list of TBK1 inhibitors, only a few has potential to control cancer. Among them, a compound BX795 is considered a potent and selective inhibitor of TBK1. We discussed the therapeutic potential of small-molecule inhibitors of TBK1, particularly those with high selectivity, which will enable further exploration in the therapeutic management of cancer and inflammatory diseases.
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Affiliation(s)
- Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, PO Box 173, Al-Kharj 11942, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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11
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Pandey P, Prasad K, Prakash A, Kumar V. Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis. J Mol Med (Berl) 2020; 98:1659-1673. [PMID: 32965508 PMCID: PMC7509052 DOI: 10.1007/s00109-020-01980-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 12/28/2022]
Abstract
Abstract The outbreak of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus continually led to infect a large population worldwide. SARS-CoV-2 utilizes its NSP6 and Orf9c proteins to interact with sigma receptors that are implicated in lipid remodeling and ER stress response, to infect cells. The drugs targeting the sigma receptors, sigma-1 and sigma-2, have emerged as effective candidates to reduce viral infectivity, and some of them are in clinical trials against COVID-19. The antipsychotic drug, haloperidol, exerts remarkable antiviral activity, but, at the same time, the sigma-1 benzomorphan agonist, dextromethorphan, showed pro-viral activity. To explore the potential mechanisms of biased binding and activity of the two drugs, haloperidol and dextromethorphan towards NSP6, we herein utilized molecular docking–based molecular dynamics simulation studies. Our extensive analysis of the protein-drug interactions, structural and conformational dynamics, residual frustrations, and molecular switches of NSP6-drug complexes indicates that dextromethorphan binding leads to structural destabilization and increase in conformational dynamics and energetic frustrations. On the other hand, the strong binding of haloperidol leads to minimal structural and dynamical perturbations to NSP6. Thus, the structural insights of stronger binding affinity and favorable molecular interactions of haloperidol towards viral NSP6 suggests that haloperidol can be potentially explored as a candidate drug against COVID-19. Key messages •Inhibitors of sigma receptors are considered as potent drugs against COVID-19. •Antipsychotic drug, haloperidol, binds strongly to NSP6 and induces the minimal changes in structure and dynamics of NSP6. •Dextromethorphan, agonist of sigma receptors, binding leads to overall destabilization of NSP6. •These two drugs bind with NSP6 differently and also induce differences in the structural and conformational changes that explain their different mechanisms of action. •Haloperidol can be explored as a candidate drug against COVID-19. Electronic supplementary material The online version of this article (10.1007/s00109-020-01980-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Preeti Pandey
- Department of Chemistry & Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019-5251, USA
| | - Kartikay Prasad
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, UP, 201303, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health (AIISH), Amity University Haryana, Gurgaon, 122413, India.
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, UP, 201303, India.
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Kumar V, Pandey P, Idrees D, Prakash A, Lynn A. Delineating the effect of mutations on the conformational dynamics of N-terminal domain of TDP-43. Biophys Chem 2019; 250:106174. [DOI: 10.1016/j.bpc.2019.106174] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/06/2019] [Accepted: 04/21/2019] [Indexed: 12/12/2022]
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Amir M, Ahmad S, Ahamad S, Kumar V, Mohammad T, Dohare R, Alajmi MF, Rehman T, Hussain A, Islam A, Ahmad F, Hassan MI. Impact of Gln94Glu mutation on the structure and function of protection of telomere 1, a cause of cutaneous familial melanoma. J Biomol Struct Dyn 2019; 38:1514-1524. [DOI: 10.1080/07391102.2019.1610500] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Mohd. Amir
- Jamia Millia Islamia, Jamia Nagar, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Shahnawaz Ahmad
- Department of Biotechnology, School of Engineering &Technology, IFTM University, Lodhipur-Rajput, Moradabad, Uttar Pradesh, India
| | - Shahzaib Ahamad
- Department of Biotechnology, School of Engineering &Technology, IFTM University, Lodhipur-Rajput, Moradabad, Uttar Pradesh, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, Uttar Pradesh, India
| | - Taj Mohammad
- Jamia Millia Islamia, Jamia Nagar, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Ravins Dohare
- Jamia Millia Islamia, Jamia Nagar, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, KSA
| | - Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, KSA
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, KSA
| | - Asimul Islam
- Jamia Millia Islamia, Jamia Nagar, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Faizan Ahmad
- Jamia Millia Islamia, Jamia Nagar, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Md. Imtaiyaz Hassan
- Jamia Millia Islamia, Jamia Nagar, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
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Prakash A, Kumar V, Meena NK, Lynn AM. Elucidation of the structural stability and dynamics of heterogeneous intermediate ensembles in unfolding pathway of the N-terminal domain of TDP-43. RSC Adv 2018; 8:19835-19845. [PMID: 35548664 PMCID: PMC9088055 DOI: 10.1039/c8ra03368d] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/14/2018] [Indexed: 11/21/2022] Open
Abstract
The N-terminal domain of the RNA binding protein TDP-43 (NTD) is essential to both physiology and proteinopathy; however, elucidation of its folding/unfolding still remains a major quest. In this study, we have investigated the biophysical behavior of intermediate ensembles employing all-atom molecular dynamics simulations in 8 M urea accelerated with high temperatures to achieve unfolded states in a confined computation time. The cumulative results of the 2.75 μs simulations show that unfolding of the NTD at 350 K evolves through different stable and meta-stable intermediate states. The free-energy landscape reveals two meta-stable intermediates (IN and IU) stabilized by non-native interactions, which are largely hydrophilic and highly energetically frustrated. A single buried tryptophan residue, W80, undergoes solvent exposure to different extents during unfolding; this suggests a structurally heterogeneous population of intermediate ensembles. Furthermore, the structure properties of the IN state show a resemblance to the molten globule (MG) state with most of the secondary structures intact. The unfolding of the NTD is initiated by the loss of β-strands, and the unfolded (U) states exhibit a population of non-native α-helices. These non-native unfolded intermediate ensembles may mediate protein oligomerization, leading to the formation of pathological, irreversible aggregates, characteristics of disease pathogenesis.
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Affiliation(s)
- Amresh Prakash
- School of Computational & Integrative Sciences, Jawaharlal Nehru University New Delhi-110067 India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia Jamia Nagar New Delhi-110025 India
| | - Naveen Kumar Meena
- School of Computational & Integrative Sciences, Jawaharlal Nehru University New Delhi-110067 India
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University New Delhi-110067 India
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