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Salamh S, Sayyed-Ahmad A. Investigating the effects of cysteine-118 oxidation on G12D KRas structure and dynamics: insights from MD simulations. J Biomol Struct Dyn 2024; 42:6968-6981. [PMID: 37480262 DOI: 10.1080/07391102.2023.2238080] [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: 06/24/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Mutations of Ras proteins are believed to be among the most prominent causes of cancer. There is increasing evidence that the activity of Ras may be controlled by the redox state of cysteine residues located within the NKCD motif. This redox signaling is critical to both physiological and pathological processes and occurs when C118 is oxidized in a reversible manner. In this study, we used atomistic molecular dynamics simulations and Markov state models to investigate the structural and conformational effects of C118 oxidation on the oncogenic mutant KRas(G12D). While both mutants share common features and exhibit some distinct conformational states and fluctuations, we have found that the oxidized variant KRas(G12D/C118SOH) is more dynamic than the unoxidized counterpart, particularly in the switch II region. Additionally, C118 oxidation is found to alter the structure of the nucleotide-binding site and the switch regions as well as perturb the conformational equilibrium between Ras active and inactive states. These conformational preferences may alter the affinity to different effectors, resulting in selective downstream activation. Our results are anticipated to help future drug development efforts aimed at KRAS-related anticancer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shimaa Salamh
- Department of Physics, Birzeit University, Birzeit, Palestine
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2
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Hashmi HF, Xuan X, Chen K, Zhang P, Shahab M, Zheng G, Younous YA, Salamatullah AM, Bourhia M. Molecular modeling and simulation approaches to characterize potential molecular targets for burdock inulin to instigate protection against autoimmune diseases. Sci Rep 2024; 14:11291. [PMID: 38760355 PMCID: PMC11101470 DOI: 10.1038/s41598-024-61387-7] [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: 03/06/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
In the current study, we utilized molecular modeling and simulation approaches to define putative potential molecular targets for Burdock Inulin, including inflammatory proteins such as iNOS, COX-2, TNF-alpha, IL-6, and IL-1β. Molecular docking results revealed potential interactions and good binding affinity for these targets; however, IL-1β, COX-2, and iNOS were identified as the best targets for Inulin. Molecular simulation-based stability assessment demonstrated that inulin could primarily target iNOS and may also supplementarily target COX-2 and IL-1β during DSS-induced colitis to reduce the role of these inflammatory mechanisms. Furthermore, residual flexibility, hydrogen bonding, and structural packing were reported with uniform trajectories, showing no significant perturbation throughout the simulation. The protein motions within the simulation trajectories were clustered using principal component analysis (PCA). The IL-1β-Inulin complex, approximately 70% of the total motion was attributed to the first three eigenvectors, while the remaining motion was contributed by the remaining eigenvectors. In contrast, for the COX2-Inulin complex, 75% of the total motion was attributed to the eigenvectors. Furthermore, in the iNOS-Inulin complex, the first three eigenvectors contributed to 60% of the total motion. Furthermore, the iNOS-Inulin complex contributed 60% to the total motion through the first three eigenvectors. To explore thermodynamically favorable changes upon mutation, motion mode analysis was carried out. The Free Energy Landscape (FEL) results demonstrated that the IL-1β-Inulin achieved a single conformation with the lowest energy, while COX2-Inulin and iNOS-Inulin exhibited two lowest-energy conformations each. IL-1β-Inulin and COX2-Inulin displayed total binding free energies of - 27.76 kcal/mol and - 37.78 kcal/mol, respectively, while iNOS-Inulin demonstrated the best binding free energy results at - 45.89 kcal/mol. This indicates a stronger pharmacological potential of iNOS than the other two complexes. Thus, further experiments are needed to use inulin to target iNOS and reduce DSS-induced colitis and other autoimmune diseases.
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Affiliation(s)
- Huma Farooque Hashmi
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Xu Xuan
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Kaoshan Chen
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Pengying Zhang
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China.
| | - Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | | | - Ahmad Mohammad Salamatullah
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, 80060, Agadir, Morocco
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Shahab M, Khan A, Khan SA, Zheng G. Unraveling the mechanisms of Sofosbuvir resistance in HCV NS3/4A protease: Structural and molecular simulation-based insights. Int J Biol Macromol 2024; 267:131629. [PMID: 38631585 DOI: 10.1016/j.ijbiomac.2024.131629] [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: 08/30/2023] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
Current management of HCV infection is based on Direct-Acting Antiviral Drugs (DAAs). However, resistance-associated mutations, especially in the NS3 and NS5B regions are gradually decreasing the efficacy of DAAs. Among the most effective HCV NS3/4A protease drugs, Sofosbuvir also develops resistance due to mutations in the NS3 and NS5B regions. Four mutations at positions A156Y, L36P, Q41H, and Q80K are classified as high-level resistance mutations. The resistance mechanism of HCV NS3/4A protease toward Sofosbuvir caused by these mutations is still unclear, as there is less information available regarding the structural and functional effects of the mutations against Sofosbuvir. In this work, we combined molecular dynamics simulation, molecular mechanics/Generalized-Born surface area calculation, principal component analysis, and free energy landscape analysis to explore the resistance mechanism of HCV NS3/4A protease due to these mutations, as well as compare interaction changes in wild-type. Subsequently, we identified that the mutant form of HCV NS3/4A protease affects the activity of Sofosbuvir. In this study, the resistance mechanism of Sofosbuvir at the atomic level is proposed. The proposed drug-resistance mechanism will provide valuable guidance for the design of HCV drugs.
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Affiliation(s)
- Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Salman Ali Khan
- Tunneling Group, Biotechnology Centre, Doctoral School, Silesian University of Technology, Akademicka 2, 44-100, Gliwice, Poland
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China.
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Nezhad NG, Jamaludin SZB, Rahman RNZRA, Yahaya NM, Oslan SN, Shariff FM, Isa NM, Leow TC. Functional expression, purification, biochemical and biophysical characterizations, and molecular dynamics simulation of a histidine acid phosphatase from Saccharomyces cerevisiae. World J Microbiol Biotechnol 2024; 40:171. [PMID: 38630327 DOI: 10.1007/s11274-024-03970-8] [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: 01/09/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
A histidine acid phosphatase (HAP) (PhySc) with 99.50% protein sequence similarity with PHO5 from Saccharomyces cerevisiae was expressed functionally with the molecular mass of ∼110 kDa through co-expression along with the set of molecular chaperones dnaK, dnaJ, GroESL. The purified HAP illustrated the optimum activity of 28.75 ± 0.39 U/mg at pH 5.5 and 40 ˚C. The Km and Kcat values towards calcium phytate were 0.608 ± 0.09 mM and 650.89 ± 3.6 s- 1. The half-lives (T1/2) at 55 and 60 ˚C were 2.75 min and 55 s, respectively. The circular dichroism (CD) demonstrated that PhySc includes 30.5, 28.1, 21.3, and 20.1% of random coils, α-Helix, β-Turns, and β-Sheet, respectively. The Tm recorded by CD for PhySc was 56.5 ± 0.34˚C. The molecular docking illustrated that His59 and Asp322 act as catalytic residues in the PhySc. MD simulation showed that PhySc at 40 ˚C has higher structural stability over those of the temperatures 60 and 80 ˚C that support the thermodynamic in vitro investigations. Secondary structure content results obtained from MD simulation indicated that PhySc consists of 34.03, 33.09, 17.5, 12.31, and 3.05% of coil, helix, turn, sheet, and helix310, respectively, which is almost consistent with the experimental results.
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Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Siti Zahra Binti Jamaludin
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Normi Mohd Yahaya
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Nurulfiza Mat Isa
- Laboratory of Vaccine and Biomolecules (VacBio), Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
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Hassan SA, Aziz DM, Abdullah MN, Bhat AR, Dongre RS, Hadda TB, Almalki FA, Kawsar SMA, Rahiman AK, Ahmed S, Abdellattif MH, Berredjem M, Sheikh SA, Jamalis J. In vitro and in vivo evaluation of the antimicrobial, antioxidant, cytotoxic, hemolytic activities and in silico POM/DFT/DNA-binding and pharmacokinetic analyses of new sulfonamide bearing thiazolidin-4-ones. J Biomol Struct Dyn 2024; 42:3747-3763. [PMID: 37402503 DOI: 10.1080/07391102.2023.2226713] [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: 11/24/2022] [Accepted: 05/11/2023] [Indexed: 07/06/2023]
Abstract
In this work, Schiff bases and Thiazolidin-4-ones, were synthesized using Sonication and Microwave techniques, respectively. The Schiff base derivatives (3a-b) were synthesized via the reaction of Sulfathiazole (1) with benzaldehyde derivatives (2a-b), followed by the synthesis of 4-thiazoledinone (4a-b) derivatives by cyclizing the synthesized Schiff bases through thioglycholic acid. All the synthesized compounds were characterized by spectroscopic techniques such as FT IR, NMR and HRMS. The synthesized compounds were tested for their in vitro antimicrobial and antioxidant and in vivo cytotoxicity and hemolysis ability. The synthesized compounds displayed better antimicrobial and antioxidant activity and low toxicity in comparison to reference drugs and negative controls, respectively. The hemolysis test revealed the compounds exhibit lower hemolytic effects and hemolytic values are comparatively low and the safety of compounds is in comparison with standard drugs. Theoretical calculations were carried out by using the molecular operating environment (MOE) and Gaussian computing software and observations were in good agreement with the in vitro and in vivo biological activities. Petra/Osiris/Molinspiration (POM) results indicate the presence of three combined antibacterial, antiviral and antitumor pharmacophore sites. The molecular docking revealed the significant binding affinities and non-bonding interactions between the compounds and Erwinia Chrysanthemi (PDB ID: 1SHK). The molecular dynamics simulation under in silico physiological conditions revealed a stable conformation and binding pattern in a stimulating environment. HighlightsNew series of Thaiazolidin-4-one derivatives have been synthesized.Sonication and microwave techniques are used.Antimicrobial, Antioxidant, cytotoxicity, and hemolysis activities were observed for all synthesized compounds.Molecular Docking and DFT/POM analyses have been predicted.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sangar Ali Hassan
- Department of Chemistry, College of Science, University of Raparin, Sulaymaniyah, Iraq
| | - Dara Muhammed Aziz
- Department of Chemistry, College of Science, University of Raparin, Sulaymaniyah, Iraq
| | | | - Ajmal R Bhat
- Department of Chemistry, R.T.M. Nagpur University, Nagpur, India
| | | | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong, Bangladesh
| | - Aziz Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | - Sumeer Ahmed
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | - Magda H Abdellattif
- Department of Chemistry, College of Science, Taif University, Al-Haweiah, Taif, Saudi Arabia
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria
| | - S A Sheikh
- Department of physics, National Institute of Technology, Srinagar, Kashmir, India
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
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Kibria MK, Ali MA, Yaseen M, Khan IA, Bhat MA, Islam MA, Mahumud RA, Mollah MNH. Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications. Pharmaceuticals (Basel) 2024; 17:432. [PMID: 38675393 PMCID: PMC11053588 DOI: 10.3390/ph17040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
SARS-CoV-2 infections, commonly referred to as COVID-19, remain a critical risk to both human life and global economies. Particularly, COVID-19 patients with weak immunity may suffer from different complications due to the bacterial co-infections/super-infections/secondary infections. Therefore, different variants of alternative antibacterial therapeutic agents are required to inhibit those infection-causing drug-resistant pathogenic bacteria. This study attempted to explore these bacterial pathogens and their inhibitors by using integrated statistical and bioinformatics approaches. By analyzing bacterial 16S rRNA sequence profiles, at first, we detected five bacterial genera and taxa (Bacteroides, Parabacteroides, Prevotella Clostridium, Atopobium, and Peptostreptococcus) based on differentially abundant bacteria between SARS-CoV-2 infection and control samples that are significantly enriched in 23 metabolic pathways. A total of 183 bacterial genes were found in the enriched pathways. Then, the top-ranked 10 bacterial genes (accB, ftsB, glyQ, hldD, lpxC, lptD, mlaA, ppsA, ppc, and tamB) were selected as the pathogenic bacterial key genes (bKGs) by their protein-protein interaction (PPI) network analysis. Then, we detected bKG-guided top-ranked eight drug molecules (Bemcentinib, Ledipasvir, Velpatasvir, Tirilazad, Acetyldigitoxin, Entreatinib, Digitoxin, and Elbasvir) by molecular docking. Finally, the binding stability of the top-ranked three drug molecules (Bemcentinib, Ledipasvir, and Velpatasvir) against three receptors (hldD, mlaA, and lptD) was investigated by computing their binding free energies with molecular dynamic (MD) simulation-based MM-PBSA techniques, respectively, and was found to be stable. Therefore, the findings of this study could be useful resources for developing a proper treatment plan against bacterial co-/super-/secondary-infection in SARS-CoV-2 infections.
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Affiliation(s)
- Md. Kaderi Kibria
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Statistics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Chemistry, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Imran Ahmad Khan
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia;
| | - Md. Ariful Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
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Kesavan LR, Kamalan BC, Sivanandan S. Targeting human inosine 5' monophosphate dehydrogenase type 2 for anti-dengue lead identification - a computational approach. J Biomol Struct Dyn 2024:1-15. [PMID: 38517251 DOI: 10.1080/07391102.2024.2331094] [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: 11/02/2023] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
Dengue is a rapidly evolving arboviral disease that mainly affects tropical and subtropical regions of the world. The lack of therapeutic drugs and effective vaccines suggests that further resources need to be investigated. The effectiveness of the existing dengue vaccine is improbable as its efficacy depends on prior exposure to the dengue virus(DENV). Although the mechanism underlying the action of bioactive compounds to limit viral replication is less studied and still needs to be further explored, medicinal plants are excellent alternatives to combat DENV infection. In the current study, an in silico screening of phytochemicals from Annona reticulata Linn. against human Impdh2 was performed using Autodock Vina. Daucosterol (-9.0 kcal/mol) and Kaurenoic acid (-8.5 kcal/mol) were chosen as the top hits based on molecular interaction analysis. The hits were further exposed to pharmacokinetics and toxicity properties to determine their drug-like parameters. Molecular dynamics simulation studies of the Impdh2-top hits were carried out to investigate their kinetic behaviour and structural stabilities. The binding free energies of the Impdh2-hit complexes were determined using MM-PBSA analysis. According to the overall conclusions of the study, Daucosterol showed good binding affinity and high structural stability to the binding site residues of the target, therefore it is recommended as a lead compound against dengue.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lekshmi Radha Kesavan
- Biotechnology and Bioinformatics Division, Saraswathy Thangavelu Extension Centre, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, A Research Centre of University of Kerala, Thiruvananthapuram, India
| | - Biju Charuvil Kamalan
- Biotechnology and Bioinformatics Division, Saraswathy Thangavelu Extension Centre, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, A Research Centre of University of Kerala, Thiruvananthapuram, India
| | - Sreekumar Sivanandan
- Biotechnology and Bioinformatics Division, Saraswathy Thangavelu Extension Centre, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, A Research Centre of University of Kerala, Thiruvananthapuram, India
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Patar AK, Borah SM, Barman J, Bora A, Baruah TJ. Dronabinol as an answer to flavivirus infections: an in-silico investigation. J Biomol Struct Dyn 2023; 41:11219-11230. [PMID: 36576139 DOI: 10.1080/07391102.2022.2160817] [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: 09/23/2021] [Accepted: 12/15/2022] [Indexed: 12/29/2022]
Abstract
Flavivirus infections are common in several parts of the world. Two major types of flaviviruses are dengue and zika viruses. Both these two viral infections have caused many fatalities around the world. There is an absence of a vaccine and an effective medication against these viruses. In this study, we analyzed the ability of dronabinol to act as a potential cure against these viral infections. We performed the docking of dronabinol with several viral proteins followed by molecular dynamics simulation, MM/PBSA and PCA analysis. We checked the ability of the polyphenol dronabinol to interfere with the binding of viral helicases to their cellular targets. We performed 2 D-QSAR studies, drug likeliness, ADMET and target prediction studies. From our study, we observed that dronabinol had the best docking ability against the helicase proteins of dengue and zika. Molecular dynamics simulation and MM/PBSA investigation confirmed the stability of the binding while PCA investigation showed a lowering of molecular motions in response to dronabinol docking to the helicases. Dronabinol interfered in the binding of the helicases to RNA. 2 D QSAR studies revealed a low IC50 value for dronabinol. Dronabinol showed favorable drug-likeness, ADMET properties and target prediction results. Thus we propose dronabinol be further investigated in-vitro as a cure against dengue and zika virus infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abani Kumar Patar
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
| | - Sapna Mayuri Borah
- Department of Plant Pathology, Assam Agricultural University, Jorhat, Assam, India
| | - Jitul Barman
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
| | - Anupam Bora
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
| | - Taranga Jyoti Baruah
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
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Toth D, Dudas B, Miteva MA, Balog E. Role of Conformational Dynamics of Sulfotransferases SULT1A1 and SULT1A3 in Substrate Specificity. Int J Mol Sci 2023; 24:16900. [PMID: 38069221 PMCID: PMC10706399 DOI: 10.3390/ijms242316900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Sulfotransferases (SULTs) are phase II metabolizing enzymes catalyzing the sulfoconjugation from the co-factor 3'-Phosphoadenosine 5'-Phosphosulfate (PAPS) to a wide variety of endogenous compounds, drugs and natural products. Although SULT1A1 and SULT1A3 share 93% identity, SULT1A1, the most abundant SULT isoform in humans, exhibits a broad substrate range with specificity for small phenolic compounds, while SULT1A3 displays a high affinity toward monoamine neurotransmitters like dopamine. To elucidate the factors determining the substrate specificity of the SULT1 isoenzymes, we studied the dynamic behavior and structural specificities of SULT1A1 and SULT1A3 by using molecular dynamics (MD) simulations and ensemble docking of common and specific substrates of the two isoforms. Our results demonstrated that while SULT1A1 exhibits a relatively rigid structure by showing lower conformational flexibility except for the lip (loop L1), the loop L2 and the cap (L3) of SULT1A3 are extremely flexible. We identified protein residues strongly involved in the recognition of different substrates for the two isoforms. Our analyses indicated that being more specific and highly flexible, the structure of SULT1A3 has particularities in the binding site, which are crucial for its substrate selectivity.
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Affiliation(s)
- Daniel Toth
- CiTCoM UMR 8038 CNRS, INSERM U1268 MCTR, Université Paris Cité, 75006 Paris, France; (D.T.); (B.D.)
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Balint Dudas
- CiTCoM UMR 8038 CNRS, INSERM U1268 MCTR, Université Paris Cité, 75006 Paris, France; (D.T.); (B.D.)
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Maria A. Miteva
- CiTCoM UMR 8038 CNRS, INSERM U1268 MCTR, Université Paris Cité, 75006 Paris, France; (D.T.); (B.D.)
| | - Erika Balog
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
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Singh J, Khanduja KL, Avti PK. Unravelling benzazepines and aminopyrimidine as multi-target therapeutic repurposing drugs for EGFR V774M mutation in neuroglioma patients. BIOIMPACTS : BI 2023; 14:28876. [PMID: 38938756 PMCID: PMC11199933 DOI: 10.34172/bi.2023.28876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/03/2023] [Accepted: 08/23/2023] [Indexed: 06/29/2024]
Abstract
Introduction Neuroglioma, a classification encompassing tumors arising from glial cells, exhibits variable aggressiveness and depends on tumor grade and stage. Unraveling the EGFR gene alterations, including amplifications (unaltered), deletions, and missense mutations (altered), is emerging in glioma. However, the precise understanding of emerging EGFR mutations and their role in neuroglioma remains limited. This study aims to identify specific EGFR mutations prevalent in neuroglioma patients and investigate their potential as therapeutic targets using FDA-approved drugs for repurposing approach. Methods Neuroglioma patient's data were analyzed to identify the various mutations and survival rates. High throughput virtual screening (HTVS) of FDA-approved (1615) drugs using molecular docking and simulation was executed to determine the potential hits. Results Neuroglioma patient samples (n=4251) analysis reveals 19% EGFR alterations with most missense mutations at V774M in exon 19. The Kaplan-Meier plots show that the overall survival rate was higher in the unaltered group than in the altered group. Docking studies resulted the best hits based on each target's higher docking score, minimum free energy (MMGBSA), minimum kd, ki, and IC50 values. MD simulations and their trajectories show that compounds ZINC000011679756 target unaltered EGFR and ZINC000003978005 targets altered EGFR, whereas ZINC000012503187 (Conivaptan, Benzazepine) and ZINC000068153186 (Dabrafenib, aminopyrimidine) target both the EGFRs. The shortlisted compounds demonstrate favorable residual interactions with their respective targets, forming highly stable complexes. Moreover, these shortlisted compounds have drug- like properties as assessed by ADMET profiling. Conclusion Therefore, compounds (ZINC000012503187 and ZINC000068153186) can effectively target both the unaltered/altered EGFRs as multi-target therapeutic repurposing drugs towards neuroglioma.
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Affiliation(s)
- Jitender Singh
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India – 160012
| | - Krishan L Khanduja
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India – 160012
| | - Pramod K Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India – 160012
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11
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Aloufi B, Alshabrmi FM, Sreeharsha N, Rehman A. Exploring therapeutic targets and drug candidates for obesity: a combined network pharmacology, bioinformatics approach. J Biomol Struct Dyn 2023:1-22. [PMID: 37811763 DOI: 10.1080/07391102.2023.2265491] [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: 08/24/2023] [Accepted: 09/24/2023] [Indexed: 10/10/2023]
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-Senna alexandrina, Capsicum annuum, Zingiber officinale, Curcuma longa, Trigonella foenum-graecum, and Foeniculum vulgare-we conducted preliminary screenings for potential bioactive compounds. We systematically compiled compound data from public databases and reviewed literature, revealing active compounds like apigenin, kaempferol, moupinamide, cyclocurcumin, chrysoeriol, isorhamnetin, rheinanthrone, cyclocurcumin, and riboflavin.Constructing a compound-target genes-obesity network unveiled their significant impact on metabolic regulation and fat accumulation, interacting notably with key proteins AKT1 and PTGS2. Molecular docking and 100 ns Molecular Dynamic (MD) simulations demonstrated robust binding affinity and stability at the docking site. Employing adipocytes as a cellular model, we gauged their viability and response to obesity-related stressors post-treatment with these native plant compounds.In conclusion, Saudi Arabia's indigenous plants hold promise as natural solutions for obesity treatment. This research opens new avenues in the battle against this pervasive health crisis by incorporating the potential of native botanicals.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bandar Aloufi
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Pharmaceutics, Vidya Siri College of Pharmacy, Bangalore, India
| | - Abdur Rehman
- Department of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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12
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Ceauranu S, Ciorsac A, Ostafe V, Isvoran A. Evaluation of the Toxicity Potential of the Metabolites of Di-Isononyl Phthalate and of Their Interactions with Members of Family 1 of Sulfotransferases-A Computational Study. Molecules 2023; 28:6748. [PMID: 37764524 PMCID: PMC10536557 DOI: 10.3390/molecules28186748] [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: 08/30/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
Di-isononyl phthalates are chemicals that are widely used as plasticizers. Humans are extensively exposed to these compounds by dietary intake, through inhalation and skin absorption. Sulfotransferases (SULTs) are enzymes responsible for the detoxification and elimination of numerous endogenous and exogenous molecules from the body. Consequently, SULTs are involved in regulating the biological activity of various hormones and neurotransmitters. The present study considers a computational approach to predict the toxicological potential of the metabolites of di-isononyl phthalate. Furthermore, molecular docking was considered to evaluate the inhibitory potential of these metabolites against the members of family 1 of SULTs. The metabolites of di-isononyl phthalate reveal a potency to cause liver damage and to inhibit receptors activated by peroxisome proliferators. These metabolites are also usually able to inhibit the activity of the members of family 1 of SULTs, except for SULT1A3 and SULT1B1. The outcomes of this study are important for an enhanced understanding of the risk of human exposure to di-isononyl phthalates.
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Affiliation(s)
- Silvana Ceauranu
- Department of Biology Chemistry, West University of Timisoara, 16 Pestalozzi, 300115 Timisoara, Romania; (S.C.); (V.O.)
- Advanced Environmental Research Laboratories, West University of Timisoara, 4 Oituz, 300086 Timisoara, Romania
| | - Alecu Ciorsac
- Department of Physical Education and Sport, University Politehnica Timisoara, 2. Piata Victoriei, 300006 Timisoara, Romania;
| | - Vasile Ostafe
- Department of Biology Chemistry, West University of Timisoara, 16 Pestalozzi, 300115 Timisoara, Romania; (S.C.); (V.O.)
- Advanced Environmental Research Laboratories, West University of Timisoara, 4 Oituz, 300086 Timisoara, Romania
| | - Adriana Isvoran
- Department of Biology Chemistry, West University of Timisoara, 16 Pestalozzi, 300115 Timisoara, Romania; (S.C.); (V.O.)
- Advanced Environmental Research Laboratories, West University of Timisoara, 4 Oituz, 300086 Timisoara, Romania
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13
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Au SX, Mohd Padzil A, Muhd Noor ND, Matsumura H, Raja Abdul Rahman RNZ, Normi YM. Probing the substrate binding modes and catalytic mechanisms of BLEG-1, a promiscuous B3 metallo-β-lactamase with glyoxalase II properties. PLoS One 2023; 18:e0291012. [PMID: 37672512 PMCID: PMC10482274 DOI: 10.1371/journal.pone.0291012] [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: 04/04/2023] [Accepted: 08/19/2023] [Indexed: 09/08/2023] Open
Abstract
BLEG-1 from Bacillus lehensis G1 is an evolutionary divergent B3 metallo-β-lactamase (MBL) that exhibited both β-lactamase and glyoxalase II (GLXII) activities. Sequence, phylogeny, biochemical and structural relatedness of BLEG-1 to B3 MBL and GLXII suggested BLEG-1 might be an intermediate in the evolutionary path of B3 MBL from GLXII. The unique active site cavity of BLEG-1 that recognizes both β-lactam antibiotics and S-D-lactoylglutathione (SLG) had been postulated as the key factor for its dual activity. In this study, dynamic ensembles of BLEG-1 and its substrate complexes divulged conformational plasticity and binding modes of structurally distinct substrates to the enzyme, providing better insights into its structure-to-function relationship and enzymatic promiscuity. Our results highlight the flexible nature of the active site pocket of BLEG-1, which is governed by concerted loop motions involving loop7+α3+loop8 and loop12 around the catalytic core, thereby moulding the binding pocket and facilitate interactions of BLEG-1 with both ampicillin and SLG. The distribution of (i) predominantly hydrophobic amino acids in the N-terminal domain, and (ii) flexible amino acids with polar and/or charged side chains in both N- and C-termini provide additional advantages to BLEG-1 in confining the aromatic group of ampicillin, and polar groups of SLG, respectively. The importance of these residues for substrates binding was further confirmed by the reduction in MBL and GLXII activities upon alanine substitutions of Ile-10, Phe-57, Arg-94, Leu-95, and Arg-159. Based on molecular dynamics simulation, mutational, and biochemical data presented herein, the catalytic mechanisms of BLEG-1 toward the hydrolysis of β-lactams and SLG were proposed.
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Affiliation(s)
- Shaw Xian Au
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Azyyati Mohd Padzil
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Hiroyoshi Matsumura
- College of Life Sciences, Ritsumeikan University, Noji-Higashi, Kusatsu, Japan
| | - Raja Noor Zaliha Raja Abdul Rahman
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yahaya M. Normi
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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14
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Kwain S, Dominy BN, Whitehead KJ, Miller BA, Whitehead DC. Exploring the interactive mechanism of acarbose with the amylase SusG in the starch utilization system of the human gut symbiont Bacteroides thetaiotaomicron through molecular modeling. Chem Biol Drug Des 2023; 102:486-499. [PMID: 37062591 DOI: 10.1111/cbdd.14251] [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: 01/24/2023] [Revised: 03/15/2023] [Accepted: 04/04/2023] [Indexed: 04/18/2023]
Abstract
The α-amylase, SusG, is a principal component of the Bacteroides thetaiotaomicron (Bt) starch utilization system (Sus) used to metabolize complex starch molecules in the human gastrointestinal (GI) tract. We previously reported the non-microbicidal growth inhibition of Bt by the acarbose-mediated arrest of the Sus as a potential therapeutic strategy. Herein, we report a computational approach using density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulation to explore the interactive mechanism between acarbose and SusG at the atomic level in an effort to understand how acarbose shuts down the Bt Sus. The docking analysis reveals that acarbose binds orthosterically to SusG with a binding affinity of -8.3 kcal/mol. The MD simulation provides evidence of conformational variability of acarbose at the active site of SusG and also suggests that acarbose interacts with the main catalytic residues via a general acid-base double-displacement catalytic mechanism. These results suggest that small molecule competitive inhibition against the SusG protein could impact the entire Bt Sus and eliminate or reduce the system's ability to metabolize starch. This computational strategy could serve as a potential avenue for structure-based drug design to discover other small molecules capable of inhibiting the Sus of Bt with high potency, thus providing a holistic approach for selective modulation of the GI microbiota.
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Affiliation(s)
- Samuel Kwain
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Brian N Dominy
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Kristi J Whitehead
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Brock A Miller
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
| | - Daniel C Whitehead
- Department of Chemistry, Clemson University, Clemson, South Carolina, USA
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15
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Mondol SM, Hasib M, Limon MBH, Alam ASMRU. Insights into Omicron's Low Fusogenicity through In Silico Molecular Studies on Spike-Furin Interactions. Bioinform Biol Insights 2023; 17:11779322231189371. [PMID: 37529484 PMCID: PMC10387760 DOI: 10.1177/11779322231189371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these mutations reside together, they exert less-efficient membrane fusion than wild type and most other variants of concern such as the Delta variant. Here, we in silico targeted these mutations to find out which of the amino acids and interactions change plays the key role in fusion. To comprehend the epistatic effect of N679 K and P681 H mutations on the spike protein, we in silico constructed three types of spike protein sequences by changing the respective amino acids on 679 and 681 positions (P681 H, N679 K, K679 N-H681 P variants). We then analyzed the binding affinity of furin and spike (Furin-Wild, Furin-Omicron, Furin-P681 H, Furin-N679 K, and Furin-K679 N/H681 P) complexes. Omicron and P681 H variants showed a similar higher binding energy trend compared to the wild type and N679 K. The variation in hydrogen, hydrophobic, and salt bridge bonds between spike protein and furin provided an explanation for the observed low fusogenicity of Omicron. The fate of the epistasis in furin binding and possible cleavage depends on the efficient interaction between FCS in spike and furin catalytic triad, and in addition, the loss of the hydrogen bond between Arg 681 (spike) and Asn 295 (furin) along with inhibitor-like ineffective higher affinity plays an important role in the enzymatic activity.
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Affiliation(s)
| | - Md Hasib
- Department of Biochemistry and Biotechnology, University of Barishal, Barishal, Bangladesh
| | | | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
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16
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Hidayatullah A, Putra WE, Sustiprijatno S, Rifa'i M, Widiastuti D, Heikal MF, Permatasari GW. Concatenation of molecular docking and dynamics simulation of human papillomavirus type 16 E7 oncoprotein targeted ligands: In quest of cervical cancer's treatment. AN ACAD BRAS CIENC 2023; 95:e20220633. [PMID: 37466536 DOI: 10.1590/0001-3765202320220633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/23/2022] [Indexed: 07/20/2023] Open
Abstract
The Human papillomaviruses type 16 E7 oncoprotein is a 98-amino-acid, 11-kilodalton acidic oncoprotein with three conserved portions. Due to its interaction with the pRb-E2F complex, CKII, CKI (mostly p21), and even HDAC1, it possesses strong transformative and carcinogenic qualities that inhibit normal differentiation and cell cycle regulation. Here, we target the E7 oncoprotein using two prior research active compounds: asarinin and thiazolo[3,2-a]benzimidazole-3(2H)-one,2-(2-fluorobenzylideno)-7,8-dimethyl (thiazolo), and valproic acid as a control. We are performing molecular docking followed by molecular dynamic analysis. By acting as competitive inhibitors in the binding site, it was hypothesized that both drugs would inhibit E7-mediated pRb degradation and E7-mediated p21 degradation, resulting in decreased cell cycle progression, immortalization, and proliferation. In addition, we expect that the direct inhibitory action of valproic acid in E7 will target the CKII-mediated phosphorylation pathway necessary for destabilizing p130 and pRb. According to the results of the dynamic simulation, stable interactions exist between every compound. Despite the instability of E7 protein, stability results indicate that both natural chemicals are preferable, with thiazolo outperforming valproic acid.
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Affiliation(s)
- Arief Hidayatullah
- United Nations Development Programme Indonesia, Health Governance Initiative, Eijkman-RSCM Building, Jakarta, 10430, Indonesia
| | - Wira E Putra
- Universitas Negeri Malang, Biotechnology Study Program, Department of Applied Sciences, Faculty of Mathematics and Natural Sciences, East Java 65145, Indonesia
| | - Sustiprijatno Sustiprijatno
- National Research and Innovation Agency, Research Center for Plant Conservation, Botanic Gardens and Forestry, Cibinong-Bogor, West Java 45262, Indonesia
| | - Muhaimin Rifa'i
- Brawijaya University, Department of Biology, Faculty of Mathematics and Natural Sciences, East Java, 65145, Indonesia
| | - Diana Widiastuti
- Universitas Pakuan, Department of Chemistry, Faculty of Mathematics and Natural Science, West Java, 45262, Indonesia
| | - Muhammad F Heikal
- Khon Kaen University, Tropical Medicine International Program, Faculty of Medicine, Khon Kaen 40000, Thailand
| | - Galuh W Permatasari
- Indonesian Research Institute for Biotechnology and Bioindustry, Bogor, West Java, 45262, Indonesia
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17
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Dey D, Hossain R, Biswas P, Paul P, Islam MA, Ema TI, Gain BK, Hasan MM, Bibi S, Islam MT, Rahman MA, Kim B. Amentoflavone derivatives significantly act towards the main protease (3CL PRO/M PRO) of SARS-CoV-2: in silico admet profiling, molecular docking, molecular dynamics simulation, network pharmacology. Mol Divers 2023; 27:857-871. [PMID: 35639226 PMCID: PMC9153225 DOI: 10.1007/s11030-022-10459-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/07/2022] [Indexed: 11/16/2022]
Abstract
SARS-CoV-2 is the foremost culprit of the novel coronavirus disease 2019 (nCoV-19 and/or simply COVID-19) and poses a threat to the continued life of humans on the planet and create pandemic issue globally. The 3-chymotrypsin-like protease (MPRO or 3CLPRO) is the crucial protease enzyme of SARS-CoV-2, which directly involves the processing and release of translated non-structural proteins (nsps), and therefore involves the development of virus pathogenesis along with outbreak the forecasting of COVID-19 symptoms. Moreover, SARS-CoV-2 infections can be inhibited by plant-derived chemicals like amentoflavone derivatives, which could be used to develop an anti-COVID-19 drug. Our research study is designed to conduct an in silico analysis on derivatives of amentoflavone (isoginkgetin, putraflavone, 4''''''-methylamentoflavone, bilobetin, ginkgetin, sotetsuflavone, sequoiaflavone, heveaflavone, kayaflavone, and sciadopitysin) for targeting the non-structural protein of SARS-CoV-2, and subsequently further validate to confirm their antiviral ability. To conduct all the in silico experiments with the derivatives of amentoflavone against the MPRO protein, both computerized tools and online servers were applied; notably the software used is UCSF Chimera (version 1.14), PyRx, PyMoL, BIOVIA Discovery Studio tool (version 4.5), YASARA (dynamics simulator), and Cytoscape. Besides, as part of the online tools, the SwissDME and pKCSM were employed. The research study was proposed to implement molecular docking investigations utilizing compounds that were found to be effective against the viral primary protease (MPRO). MPRO protein interacted strongly with 10 amentoflavone derivatives. Every time, amentoflavone compounds outperformed the FDA-approved antiviral medicine that is currently underused in COVID-19 in terms of binding affinity (- 8.9, - 9.4, - 9.7, - 9.1, - 9.3, - 9.0, - 9.7, - 9.3, - 8.8, and - 9.0 kcal/mol, respectively). The best-selected derivatives of amentoflavone also possessed potential results in 100 ns molecular dynamic simulation (MDS) validation. It is conceivable that based on our in silico research these selected amentoflavone derivatives more precisely 4''''''-methylamentoflavone, ginkgetin, and sequoiaflavone have potential for serving as promising lead drugs against SARS-CoV-2 infection. In consequence, it is recommended that additional in vitro as well as in vivo research studies have to be conducted to support the conclusions of this current research study.
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Affiliation(s)
- Dipta Dey
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka, 8100, Bangladesh
| | - Rajib Hossain
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka, 8100, Bangladesh
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore, 7408, Bangladesh.
| | - Priyanka Paul
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka, 8100, Bangladesh
| | - Md Aminul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore, 7408, Bangladesh
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | - Bibhuti Kumar Gain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore, 7408, Bangladesh
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Shabana Bibi
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Muhammad Torequl Islam
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka, 8100, Bangladesh
| | - Md Ataur Rahman
- Global Biotechnology & Biomedical Research Network (GBBRN), Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea.
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea.
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Biswas P, Bibi S, Yousafi Q, Mehmood A, Saleem S, Ihsan A, Dey D, Hasan Zilani MN, Hasan MN, Saleem R, Awaji AA, Fahmy UA, Abdel-Daim MM. Study of MDM2 as Prognostic Biomarker in Brain-LGG Cancer and Bioactive Phytochemicals Inhibit the p53-MDM2 Pathway: A Computational Drug Development Approach. Molecules 2023; 28:molecules28072977. [PMID: 37049742 PMCID: PMC10095937 DOI: 10.3390/molecules28072977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/02/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
An evaluation of the expression and predictive significance of the MDM2 gene in brain lower-grade glioma (LGG) cancer was carried out using onco-informatics pipelines. Several transcriptome servers were used to measure the differential expression of the targeted MDM2 gene and search mutations and copy number variations. GENT2, Gene Expression Profiling Interactive Analysis, Onco-Lnc, and PrognoScan were used to figure out the survival rate of LGG cancer patients. The protein–protein interaction networks between MDM2 gene and its co-expressed genes were constructed by Gene-MANIA tool. Identified bioactive phytochemicals were evaluated through molecular docking using Schrödinger Suite Software, with the MDM2 (PDB ID: 1RV1) target. Protein–ligand interactions were observed with key residues of the macromolecular target. A molecular dynamics simulation of the novel bioactive compounds with the targeted protein was performed. Phytochemicals targeting MDM2 protein, such as Taxifolin and (-)-Epicatechin, have been shown with more highly stable results as compared to the control drug, and hence, concluded that phytochemicals with bioactive potential might be alternative therapeutic options for the management of LGG patients. Our once informatics-based designed pipeline has indicated that the MDM2 gene may have been a predictive biomarker for LGG cancer and selected phytochemicals possessed outstanding interaction results within the macromolecular target’s active site after utilizing in silico approaches. In vitro and in vivo experiments are recommended to confirm these outcomes.
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Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database. Comput Biol Chem 2023; 102:107800. [PMID: 36516617 DOI: 10.1016/j.compbiolchem.2022.107800] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/07/2022]
Abstract
Antimicrobial peptides (AMPs) are short peptides with a broad spectrum of antimicrobial activity. They play a key role in the host innate immunity of many organisms. The growing threat of microorganisms resistant to antimicrobial agents and the lack of new commercially available antibiotics have made in silico discovery of AMPs increasingly important. Machine learning (ML) has improved the speed and efficiency of AMP discovery while reducing the cost of experimental approaches. Despite various ML platforms developed, there is still a lack of integrative use of ML platforms for AMP discovery from publicly available protein databases. Therefore, our study aims to screen potential AMPs with antibiofilm properties from databases using ML platforms, followed by protein-peptide molecular docking analysis and molecular dynamics (MD) simulations. A total of 5850 peptides classified as non-AMP were screened from UniProtKB and analyzed using various online ML platforms (e.g., CAMPr3, DBAASP, dPABBs, Hemopred, and ToxinPred). Eight potential AMP peptides against Klebsiella pneumoniae with antibiofilm, non-toxic and non-hemolytic properties were then docked to MrkH, a transcriptional regulator of type 3 fimbriae involved in biofilm formation. Five of eight peptides bound more strongly than the native MrkH ligand when analyzed using HADDOCK and HPEPDOCK. Following the docking studies, our MD simulated that a Neuropeptide B (Peptide 3) bind strongly to the MrkH active sites. The discovery of putative AMPs that exceed the binding energies of the native ligand underscores the utility of the combined ML and molecular simulation strategies for discovering novel AMPs with antibiofilm properties.
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20
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Muthu SA, Sharma R, Qureshi A, Parvez S, Ahmad B. Mechanistic insights into monomer level prevention of amyloid aggregation of lysozyme by glycyrrhizic acid. Int J Biol Macromol 2023; 227:884-895. [PMID: 36549619 DOI: 10.1016/j.ijbiomac.2022.12.166] [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: 10/19/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
As the primary bioactive compound of glycyrrhiza rhizome, the triterpene glycoside conjugate Glycyrrhizic acid (GA) has demonstrated neuroprotective effects in vivo. This study evaluates the effectiveness of GA as an inhibitor of GuHCl-induced amyloid aggregation of hen egg white lysozyme (HEWL). Fibril formation as measured by Thioflavin-T fluorescence, 900 light scattering, and 8-Anilinonaphthalene-1-sulfonic acid (ANS) fluorescence illustrated ∼90 % prevention of fibrils at [GA]/[HEWL] ≥2:1. Images of Transmission electron microscopy evidence for the absence of any fibril or amorphous aggregation products. The spectral characteristics of soluble HEWL were in close resemblance to unfolded monomer. Computational and fluorescence investigations performed to analyse GA-HEWL interactions demonstrated slightly higher affinity of GA to unfolded HEWL and aggregation-prone regions. The likely mechanism of monomer level aggregation prevention by GA as dermined by computational, stability, and ANS experiments illustrated that GA modulated the compactness, solvent-accessible surface, and solvent-exposed hydrophobic surfaces of aggregation-prone state of HEWL. Our findings corroborate GA as an effective inhibitor of HEWL amyloid formation. To our knowledge, GA interaction-induced inhibition of aggregation-prone states has not been previously discussed. GA's modulation of aggregation-prone states of disease-related proteins will successfully develop GA as an amyloid inhibitor for clinical trials of amyloidosis and neurodegenerative illnesses.
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Affiliation(s)
- Shivani A Muthu
- Protein Assembly Laboratory, Department of Medical Entomology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard, New Delhi 110062, India
| | - Rahul Sharma
- Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard, New Delhi 110062, India
| | - Afnaan Qureshi
- Protein Assembly Laboratory, Department of Medical Entomology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Suhel Parvez
- Department of Medical Entomology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Basir Ahmad
- Protein Assembly Laboratory, Department of Medical Entomology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India.
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21
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Ali MC, Khatun MS, Jahan SI, Das R, Munni YA, Rahman MM, Dash R. In silico design of epitope-based peptide vaccine against non-typhoidal Salmonella through immunoinformatic approaches. J Biomol Struct Dyn 2022; 40:10696-10714. [PMID: 36529187 DOI: 10.1080/07391102.2021.1947381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Non-typhoidal Salmonella (NTS) is one of the leading bacterial causes of many invasive human infections with a high antibiotic resistance profile. With this concern, the current study aimed to design an effective epitope-based peptide vaccine against NTS species as a successive and substitutive protective measure of invasive NTS disease. To design rationally, the current study considered a comprehensive in silico workflow combination of both immunoinformatics and molecular modeling approaches, including molecular docking and molecular dynamics (MD) simulation. We identified the two most promising T cell epitopes KVLYGIFAI and YGIFAITAL, and three B cell epitopes AAPVQVGEAAGS, TGGGDGSNT, and TGGGDGSNTGTTTT, in the outer membrane of NTS. Using these epitopes, a multiepitope vaccine was subsequently constructed along with appropriate adjuvant and linkers, which showed a good binding affinity and stability with toll-like receptor 2 (TLR2) in both molecular docking and MD simulation. Furthermore, in silico immune simulation described a strong immune response with a high number of antibodies, interferon-γ, and activated B and T cells. This study collectively suggests that predicted vaccine constructs could be considered potential vaccine candidates against common NTS species.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Chayan Ali
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Mst Shanzeda Khatun
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Sultana Israt Jahan
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Raju Das
- Department of Physiology, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Md Mafizur Rahman
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
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22
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Isvoran A, Peng Y, Ceauranu S, Schmidt L, Nicot AB, Miteva MA. Pharmacogenetics of human sulfotransferases and impact of amino acid exchange on Phase II drug metabolism. Drug Discov Today 2022; 27:103349. [PMID: 36096358 DOI: 10.1016/j.drudis.2022.103349] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/27/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022]
Abstract
Sulfotransferases (SULTs) are Phase II drug-metabolizing enzymes (DMEs) catalyzing the sulfation of a variety of endogenous compounds, natural products, and drugs. Various drugs, such as nonsteroidal anti-inflammatory drugs (NSAIDS) can inhibit SULTs, affecting drug-drug interactions. Several polymorphisms have been identified for SULTs that might be crucial for interindividual variability in drug response and toxicity or for increased disease risk. Here, we review current knowledge on non-synonymous single nucleotide polymorphisms (nsSNPs) of human SULTs, focusing on the coded SULT allozymes and molecular mechanisms explaining their variable activity, which is essential for personalized medicine. We discuss the structural and dynamic bases of key amino acid (AA) variants implicated in the impacts on drug metabolism in the case of SULT1A1, as revealed by molecular modeling approaches.
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Affiliation(s)
- Adriana Isvoran
- Department of Biology-Chemistry and Advanced Environmental Research Laboratories, West University of Timisoara, 16 Pestalozzi, 300115 Timisoara, Romania
| | - Yunhui Peng
- INSERM U1268 Medicinal Chemistry and Translational Research, CiTCoM UMR 8038 CNRS - Université Paris Cité, 75006 Paris, France
| | - Silvana Ceauranu
- Department of Biology-Chemistry and Advanced Environmental Research Laboratories, West University of Timisoara, 16 Pestalozzi, 300115 Timisoara, Romania
| | - Leon Schmidt
- Department of Biology-Chemistry and Advanced Environmental Research Laboratories, West University of Timisoara, 16 Pestalozzi, 300115 Timisoara, Romania
| | - Arnaud B Nicot
- INSERM, Nantes Université, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France.
| | - Maria A Miteva
- INSERM U1268 Medicinal Chemistry and Translational Research, CiTCoM UMR 8038 CNRS - Université Paris Cité, 75006 Paris, France.
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23
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Anowar Hosen M, Sultana Munia N, Al-Ghorbani M, Baashen M, Almalki FA, Ben Hadda T, Ali F, Mahmud S, Abu Saleh M, Laaroussi H, Kawsar SMA. Synthesis, antimicrobial, molecular docking and molecular dynamics studies of lauroyl thymidine analogs against SARS-CoV-2: POM study and identification of the pharmacophore sites. Bioorg Chem 2022; 125:105850. [PMID: 35533581 PMCID: PMC9065685 DOI: 10.1016/j.bioorg.2022.105850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/21/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022]
Abstract
Nucleoside precursors and nucleoside analogs occupy an important place in the treatment of viral respiratory pathologies, especially during the current COVID-19 pandemic. From this perspective, the present study has been designed to explore and evaluate the synthesis and spectral characterisation of 5́-O-(lauroyl) thymidine analogs 2–6 with different aliphatic and aromatic groups through comprehensive in vitro antimicrobial screening, cytotoxicity assessment, physicochemical aspects, molecular docking and molecular dynamics analysis, along with pharmacokinetic prediction. A unimolar one-step lauroylation of thymidine under controlled conditions furnished the 5́-O-(lauroyl) thymidine and indicated the selectivity at C-5́ position and the development of thymidine based potential antimicrobial analogs, which were further converted into four newer 3́-O-(acyl)-5́-O-(lauroyl) thymidine analogs in reasonably good yields. The chemical structures of the newly synthesised analogs were ascertained by analysing their physicochemical, elemental, and spectroscopic data. In vitro antimicrobial tests against five bacteria and two fungi, along with the prediction of activity spectra for substances (PASS), indicated promising antibacterial functionality for these thymidine analogs compared to antifungal activity. In support of this observation, molecular docking experiments have been performed against the main protease of SARS-CoV-2, and significant binding affinities and non-bonding interactions were observed against the main protease (6LU7, 6Y84 and 7BQY), considering hydroxychloroquine (HCQ) as standard. Moreover, the 100 ns molecular dynamics simulation process was performed to monitor the behaviour of the complex structure formed by the main protease under in silico physiological conditions to examine its stability over time, and this revealed a stable conformation and binding pattern in a stimulating environment of thymidine analogs. Cytotoxicity determination confirmed that compounds were found less toxic. Pharmacokinetic predictions were investigated to evaluate their absorption, distribution, metabolism and toxic properties, and the combination of pharmacokinetic and drug-likeness predictions has shown promising results in silico. The POM analysis shows the presence of an antiviral (O1δ-, O2δ-) pharmacophore site. Overall, the current study should be of great help in the development of thymidine-based, novel, multiple drug-resistant antimicrobial and COVID-19 drugs.
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Affiliation(s)
- Mohammed Anowar Hosen
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Nasrin Sultana Munia
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Mohammed Al-Ghorbani
- Department of Chemistry, Faculty of Science and Arts, Ulla, Taibah University, Medina, Saudi Arabia
| | - Mohammed Baashen
- Department of Chemistry, Science and Humanities College, Shaqra University, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, 21955 Makkah, Saudi Arabia
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, 21955 Makkah, Saudi Arabia; Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco
| | - Ferdausi Ali
- Department of Microbiology, Faculty of Biological Science, University of Chittagong, V, Bangladesh
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh.
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24
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Dey D, Biswas P, Paul P, Mahmud S, Ema TI, Khan AA, Ahmed SZ, Hasan MM, Saikat ASM, Fatema B, Bibi S, Rahman MA, Kim B. Natural flavonoids effectively block the CD81 receptor of hepatocytes and inhibit HCV infection: a computational drug development approach. Mol Divers 2022:10.1007/s11030-022-10491-9. [PMID: 35821161 DOI: 10.1007/s11030-022-10491-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/24/2022] [Indexed: 12/15/2022]
Abstract
Hepatitis C virus (HCV) infection is a major public health concern, and almost two million people are infected per year globally. This is occurred by the diverse spectrum of viral genotypes, which are directly associated with chronic liver disease (fibrosis, and cirrhosis). Indeed, the viral genome encodes three principal proteins as sequentially core, E1, and E2. Both E1 and E2 proteins play a crucial role in the attachment of the host system, but E2 plays a more fundamental role in attachment. The researchers have found the "E2-CD81 complex" at the entry site, and therefore, CD81 is the key receptor for HCV entrance in both humans, and chimpanzees. So, the researchers are trying to block the host CD81 receptor and halt the virus entry within the cellular system via plant-derived compounds. Perhaps that is why the current research protocol is designed to perform an in silico analysis of the flavonoid compounds for targeting the tetraspanin CD81 receptor of hepatocytes. To find out the best flavonoid compounds from our library, web-based tools (Swiss ADME, pKCSM), as well as computerized tools like the PyRx, PyMOL, BIOVIA Discovery Studio Visualizer, Ligplot+ V2.2, and YASARA were employed. For molecular docking studies, the flavonoid compounds docked with the targeted CD81 protein, and herein, the best-outperformed compounds are Taxifolin, Myricetin, Puerarin, Quercetin, and (-)-Epicatechin, and outstanding binding affinities are sequentially - 7.5, - 7.9, - 8.2, - 8.4, and - 8.5 kcal/mol, respectively. These compounds have possessed more interactions with the targeted protein. To validate the post docking data, we analyzed both 100 ns molecular dynamic simulation, and MM-PBSA via the YASARA simulator, and finally finds the more significant outcomes. It is concluded that in the future, these compounds may become one of the most important alternative antiviral agents in the fight against HCV infection. It is suggested that further in vivo, and in vitro research studies should be done to support the conclusions of this in silico research workflow.
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Affiliation(s)
- Dipta Dey
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore, 7408, Bangladesh.
| | - Priyanka Paul
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6204, Bangladesh
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | - Arysha Alif Khan
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | - Shahlaa Zernaz Ahmed
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Abu Saim Mohammad Saikat
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Babry Fatema
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Shabana Bibi
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Md Ataur Rahman
- Global Biotechnology & Biomedical Research Network (GBBRN), Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea.
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, 02447, Korea.
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25
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Mahtarin R, Islam S, Islam MJ, Ullah MO, Ali MA, Halim MA. Structure and dynamics of membrane protein in SARS-CoV-2. J Biomol Struct Dyn 2022; 40:4725-4738. [PMID: 33353499 PMCID: PMC7784837 DOI: 10.1080/07391102.2020.1861983] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/05/2020] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 membrane (M) protein performs a variety of critical functions in virus infection cycle. However, the expression and purification of membrane protein structure is difficult despite tremendous progress. In this study, the 3 D structure is modeled followed by intensive validation and molecular dynamics simulation. The lack of suitable homologous templates (>30% sequence identities) leads us to construct the membrane protein models using template-free modeling (de novo or ab initio) approach with Robetta and trRosetta servers. Comparing with other model structures, it is evident that trRosetta (TM-score: 0.64; TM region RMSD: 2 Å) can provide the best model than Robetta (TM-score: 0.61; TM region RMSD: 3.3 Å) and I-TASSER (TM-score: 0.45; TM region RMSD: 6.5 Å). 100 ns molecular dynamics simulations are performed on the model structures by incorporating membrane environment. Moreover, secondary structure elements and principal component analysis (PCA) have also been performed on MD simulation data. Finally, trRosetta model is utilized for interpretation and visualization of interacting residues during protein-protein interactions. The common interacting residues including Phe103, Arg107, Met109, Trp110, Arg131, and Glu135 in the C-terminal domain of M protein are identified in membrane-spike and membrane-nucleocapsid protein complexes. The active site residues are also predicted for potential drug and peptide binding. Overall, this study might be helpful to design drugs and peptides against the modeled membrane protein of SARS-CoV-2 to accelerate further investigation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rumana Mahtarin
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shafiqul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md. Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Physical Sciences, University of Arkansas - Fort Smith, Fort Smith, AR, USA
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26
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Dash R, Munni YA, Mitra S, Choi HJ, Jahan SI, Chowdhury A, Jang TJ, Moon IS. Dynamic insights into the effects of nonsynonymous polymorphisms (nsSNPs) on loss of TREM2 function. Sci Rep 2022; 12:9378. [PMID: 35672339 PMCID: PMC9174165 DOI: 10.1038/s41598-022-13120-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
Single nucleotide variations in Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) are associated with many neurodegenerative diseases, including Nasu-Hakola disease (NHD), frontotemporal dementia (FTD), and late-onset Alzheimer's disease because they disrupt ligand binding to the extracellular domain of TREM2. However, the effects of nonsynonymous single nucleotide polymorphisms (nsSNPs) in TREM2 on disease progression remain unknown. In this study, we identified several high-risk nsSNPs in the TREM2 gene using various deleterious SNP predicting algorithms and analyzed their destabilizing effects on the ligand recognizing region of the TREM2 immunoglobulin (Ig) domain by molecular dynamics (MD) simulation. Cumulative prediction by all tools employed suggested the three most deleterious nsSNPs involved in loss of TREM2 function are rs549402254 (W50S), rs749358844 (R52C), and rs1409131974 (D104G). MD simulation showed that these three variants cause substantial structural alterations and conformational remodeling of the apical loops of the TREM2 Ig domain, which is responsible for ligand recognition. Detailed analysis revealed that these variants substantially increased distances between apical loops and induced conformation remodeling by changing inter-loop nonbonded contacts. Moreover, all nsSNPs changed the electrostatic potentials near the putative ligand-interacting region (PLIR), which suggested they might reduce specificity or loss of binding affinity for TREM2 ligands. Overall, this study identifies three potential high-risk nsSNPs in the TREM2 gene. We propose further studies on the molecular mechanisms responsible for loss of TREM2 function and the associations between TREM2 nsSNPs and neurodegenerative diseases.
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Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Sarmistha Mitra
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Ho Jin Choi
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Sultana Israt Jahan
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Apusi Chowdhury
- Department of Pharmaceutical Science, North-South University, Dhaka, 1229, Bangladesh
| | - Tae Jung Jang
- Department of Pathology, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
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27
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In vitro antioxidant and cytotoxicity activities and in silico anticancer property of methanolic leaf extract of Leucas indica. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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28
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Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study. J Mol Graph Model 2022; 114:108192. [PMID: 35468453 PMCID: PMC9007924 DOI: 10.1016/j.jmgm.2022.108192] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
COVID-19 pandemic has emerged as a global threat with its highly contagious and mutating nature. Several existing antiviral drugs has been worked on, without proper results and meanwhile the virus is mutating rapidly to create more infectious variant. In order to find some alternatives, phytocompounds can be opted as good one. In this study, three hundred phytocompounds were screened virtually against two viral proteins namely main protease and spike protein. Molecular docking and dynamic simulation study was used to find binding affinity, structural stability and flexibility of the complex. Pharmacokinetic properties were studied through ADMET analysis. To understand energy variation of the complex structure free energy landscape analysis was performed. Among three hundred phytocompounds virtual screening, three phytocompounds were selected for detailed molecular interaction analysis. Oleanderolide, Proceragenin A and Balsaminone A, showed strong binding affinity against both the target proteins and reflected conformational stability throughout the MD run. Oleanderolide, proceragenin A and balsaminone A has docking score −9.4 kcal/mol, −8.6 kcal/mol, and −8.1 kcal/mol respectively against main protease and same −8.3 kcal/mol docking score against spike protein. These three phytocompounds has high gastrointestinal absorption capacity. They were unexplored till now for their antiviral activity. Their promising in silico results suggests that they can be promoted in the long run for development of new antiviral drugs.
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29
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Structural Consequence of Non-Synonymous Single-Nucleotide Variants in the N-Terminal Domain of LIS1. Int J Mol Sci 2022; 23:ijms23063109. [PMID: 35328531 PMCID: PMC8955593 DOI: 10.3390/ijms23063109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Disruptive neuronal migration during early brain development causes severe brain malformation. Characterized by mislocalization of cortical neurons, this condition is a result of the loss of function of migration regulating genes. One known neuronal migration disorder is lissencephaly (LIS), which is caused by deletions or mutations of the LIS1 (PAFAH1B1) gene that has been implicated in regulating the microtubule motor protein cytoplasmic dynein. Although this class of diseases has recently received considerable attention, the roles of non-synonymous polymorphisms (nsSNPs) in LIS1 on lissencephaly progression remain elusive. Therefore, the present study employed combined bioinformatics and molecular modeling approach to identify potential damaging nsSNPs in the LIS1 gene and provide atomic insight into their roles in LIS1 loss of function. Using this approach, we identified three high-risk nsSNPs, including rs121434486 (F31S), rs587784254 (W55R), and rs757993270 (W55L) in the LIS1 gene, which are located on the N-terminal domain of LIS1. Molecular dynamics simulation highlighted that all variants decreased helical conformation, increased the intermonomeric distance, and thus disrupted intermonomeric contacts in the LIS1 dimer. Furthermore, the presence of variants also caused a loss of positive electrostatic potential and reduced dimer binding potential. Since self-dimerization is an essential aspect of LIS1 to recruit interacting partners, thus these variants are associated with the loss of LIS1 functions. As a corollary, these findings may further provide critical insights on the roles of LIS1 variants in brain malformation.
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30
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Ahsan T, Shoily SS, Fatema K, Sajib AA. Impacts of 119 missense variants at functionally important sites of drug-metabolizing human cytosolic sulfotransferase SULT1A1: An in silico study. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2021.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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31
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Mahato RK, Mahanty AK, Kotakonda M, Prasad S, Bhattacharyya S, Biswas B. A hydrated 2,3-diaminophenazinium chloride as a promising building block against SARS-CoV-2. Sci Rep 2021; 11:23122. [PMID: 34848758 PMCID: PMC8633378 DOI: 10.1038/s41598-021-02280-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022] Open
Abstract
Phenazine scaffolds are the versatile secondary metabolites of bacterial origin. It functions in the biological control of plant pathogens and contributes to the producing strains ecological fitness and pathogenicity. In the light of the excellent therapeutic properties of phenazine, we have synthesized a hydrated 2,3-diaminophenazinium chloride (DAPH+Cl-·3H2O) through direct catalytic oxidation of o-phenylenediamine with an iron(III) complex, [Fe(1,10-phenanthroline)2Cl2]NO3 in ethanol under aerobic condition. The crystal structure, molecular complexity and supramolecular aspects of DAPH+Cl- were confirmed and elucidated with different spectroscopic methods and single crystal X-ray structural analysis. Crystal engineering study on DAPH+Cl- exhibits a fascinating formation of (H2O)2…Cl-…(H2O) cluster and energy framework analysis of defines the role of chloride ions in the stabilization of DAPH+Cl-. The bactericidal efficiency of the compound has been testified against few clinical bacteria like Streptococcus pneumoniae, Escherichia coli, K. pneumoniae using the disc diffusion method and the results of high inhibition zone suggest its excellent antibacterial properties. The phenazinium chloride exhibits a significant percentage of cell viability and a considerable inhibition property against SARS-CoV-2 at non-cytotoxic concentration compared to remdesivir. Molecular docking studies estimate a good binding propensity of DAPH+Cl- with non-structural proteins (nsp2 and nsp7-nsp-8) and the main protease (Mpro) of SARS-CoV-2. The molecular dynamics simulation studies attribute the conformationally stable structures of the DAPH+Cl- bound Mpro and nsp2, nsp7-nsp8 complexes as evident from the considerable binding energy values, - 19.2 ± 0.3, - 25.7 ± 0.1, and - 24.5 ± 0.7 kcal/mol, respectively.
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Affiliation(s)
- Rajani Kanta Mahato
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Ayan Kumar Mahanty
- Department of Biotechnology, University of North Bengal, Darjeeling, 734013, India
| | | | - Sunnapu Prasad
- Department of Pharmaceutical Chemistry, Sri Ramakrishna Institute of Paramedical Science, Coimbatore, 641044, India
| | | | - Bhaskar Biswas
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India.
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Rahman MM, Junaid M, Hosen SMZ, Mostafa M, Liu L, Benkendorff K. Mollusc-Derived Brominated Indoles for the Selective Inhibition of Cyclooxygenase: A Computational Expedition. Molecules 2021; 26:molecules26216538. [PMID: 34770946 PMCID: PMC8587571 DOI: 10.3390/molecules26216538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Inflammation plays an important role in different chronic diseases. Brominated indoles derived from the Australian marine mollusk Dicathais orbita (D. orbita) are of interest for their anti-inflammatory properties. This study evaluates the binding mechanism and potentiality of several brominated indoles (tyrindoxyl sulfate, tyrindoleninone, 6-bromoisatin, and 6,6′-dibromoindirubin) against inflammatory mediators cyclooxygenases-1/2 (COX-1/2) using molecular docking, followed by molecular dynamics simulation, along with physicochemical, drug-likeness, pharmacokinetic (pk), and toxicokinetic (tk) properties. Molecular docking identified that these indole compounds are anchored, with the main amino acid residues, positioned in the binding pocket of the COX-1/2, required for selective inhibition. Moreover, the molecular dynamics simulation based on root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), and root mean square fluctuation (RMSF) analyses showed that these natural brominated molecules transit rapidly to a progressive constant configuration during binding with COX-1/2 and seem to accomplish a consistent dynamic behavior by maintaining conformational stability and compactness. The results were comparable to the Food and Drug Administration (FDA)-approved selective COX inhibitor, aspirin. Furthermore, the free energy of binding for the compounds assessed by molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) confirmed the binding capacity of indoles towards COX-1/2, with suitable binding energy values except for the polar precursor tyrindoxyl sulfate (with COX-1). The physicochemical and drug-likeness analysis showed zero violations of Lipinski’s rule, and the compounds are predicted to have excellent pharmacokinetic profiles. These indoles are projected to be non-mutagenic and free from hepatotoxicity, with no inhibition of human ether-a-go–go gene (hERG) I inhibitors, and the oral acute toxicity LD50 in rats is predicted to be similar or lower than aspirin. Overall, this work has identified a plausible mechanism for selective COX inhibition by natural marine indoles as potential therapeutic candidates for the mitigation of inflammation.
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Affiliation(s)
- Md. Mominur Rahman
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Md. Junaid
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - S. M. Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
- Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for AppliedMedical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mohammad Mostafa
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - Lei Liu
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW 2450, Australia
- Correspondence:
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Walia HK, Singh N, Sharma S. Genetic polymorphism of Arg213His variant in the SULT1A1 gene is associated with reduced susceptibility to lung cancer in North Indian population. Xenobiotica 2021; 51:1071-1080. [PMID: 34328372 DOI: 10.1080/00498254.2021.1963008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sulfotransferases (SULTs) are phase II detoxification enzymes that is involved in the biotransformation of many compounds including tobacco carcinogens. A polymorphism in the SULT1A1 (Arg213His) gene results in reduced enzyme activity.We investigated the association between the SULT1A1 (Arg213/His) genotype and lung cancer (LC). This case-control study comprised of 550 cases and controls, matched on age, gender and smoking status.The variant genotype exhibited no association with LC risk, even after stratification on basis of histological subtypes. Male LC patients carrying the variant His213 allele (p = 0.02) did not exhibit an increased risk towards LC. Smokers harbouring the Arg/His genotype did demonstrate a reduced risk towards LC (AOR = 0.70; p = 0.019). Furthermore, the LC subjects who were heavy smokers and harbouring the Arg/His genotype (AOR = 0.28; p = 0.019) did not show a genetic predisposition towards LC susceptibility. The subjects who smoked pack years of above 40 and carrying the His/His (AOR = 0.28; p = 0.036) genotype were found to have a reduced risk for LC. Furthermore, 473 subjects were analysed in regards to overall survival, wherein the His/His genotype exhibited better OS than Arg/Arg genotype (11.30 vs. 8.07 months).This study provides evidence of no genetic predisposition towards LC risk associated with SULT1A1 Arg213His polymorphism in relation to tobacco smoking.
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Affiliation(s)
- Harleen Kaur Walia
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, India
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Dash R, Mitra S, Munni YA, Choi HJ, Ali MC, Barua L, Jang TJ, Moon IS. Computational Insights into the Deleterious Impacts of Missense Variants on N-Acetyl-d-glucosamine Kinase Structure and Function. Int J Mol Sci 2021; 22:8048. [PMID: 34360815 PMCID: PMC8347710 DOI: 10.3390/ijms22158048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/05/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022] Open
Abstract
An enzyme of the mammalian amino-sugar metabolism pathway, N-acetylglucosamine kinase (NAGK), that synthesizes N-acetylglucosamine (GlcNAc)-6-phosphate, is reported to promote dynein functions during mitosis, axonal and dendritic growth, cell migration, and selective autophagy, which all are unrelated to its enzyme activity. As non-enzymatic structural functions can be altered by genetic variation, we made an effort in this study aimed at deciphering the pathological effect of nonsynonymous single-nucleotide polymorphisms (nsSNPs) in NAGK gene. An integrated computational approach, including molecular dynamics (MD) simulation and protein-protein docking simulation, was used to identify the damaging nsSNPs and their detailed structural and functional consequences. The analysis revealed the four most damaging variants (G11R, G32R, G120E, and A156D), which are highly conserved and functional, positioned in both small (G11R and G32R) and large (G120E and A156D) domains of NAGK. G11R is located in the ATP binding region, while variants present in the large domain (G120E and A156D) were found to induce substantial alterations in the structural organizations of both domains, including the ATP and substrate binding sites. Furthermore, all variants were found to reduce binding energy between NAGK and dynein subunit DYNLRB1, as revealed by protein-protein docking and MM-GBSA binding energy calculation supporting their deleteriousness on non-canonical function. We hope these findings will direct future studies to gain more insight into the role of these variants in the loss of NAGK function and their role in neurodevelopmental disorders.
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Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Sarmistha Mitra
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Ho Jin Choi
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Md. Chayan Ali
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh;
| | - Largess Barua
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
| | - Tae Jung Jang
- Department of Pathology, Dongguk University College of Medicine, Gyeongju 38066, Korea;
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
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Pirzada RH, Haseeb M, Batool M, Kim M, Choi S. Remdesivir and Ledipasvir among the FDA-Approved Antiviral Drugs Have Potential to Inhibit SARS-CoV-2 Replication. Cells 2021; 10:1052. [PMID: 33946869 PMCID: PMC8146643 DOI: 10.3390/cells10051052] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022] Open
Abstract
The rapid spread of the virus, the surge in the number of deaths, and the unavailability of specific SARS-CoV-2 drugs thus far necessitate the identification of drugs with anti-COVID-19 activity. SARS-CoV-2 enters the host cell and assembles a multisubunit RNA-dependent RNA polymerase (RdRp) complex of viral nonstructural proteins that plays a substantial role in the transcription and replication of the viral genome. Therefore, RdRp is among the most suitable targets in RNA viruses. Our aim was to investigate the FDA approved antiviral drugs having potential to inhibit the viral replication. The methodology adopted was virtual screening and docking of FDA-approved antiviral drugs into the RdRp protein. Top hits were selected and subjected to molecular dynamics simulations to understand the dynamics of RdRp in complex with these drugs. The antiviral activity of the drugs against SARS-CoV-2 was assessed in Vero E6 cells. Notably, both remdesivir (half-maximal effective concentration (EC50) 6.6 μM, 50% cytotoxicity concentration (CC50) > 100 µM, selectivity index (SI) = 15) and ledipasvir (EC50 34.6 μM, CC50 > 100 µM, SI > 2.9) exerted antiviral action. This study highlights the use of direct-acting antiviral drugs, alone or in combination, for better treatments of COVID-19.
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Affiliation(s)
- Rameez Hassan Pirzada
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (R.H.P.); (M.H.); (M.B.); (M.K.)
| | - Muhammad Haseeb
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (R.H.P.); (M.H.); (M.B.); (M.K.)
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (R.H.P.); (M.H.); (M.B.); (M.K.)
- S&K Therapeutics, Woncheon Hall 135, Ajou University, Suwon 16499, Korea
| | - MoonSuk Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (R.H.P.); (M.H.); (M.B.); (M.K.)
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (R.H.P.); (M.H.); (M.B.); (M.K.)
- S&K Therapeutics, Woncheon Hall 135, Ajou University, Suwon 16499, Korea
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36
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Respiratory Mycoses in COPD and Bronchiectasis. Mycopathologia 2021; 186:623-638. [PMID: 33709335 DOI: 10.1007/s11046-021-00539-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) and bronchiectasis represent chronic airway diseases associated with significant morbidity and mortality. Bacteria and viruses are commonly implicated in acute exacerbations; however the significance of fungi in these airways remains poorly defined. While COPD and bronchiectasis remain recognized risk factors for the occurrence of Aspergillus-associated disease including chronic and invasive aspergillosis, underlying mechanisms that lead to the progression from colonization to invasive disease remain uncertain. Nonetheless, advances in molecular technologies have improved our detection, identification and understanding of resident fungi characterizing these airways. Mycobiome sequencing has revealed the complex varied and myriad profile of airway fungi in COPD and bronchiectasis, including their association with disease presentation, progression, and mortality. In this review, we outline the emerging evidence for the clinical importance of fungi in COPD and bronchiectasis, available diagnostic modalities, mycobiome sequencing approaches and association with clinical outcomes.
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Islam MA, Choi HJ, Dash R, Sharif SR, Oktaviani DF, Seog DH, Moon IS. N-Acetyl- D-Glucosamine Kinase Interacts with NudC and Lis1 in Dynein Motor Complex and Promotes Cell Migration. Int J Mol Sci 2020; 22:ijms22010129. [PMID: 33374456 PMCID: PMC7795690 DOI: 10.3390/ijms22010129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/17/2020] [Accepted: 12/20/2020] [Indexed: 12/18/2022] Open
Abstract
Recently, we showed that N-acetylglucosamine kinase (NAGK), an enzyme of amino sugar metabolism, interacts with dynein light chain roadblock type 1 (DYNLRB1) and promotes the functions of dynein motor. Here, we report that NAGK interacts with nuclear distribution protein C (NudC) and lissencephaly 1 (Lis1) in the dynein complex. Yeast two-hybrid assays, pull-down assays, immunocytochemistry, and proximity ligation assays revealed NAGK-NudC-Lis1-dynein complexes around nuclei, at the leading poles of migrating HEK293T cells, and at the tips of migratory processes of cultured rat neuroblast cells. The exogenous expression of red fluorescent protein (RFP)-tagged NAGK accelerated HEK293T cell migration during in vitro wound-healing assays and of neurons during in vitro neurosphere migration and in utero electroporation assays, whereas NAGK knockdown by short hairpin RNA (shRNA) delayed migration. Finally, a small NAGK peptide derived from the NudC interacting domain in in silico molecular docking analysis retarded the migrations of HEK293T and SH-SY5Y cells. These data indicate a functional interaction between NAGK and dynein-NudC-Lis1 complex at the nuclear envelope is required for the regulation of cell migration.
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Affiliation(s)
- Md. Ariful Islam
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
| | - Ho Jin Choi
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
| | - Syeda Ridita Sharif
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
| | - Diyah Fatimah Oktaviani
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
| | - Dae-Hyun Seog
- Department of Biochemistry, Dementia and Neurodegenerative Disease Research Center, Inje University College of Medicine, Busan 47392, Korea;
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (M.A.I.); (H.J.C.); (R.D.); (S.R.S.); (D.F.O.)
- Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju 38066, Korea
- Correspondence: ; Tel.: +82-54-770-2414; Fax: +82-54-770-2447
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Munni YA, Ali MC, Selsi NJ, Sultana M, Hossen M, Bipasha TH, Rahman M, Uddin MN, Hosen SMZ, Dash R. Molecular simulation studies to reveal the binding mechanisms of shikonin derivatives inhibiting VEGFR-2 kinase. Comput Biol Chem 2020; 90:107414. [PMID: 33191109 DOI: 10.1016/j.compbiolchem.2020.107414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/17/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022]
Abstract
Traditional vascular endothelial growth factor receptor 2 (VEGFR-2) inhibitors can manage angiogenesis; however, severe toxicity and resistance limit their long-term applications in clinical therapy. Shikonin (SHK) and its derivatives could be promising to inhibit the VEGFR-2 mediated angiogenesis, as they are reported to bind in the catalytic kinase domain with low affinity. However, the detailed molecular insights and binding dynamics of these natural inhibitors are unknown, which is crucial for potential SHK based lead design. Therefore, the present study employed molecular modeling and simulations techniques to get insight into the binding behaviors of SHK and its two derivates, β-hydroxyisovalerylshikonin (β-HIVS) and acetylshikonin (ACS). Here the intermolecular interactions between protein and ligands were studied by induced fit docking approach, which were further evaluated by treating QM/MM (quantum mechanics/molecular mechanics) and molecular dynamics (MD) simulation. The result showed that the naphthazarin ring of the SHK derivates is vital for strong binding to the catalytic domain; however, the binding stability can be modulated by the side chain modification. Because of having electrostatic potential, this ring makes essential interactions with the DFG (Asp1046 and Phe1047) motif and also allows interacting with the allosteric binding site. Taken together, the studies will advance our knowledge and scope for the development of new selective VEGFR-2 inhibitors based on SHK and its analogs.
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Affiliation(s)
- Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
| | - Md Chayan Ali
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh.
| | - Nusrat Jahan Selsi
- Department of Pharmacy, University of Science & Technology, Chittagong, 4202, Bangladesh.
| | - Marium Sultana
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Md Hossen
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Tanjiba Harun Bipasha
- Department of Pharmacy, University of Science & Technology, Chittagong, 4202, Bangladesh.
| | - Mahbubur Rahman
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Md Nazim Uddin
- Department of Pharmacy, Southern University Bangladesh, Chittagong, 4000, Bangladesh.
| | - S M Zahid Hosen
- Pancreatic Research Group, South Western Sydney Clinical School, University of New South Wales, and Ingham Institute for Applied Medical Research, Liverpool, NSW, 2170, Australia.
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
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Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter. Int J Mol Sci 2020; 21:ijms21207606. [PMID: 33066695 PMCID: PMC7589834 DOI: 10.3390/ijms21207606] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
The ATP-binding cassette transporter A1 (ABCA1) is a membrane-bound exporter protein involved in regulating serum HDL level by exporting cholesterol and phospholipids to load up in lipid-poor ApoA-I and ApoE, which allows the formation of nascent HDL. Mutations in the ABCA1 gene, when presents in both alleles, disrupt the canonical function of ABCA1, which associates with many disorders related to lipid transport. Although many studies have reported the phenotypic effects of a large number of ABCA1 variants, the pathological effect of non-synonymous polymorphisms (nsSNPs) in ABCA1 remains elusive. Therefore, aiming at exploring the structural and functional consequences of nsSNPs in ABCA1, in this study, we employed an integrated computational approach consisting of nine well-known in silico tools to identify damaging SNPs and molecular dynamics (MD) simulation to get insights into the magnitudes of the damaging effects. In silico tools revealed four nsSNPs as being most deleterious, where the two SNPs (G1050V and S1067C) are identified as the highly conserved and functional disrupting mutations located in the NBD1 domain. MD simulation suggested that both SNPs, G1050V and S1067C, changed the overall structural flexibility and dynamics of NBD1, and induced substantial alteration in the structural organization of ATP binding site. Taken together, these findings direct future studies to get more insights into the role of these variants in the loss of the ABCA1 function.
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Subburaj S, Nagrale TA, Khan MM, James N, Karuppasamy R, Veerappapillai S. Discovery of anaplastic lymphoma kinase inhibitors from natural product library: A holistic in silico approach. Biotechnol Appl Biochem 2020; 68:1185-1191. [PMID: 32969554 DOI: 10.1002/bab.2040] [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: 07/12/2020] [Accepted: 09/17/2020] [Indexed: 11/06/2022]
Abstract
Over the years, phytochemical compounds have shown compelling evidences in exhibiting powerful antitumor properties. Moreover, due to the lack of safety and high cost of cancer therapies, opportunities are being sought out in these compounds as an alternative treatment modality. Therefore, in the present study, 1,574 compounds from NPACT library were examined to excavate potent and nontoxic anaplastic lymphoma kinase (ALK) inhibitors. Notably, two pharmacophore hypotheses (AAAHP and DDRRR) were generated using ligand-based and energy-based techniques, respectively, to eliminate false-positive prediction in database screening. Furthermore, molecular docking and Prime MM/GBSA analysis were performed on the screened compounds to examine inhibitory activity against ALK. The analysis revealed that the two hits, namely, NPACT00018 and NPACT01077, exhibited better docking scores, binding energies, and also ensured excellent drug-likeness properties than the reference compound, crizotinib. Finally, the results were subjected to molecular dynamics studies to gain insight into the stability of these compounds in the binding pocket of ALK protein. Indeed, the useful predictions generated by the present computational models are of immense importance and could further speed up the anticancer drug development in the near future.
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Affiliation(s)
- Saranyadevi Subburaj
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Tanvi Anand Nagrale
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Mohd Mustufa Khan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Nivya James
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
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Ripon MKH, Lee H, Dash R, Choi HJ, Oktaviani DF, Moon IS, Haque MN. N-acetyl-D-glucosamine kinase binds dynein light chain roadblock 1 and promotes protein aggregate clearance. Cell Death Dis 2020; 11:619. [PMID: 32796833 PMCID: PMC7427805 DOI: 10.1038/s41419-020-02862-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022]
Abstract
Emerging evidence indicates that neurodegenerative diseases (NDs) result from a failure to clear toxic protein aggregates rather than from their generation. We previously showed N-acetylglucosamine kinase (NAGK) promotes dynein functionality and suggested this might promote aggregate removal and effectively address proteinopathies. Here, we report NAGK interacts with dynein light chain roadblock type 1 (DYNLRB1) and efficiently suppresses mutant huntingtin (mHtt) (Q74) and α-synuclein (α-syn) A53T aggregation in mouse brain cells. A kinase-inactive NAGKD107A also efficiently cleared Q74 aggregates. Yeast two-hybrid selection and in silico protein-protein docking analysis showed the small domain of NAGK (NAGK-DS) binds to the C-terminal of DYNLRB1. Furthermore, a small peptide derived from NAGK-DS interfered with Q74 clearance. We propose binding of NAGK-DS to DYNLRB1 'pushes up' the tail of dynein light chain and confers momentum for inactive phi- to active open-dynein transition.
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Affiliation(s)
- Md Kamal Hossain Ripon
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - HyunSook Lee
- Section of Neuroscience, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Raju Dash
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Ho Jin Choi
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Diyah Fatimah Oktaviani
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Il Soo Moon
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
- Section of Neuroscience, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
| | - Md Nazmul Haque
- Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
- Department of Fisheries Biology and Genetics, Patuakhali Science and Technology University, Patuakhali, 8602, Bangladesh
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