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Hoda A, Bixheku X, Lika Çekani M. Computational analysis of non-synonymous single nucleotide polymorphism in the bovine PKLR geneComputational analysis of bovine PKLR gene. J Biomol Struct Dyn 2024; 42:4155-4168. [PMID: 37278385 DOI: 10.1080/07391102.2023.2219315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/23/2023] [Indexed: 06/07/2023]
Abstract
Pyruvate kinase (PKLR) is a potential candidate gene for milk production traits in cows. The main aim of this work is to investigate the potentially deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in the PKLR gene by using several computational tools. In silico tools including SIFT, Polyphen-2, SNAP2 and Panther indicated only 18 nsSNPs out of 170 were considered deleterious. The analysis of proteins' stability change due to amino acid substitution performed by the use of the I-mutant, MUpro, CUPSTAT, SDM and Dynamut confirmed that 9 nsSNPs decreased protein stability. ConSurf analysis predicted that all 18 nsSNPs were evolutionary moderately or highly conserved. Two different domains of PKLR protein were revealed by the InterPro tool with 12 nsSNPs positioned in the Pyruvate Kinase barrel domain and 6 nsSNP present in the Pyruvate Kinase C Terminal. The PKLR 3D model was predicted by MODELLER software and validated via Ramachandran plot and Prosa which indicated a good quality model. The analysis of energy minimizations for the native and mutated structures was performed by SWISS PDB viewer with GROMOS 96 program and showed that 3 structural and 4 functional residues had total energy higher than the native model. These findings indicate that these mutant structures (rs441424814, rs449326723, rs476805413, rs472263384, rs474320860, rs475521477, rs441633284) were less stable than the native model. Molecular Dynamics simulations were performed to confirm the impact of nsSNPs on the protein structure and function. The present study provides useful information about functional SNPs that have an impact on PKLR protein in cattle.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anila Hoda
- Agricultural University of Tirana, Tirana, Albania
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Aribisala JO, S'thebe NW, Sabiu S. In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae. Sci Rep 2024; 14:8788. [PMID: 38627456 PMCID: PMC11021432 DOI: 10.1038/s41598-024-59489-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
Infections caused by multidrug-resistant Streptococcus pneumoniae remain the leading cause of pneumonia-related deaths in children < 5 years globally, and mutations in penicillin-binding protein (PBP) 2 × have been identified as the major cause of resistance in the organism to beta-lactams. Thus, the development of new modulators with enhanced binding of PBP2x is highly encouraged. In this study, phenolics, due to their reported antibacterial activities, were screened against the active site of PBP2x using structure-based pharmacophore and molecular docking techniques, and the ability of the top-hit phenolics to inhibit the active and allosteric sites of PBP2x was refined through 120 ns molecular dynamic simulation. Except for gallocatechin gallate and lysidicichin, respectively, at the active and allosteric sites of PBP2x, the top-hit phenolics had higher negative binding free energy (ΔGbind) than amoxicillin [active site (- 19.23 kcal/mol), allosteric site (- 33.75 kcal/mol)]. Although silicristin had the best broad-spectrum effects at the active (- 38.41 kcal/mol) and allosteric (- 50.54 kcal/mol) sites of PBP2x, the high thermodynamic entropy (4.90 Å) of the resulting complex might suggest the need for its possible structural refinement for enhanced potency. Interestingly, silicristin had a predicted synthetic feasibility score of < 5 and quantum calculations using the DFT B3LYP/6-31G+ (dp) revealed that silicristin is less stable and more reactive than amoxicillin. These findings point to the possible benefits of the top-hit phenolics, and most especially silicristin, in the direct and synergistic treatment of infections caused by S. pneumoniae. Accordingly, silicristin is currently the subject of further confirmatory in vitro research.
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Affiliation(s)
- Jamiu Olaseni Aribisala
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Nosipho Wendy S'thebe
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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Wahhab BH, Oyewusi HA, Wahab RA, Mohammad Hood MH, Abdul Hamid AA, Al-Nimer MS, Edbeib MF, Kaya Y, Huyop F. Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey. J Biomol Struct Dyn 2024; 42:1429-1442. [PMID: 37038649 DOI: 10.1080/07391102.2023.2199870] [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: 08/13/2022] [Accepted: 04/01/2023] [Indexed: 04/12/2023]
Abstract
This study presents the initial structural model of L-haloacid dehalogenase (DehLBHS1) from Bacillus megaterium BHS1, an alkalotolerant bacterium known for its ability to degrade halogenated environmental pollutants. The model provides insights into the structural features of DehLBHS1 and expands our understanding of the enzymatic mechanisms involved in the degradation of these hazardous pollutants. Key amino acid residues (Arg40, Phe59, Asn118, Asn176, and Trp178) in DehLBHS1 were identified to play critical roles in catalysis and molecular recognition of haloalkanoic acid, essential for efficient binding and transformation of haloalkanoic acid molecules. DehLBHS1 was modeled using I-TASSER, yielding a best TM-score of 0.986 and an RMSD of 0.53 Å. Validation of the model using PROCHECK revealed that 89.2% of the residues were located in the most favored region, providing confidence in its structural accuracy. Molecular docking simulations showed that the non-simulated DehLBHS1 preferred 2,2DCP over other substrates, forming one hydrogen bond with Arg40 and exhibiting a minimum energy of -2.5 kJ/mol. The simulated DehLBHS1 exhibited a minimum energy of -4.3 kJ/mol and formed four hydrogen bonds with Arg40, Asn176, Asp9, and Tyr11, further confirming the preference for 2,2DCP. Molecular dynamics simulations supported this preference, based on various metrics, including RMSD, RMSF, gyration, hydrogen bonding, and molecular distance. MM-PBSA calculations showed that the DehLBHS1-2,2-DCP complex had a markedly lower binding energy (-21.363 ± 1.26 kcal/mol) than the DehLBHS1-3CP complex (-14.327 ± 1.738 kcal/mol). This finding has important implications for the substrate specificity and catalytic function of DehLBHS1, particularly in the bioremediation of 2,2-DCP in contaminated alkaline environments. These results provide a detailed view of the molecular interactions between the enzyme and its substrate and may aid in the development of more efficient biocatalytic strategies for the degradation of halogenated compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Batool Hazim Wahhab
- Department of Microbiology, Faculty of Medicine, Al-Mustansiriyah University, Iraq
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Mohammad Hakim Mohammad Hood
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Marwan Salih Al-Nimer
- Department of Pharmacology, College of Medicine, University of Diyala, Baqubah, Iraq
| | - Mohamed Faraj Edbeib
- Department of Medical Laboratories, Faculty of Medical Technology, Bani Walid University, Libya
| | - Yilmaz Kaya
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
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Roxas JDP, San Juan MAD, Villagracia ARC, Espiritu RA. An in silico analysis of the interaction of marine sponge-derived bioactive compounds with type 2 diabetes mellitus targets DPP-4 and PTP1B. J Biomol Struct Dyn 2024:1-14. [PMID: 38189304 DOI: 10.1080/07391102.2024.2301751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Type 2 diabetes is a medical condition involving elevated blood glucose levels resulting from impaired or improper insulin utilization. As the number of type 2 diabetes cases increases each year, there is an urgent need to develop novel drugs having new targets and/or complementing existing therapeutic protocols. In this regard, marine sponge-derived compounds hold great potential due to their potent biological activity and structural diversity. In this study, a small library of 50 marine sponge-derived compounds were examined for their activity towards type 2 diabetes targets, namely dipeptidyl peptidase-4 (DPP-4) and protein tyrosine phosphatase 1B (PTP1B). The compounds were first subjected to molecular docking on protein models based on their respective co-crystal structures to assess binding free energies (BFE) and conformations. Clustering analysis yielded BFE that ranged from 24.54 kcal/mol to -9.97 kcal/mol for DPP-4, and from -4.98 kcal/mol to -8.67 kcal/mol for PTP1B. Interaction analysis on the top ten compounds with the most negative BFE towards each protein target showed similar intermolecular interactions and key interacting residues as in the previously solved co-crystal structure. These compounds were subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling to characterize drug-likeness and combining the results from these analyses, (S)-6'-debromohamacanthin B was identified as a potential multi-target inhibitor of DPP-4 and PTP1B, having favorable protein interaction, no Lipinski violations, good gastrointestinal (GI) tract absorption, blood-brain barrier (BBB) penetration, and no predicted toxicity. Finally, the interaction of (S)-6'-debromohamacanthin B with the two proteins was validated using molecular dynamics simulations over 100 ns through RMSD, radius of gyration, PCA, and molecular mechanics Poisson-Boltzmann surface area (MMPBSA) confirming favorable interactions with the respective proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Al Rey C Villagracia
- Department of Physics, De La Salle University, Manila, Philippines
- Advanced Nanomaterials Investigation and Molecular Simulations (ANIMoS) Research Unit, CENSER, De La Salle University, Manila, Philippines
| | - Rafael A Espiritu
- Department of Chemistry, De La Salle University, Manila, Philippines
- Translational Research and Medicine (TRaM) Research Unit, CENSER, De La Salle University, Manila, Philippines
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Krishnamoorthy HR, Karuppasamy R. A multitier virtual screening of antagonists targeting PD-1/PD-L1 interface for the management of triple-negative breast cancer. Med Oncol 2023; 40:312. [PMID: 37777635 DOI: 10.1007/s12032-023-02183-7] [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: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 10/02/2023]
Abstract
Immunotherapies are promising therapeutic options for the management of triple-negative breast cancer because of its high mutation rate and genomic instability. Of note, the blockade of the immune checkpoint protein PD-1 and its ligand PD-L1 has been proven to be an efficient and potent strategy to combat triple-negative breast cancer. To date, various anti-PD-1/anti-PD-L1 antibodies have been approved. However, the intrinsic constraints of these therapeutic antibodies significantly limit their application, making small molecules a potentially significant option for PD-1/PD-L1 inhibition. In light of this, the current study aims to use a high-throughput virtual screening technique to identify potential repurposed candidates as PD-L1 inhibitors. Thus, the present study explored binding efficiency of 2509 FDA-approved compounds retrieved from the drug bank database against PD-L1 protein. The binding affinity of the compounds was determined using the glide XP docking programme. Furthermore, prime-MM/GBSA, DFT calculations, and RF score were used to precisely re-score the binding free energy of the docked complexes. In addition, the ADME and toxicity profiles for the lead compounds were also examined to address PK/PD characteristics. Altogether, the screening process identified three molecules, namely DB01238, DB06016 and DB01167 as potential therapeutics for the PD-L1 protein. To conclude, a molecular dynamic simulation of 100 ns was run to characterise the stability and inhibitory action of the three lead compounds. The results from the simulation study confirm the robust structural and thermodynamic stability of DB01238 than other investigated molecules. Thus, our findings hypothesize that DB01238 could serve as potential PD-L1 inhibitor in the near future for triple-negative breast cancer patients.
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Affiliation(s)
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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Elnageeb ME, Elfaki I, Adam KM, Ahmed EM, Elkhalifa EM, Abuagla HA, Ahmed AAEM, Ali EW, Eltieb EI, Edris AM. In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies. Diseases 2023; 11:115. [PMID: 37754311 PMCID: PMC10529770 DOI: 10.3390/diseases11030115] [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: 07/30/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023] Open
Abstract
Alpha synuclein (α-Syn) is a neuronal protein encoded by the SNCA gene and is involved in the development of Parkinson's disease (PD). The objective of this study was to examine in silico the functional implications of non-synonymous single nucleotide polymorphisms (nsSNPs) in the SNCA gene. We used a range of computational algorithms such as sequence conservation, structural analysis, physicochemical properties, and machine learning. The sequence of the SNCA gene was analyzed, resulting in the mapping of 42,272 SNPs that are classified into different functional categories. A total of 177 nsSNPs were identified within the coding region; there were 20 variants that may influence the α-Syn protein structure and function. This identification was made by employing different analytical tools including SIFT, PolyPhen2, Mut-pred, SNAP2, PANTHER, PhD-SNP, SNP&Go, MUpro, Cosurf, I-Mut, and HOPE. Three mutations, V82A, K80E, and E46K, were selected for further examinations due to their spatial positioning within the α-Syn as determined by PyMol. Results indicated that these mutations may affect the stability and function of α-Syn. Then, a molecular dynamics simulation was conducted for the SNCA wildtype and the four mutant variants (p.A18G, p.V82A, p.K80E, and p.E46K). The simulation examined temperature, pressure, density, root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (Rg). The data indicate that the mutations p.V82A, p.K80E, and p.E46K reduce the stability and functionality of α-Syn. These findings highlight the importance of understanding the impact of nsSNPs on α-syn structure and function. Our results required verifications in further protein functional and case-control studies. After being verified these findings can be used in genetic testing for the early diagnosis of PD, the evaluation of the risk factors, and therapeutic approaches.
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Affiliation(s)
- Mohamed E. Elnageeb
- Department of Basic Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, P.O. Box 741, Tabuk 71491, Saudi Arabia
| | - Khalid M. Adam
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Elsadig Mohamed Ahmed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
- Department of Clinical Chemistry, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti 27711, Sudan
| | - Elkhalifa M. Elkhalifa
- Department of Anatomy, Faculty of Medicine and Health Sciences, Nile Valley University, Atbara 46611, Sudan
| | - Hytham A. Abuagla
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Abubakr Ali Elamin Mohamed Ahmed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Elshazali Widaa Ali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Elmoiz Idris Eltieb
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Ali M. Edris
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
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Mohd Azrin NA, Mohamad Ali MS, Raja Abd Rahman RNZ, Mohd Shariff F, Ahmad Kamarudin NH, Muhd Noor ND. Effect of cysteine mutation at Ca 2+ coordinating residues to the autolysis, folding and hydrophobicity of full length and mature Rand protease: molecular dynamics simulation and essential dynamics. J Biomol Struct Dyn 2023:1-13. [PMID: 37608543 DOI: 10.1080/07391102.2023.2249105] [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: 04/10/2023] [Accepted: 08/12/2023] [Indexed: 08/24/2023]
Abstract
Rand protease is a serine protease that shared common characteristics with members of the MEROPS S8 subtilisin family. It is thermostable, highly stable in organic solvent and broad in specificity. Many structures of homologous protein solved by X-ray crystallography and NMR have been deposited to Protein Data Bank (PDB) which allowed this study to rely on structure prediction by deep learning to build three-dimensional (3D) structure of full length and mature Rand protease (flRP and mRP). In silico cysteine mutation to 7 predicted high affinity Ca2+ coordinating residues were introduced, and the mutants were subjected to molecular dynamics simulation to study its effect on flRP and mRP. MD simulation showed a marked increase in flexibility of the pro-peptide segment indicating the impact of single cysteine substitution at high affinity Ca2+ coordinating residues to autolysis of flRP. MD simulation for mRP reaffirmed the role of Ca2+ coordinating sites in providing stability to Rand protease. In addition, these residues also affect the autolysis, folding and hydrophobicity of RP. Essential dynamics observed large contribution of the first few eigenvectors of flRP, mRP and their high affinity Ca2+ coordinating residues mutants to the TMSF values which indicates that these values account for a large portion of the overall atomic fluctuations. These results have given a more comprehensive understanding on the role of cysteine substituted Ca2+ coordinating surface loop to the structure of flRP and mRP which are important in contributing to the structural stability of subtilisin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nur Aliyah Mohd Azrin
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Biochemistry, Universiti Putra Malaysia, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Microbiology, Universiti Putra Malaysia, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Microbiology, Universiti Putra Malaysia, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Biochemistry, Universiti Putra Malaysia, Selangor, Malaysia
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Ganai SA, Rajamanikandan S, Shah BA, Lone A, Arwa F, Malik FA. Comparative structural study of selective and non-selective NSAIDs against the enzyme cyclooxygenase-2 through real-time molecular dynamics linked to post-dynamics MM-GBSA and e-pharmacophores mapping. J Mol Model 2023; 29:192. [PMID: 37256432 DOI: 10.1007/s00894-023-05603-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Inflammation-provoked disorders including cancer are arbitrated by cyclooxygenase-2 (COX-2). Celecoxib and niflumic acid are among the potent and selective inhibitors of this enzyme while aspirin (acetylsalicylic acid) and sodium salicylate are its non-selective and lesser potent inhibitors. Despite these proven studies, the comparative structural study of these selective and non-selective molecules at atomistic scale in complex state with COX-2 that may answer this differential inhibitory behavior has not been accomplished spotlighting the imperative need of additional research in this area. Thus, this study was framed to provide a strong explanation for the enigma of higher inhibitory activity of celecoxib-niflumic acid duo in comparison to aspirin and sodium salicylate towards COX-2. METHODS A contemporary approach including advanced molecular docking against COX2, molecular dynamics of receptor-ligand complexes, simulation-trajectory-backed MMGBSA for different time points, radius of gyration (Rg) calculations, and e-pharmacophores approach was employed to attain a rational conclusion. RESULTS Our findings demonstrated the higher binding affinity of celecoxib and niflumic acid over aspirin and sodium salicylate against COX-2. Although both selective and non-selective COX-2 inhibitors manifested nearly the same stability in the active site of this enzyme but the e-pharmocophoric features found in the case of selective inhibitors scored over non-selective ones. Thus, our findings excluded the differential stability to be the cause of stronger potency of selective inhibitors but attributed their potency to greater number of complementary features present in these inhibitors against the active site of inflammation engendering COX-2.
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Affiliation(s)
- Shabir Ahmad Ganai
- Research Centre for Residue and Quality Analysis, FoH, SKUAST-Kashmir, Shalimar, Srinagar, 190025, Jammu & Kashmir, India.
| | - Sundararaj Rajamanikandan
- Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, 641021, Tamil Nadu, India
- Centre for Drug Discovery, Karpagam Academy of Higher Education, Coimbatore, 641021, Tamil Nadu, India
| | - Basit Amin Shah
- Department of Biotechnology, University of Kashmir, Srinagar, 190006, Jammu & Kashmir, India
| | - Asif Lone
- Department of Biochemistry, Deshbandhu College, University of Delhi, 110019, New Delhi, India
| | - Faieza Arwa
- Department of Veterinary Physiology, SKUAST-J-180009, Jammu, Jammu & Kashmir, India
| | - Firdose Ahmad Malik
- College of Temperate Sericulture, SKUAST-Kashmir, Mirgund, 193121, Jammu & Kashmir, India
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Agarwal V, Yadav TC, Tiwari A, Varadwaj P. Detailed investigation of catalytically important residues of class A β-lactamase. J Biomol Struct Dyn 2023; 41:2046-2073. [PMID: 34986744 DOI: 10.1080/07391102.2021.2023645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
An increasing global health challenge is antimicrobial resistance. Bacterial infections are often treated by using β-lactam antibiotics. But several resistance mechanisms have evolved in clinically mutated bacteria, which results in resistance against such antibiotics. Among which production of novel β-lactamase is the major one. This results in bacterial resistance against penicillin, cephalosporin, and carbapenems, which are considered to be the last resort of antibacterial treatment. Hence, β-lactamase enzymes produced by such bacteria are called extended-spectrum β-lactamase and carbapenemase enzymes. Further, these bacteria have developed resistance against many β-lactamase inhibitors as well. So, investigation of important residues that play an important role in altering and expanding the spectrum activity of these β-lactamase enzymes becomes necessary. This review aims to gather knowledge about the role of residues and their mutations in class A β-lactamase, which could be responsible for β-lactamase mediated resistance. Class A β-lactamase enzymes contain most of the clinically significant and expanded spectrum of β-lactamase enzymes. Ser70, Lys73, Ser130, Glu166, and Asn170 residues are mostly conserved and have a role in the enzyme's catalytic activity. In-depth investigation of 69, 130, 131, 132, 164, 165, 166, 170, 171, 173, 176, 178, 179, 182, 237, 244, 275 and 276 residues were done along with its kinetic analysis for knowing its significance. Further, detailed information from many previous studies was gathered to know the effect of mutations on the kinetic activity of class A β-lactamase enzymes with β-lactam antibiotics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vidhu Agarwal
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, Jhalwa, Uttar Pradesh, India
| | - Tara Chand Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Akhilesh Tiwari
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, Jhalwa, Uttar Pradesh, India
| | - Pritish Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, Jhalwa, Uttar Pradesh, India
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El-Tokhy FS, Abdel-Mottaleb MMA, Abdel Mageed SS, Mahmoud AMA, El-Ghany EA, Geneidi AS. Boosting the In Vivo Transdermal Bioavailability of Asenapine Maleate Using Novel Lavender Oil-Based Lipid Nanocapsules for Management of Schizophrenia. Pharmaceutics 2023; 15:pharmaceutics15020490. [PMID: 36839811 PMCID: PMC9963881 DOI: 10.3390/pharmaceutics15020490] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/23/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Lipid nanocapsules (LNCs) are promising for transdermal drug delivery due to their higher permeability-enhancing effects compared to polymeric nanoparticles. Lavender oil is an essential oil consisting of several terpenes (primarily linalool and linalyl acetate) known for their profound permeation-enhancing action. In the present work, we successfully encapsulated asenapine maleate (a second-generation antipsychotic that is highly metabolized by the liver, reducing its oral bioavailability) into biocompatible LNCs for transdermal application using a novel oily phase, i.e., lavender oil (LO-LNCs). A comparative study was conducted to determine the effects of different oily phases (i.e., Miglyol® 812, Labrafil® M1944CS, and Labrafac™ PG) on the LNCs. Surfactant types (Kolliphor® HS15, Kolliphor® EL and Tween80) and oil:surfactant ratios were studied. Blank and asenapine-loaded LNCs were optimized for particle size, polydispersity index, zeta potential, drug content and ex vivo skin permeation. Lavender oil and Labrafil® showed smaller vesicular sizes, while LO-LNCs increased the permeation of ASP across rat skin. In vivo pharmacokinetics revealed that LO-LNCs could increase the ASP Cmax via transdermal application by fourfold compared to oral suspension. They increased the bioavailability of ASP by up to 52% and provided sustained release for three days. The pharmacokinetic profile of the LO-LNCs was compared to ASP-loaded invasomes (discussed in a previous study) to emphasize LNCs' transdermal delivery behavior.
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Affiliation(s)
- Fatma Sa’eed El-Tokhy
- Department of Pharmaceutics, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City 11829, Egypt
| | - Mona M. A. Abdel-Mottaleb
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
- Correspondence: ; Tel.: +2-010-11-640-470
| | - Sherif S. Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo, Badr City 11829, Egypt
| | - Abdulla M. A. Mahmoud
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo, Badr City 11829, Egypt
| | - Elsayed A. El-Ghany
- Department of Pharmaceutics, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City 11829, Egypt
| | - Ahmed S. Geneidi
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
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11
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Madhana Priya N, Balasundaram A, Sidharth Kumar N, Udhaya Kumar S, Thirumal Kumar D, Magesh R, Zayed H, George Priya Doss C. Controlling cell proliferation by targeting cyclin-dependent kinase 6 using drug repurposing approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:97-124. [PMID: 37061342 DOI: 10.1016/bs.apcsb.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Cyclin-dependent kinase 6 (CDK6) is an essential kinase in cell cycle progression, which is a viable target for inhibitors in various malignancies, including breast cancer. This study aimed to virtually screen efficient compounds as new leads in treating breast cancer using a drug repurposing approach. Apoptosis regulatory compounds were taken from the seleckchem database. Molecular docking experiments were carried out in the presence of abemaciclib, a routinely used FDA drug. Compared to conventional drugs, the two compounds demonstrated a higher binding affinity for CDK6. Compounds (N-benzyl-6-[(4-hydroxyphenyl)methyl]-8-(naphthalen-1-ylmethyl)-4,7-dioxo-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide) and (1'-[4-[1-(4-fluorophenyl)indol-3-yl]butyl]spiro[1H-2-benzofuran-3,4'-piperidine]) were discovered to have an inhibitory effect against CDK6 at -8.49 and -6.78kcal/mol, respectively, compared to -8.09kcal/mol of the control molecule, the interacting residues of these two new compounds were found to fall within the binding site of the CDK6 molecule. Both compounds exhibited equal ADME features compared with abemaciclib and would be well distributed and metabolized by the body with an appropriate druglikeness range. Lastly, molecular dynamics was initiated for 200ns for the selected potent inhibitors and abemaciclib as complexed with CDK6. The RMSD, RMSF, Rg, H-Bond interactions, SASA, PCA, FEL, and MM/PBSA analysis were performed for the complexes to assess the stability, fluctuations, radius of gyration, hydrogen bond interaction, solvent accessibility, essential dynamics, free energy landscape, and MM/PBSA. The selected two compounds are small molecules in the appropriate druglikeness range. The results observed in molecular docking and molecular dynamics simulations were most promising for two compounds, suggesting their potent inhibitory effect against CDK6. We propose that these candidate compounds can undergo in vitro validation and in vivo testing for their further use against cancer.
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Sahu SN, Satpathy SS, Pattnaik S, Mohanty C, Pattanayak SK. Boerhavia diffusa plant extract can be a new potent therapeutics against mutant nephrin protein responsible for type1 nephrotic syndrome: Insight into hydrate-ligand docking interactions and molecular dynamics simulation study. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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13
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Addressing the Role of Angiogenesis in Patients with Advanced Pancreatic Neuroendocrine Tumors Treated with Everolimus: A Biological Prospective Analysis of Soluble Biomarkers and Clinical Outcomes. Cancers (Basel) 2022; 14:cancers14184471. [PMID: 36139632 PMCID: PMC9497075 DOI: 10.3390/cancers14184471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022] Open
Abstract
Background: The success of targeted therapies in the treatment of pancreatic neuroendocrine tumors has emphasized the strategy of targeting angiogenesis and the PI3K/AKT/mTOR pathway. However, the major challenge in the targeted era remains the early identification of resistant tumors especially when the efficacy is rarely associated to a clear tumor shrinkage at by imaging assessment. Methods: In this prospective study (NCT02305810) we investigated the predictive and prognostic role of soluble biomarkers of angiogenesis turnover (VEGF, bFGF, VEGFR2, TSP-1) circulating endothelial cells and progenitors, in 43 patients with metastatic panNET receiving everolimus. Results: Among all tested biomarkers, we found a specific subpopulation of circulating cells, CD31+CD140b-, with a significantly increased tumor progression hazard for values less or equal to the first quartile. Conclusion: Our study suggested the evidence that circulating cells might be surrogate biomarkers of angiogenesis activity in patients treated with everolimus and their baseline levels can be correlated with survival. However, further studies are now needed to validate the role of these cells as surrogate markers for the selection of patients to be candidates for antiangiogenic treatments.
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Aribisala JO, Sabiu S. Cheminformatics Identification of Phenolics as Modulators of Penicillin-Binding Protein 2a of Staphylococcus aureus: A Structure–Activity-Relationship-Based Study. Pharmaceutics 2022; 14:pharmaceutics14091818. [PMID: 36145565 PMCID: PMC9503099 DOI: 10.3390/pharmaceutics14091818] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 01/16/2023] Open
Abstract
The acquisition of penicillin-binding protein (PBP) 2a in resistant strains of Staphylococcus aureus allows for the continuous production of cell walls even after the inactivation of intrinsic PBPs. Thus, the discovery of novel therapeutics with enhanced modulatory activity on PBP2a is crucial, and plant secondary metabolites, such as phenolics, have found relevance in this regard. In this study, using computational techniques, phenolics were screened against the active site of PBP2a, and the ability of the lead phenolics to modulate PBP2a’s active and allosteric sites was studied. The top-five phenolics (leads) identified through structure–activity-based screening, pharmacokinetics and synthetic feasibility evaluations were subjected to molecular dynamics simulations. Except for propan-2-one at the active site, the leads had a higher binding free energy at both the active and allosteric sites of PBP2a than amoxicillin. The leads, while promoting the thermodynamic stability of PBP2a, showed a more promising affinity at the allosteric site than the active site, with silicristin (−25.61 kcal/mol) and epicatechin gallate (−47.65 kcal/mol) having the best affinity at the active and allosteric sites, respectively. Interestingly, the modulation of Tyr446, the active site gatekeeper residue in PBP2a, was noted to correlate with the affinity of the leads at the allosteric site. Overall, these observations point to the leads’ ability to inhibit PBP2a, either directly or through allosteric modulation with conventional drugs. Further confirmatory in vitro studies on the leads are underway.
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15
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Olubode SO, Bankole MO, Akinnusi PA, Adanlawo OS, Ojubola KI, Nwankwo DO, Edjebah OE, Adebesin AO, Ayodele AO. Molecular Modeling Studies of Natural Inhibitors of Androgen Signaling in Prostate Cancer. Cancer Inform 2022; 21:11769351221118556. [PMID: 35983016 PMCID: PMC9379963 DOI: 10.1177/11769351221118556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Prostate cancer is the second most common disease in men and the sixth leading cause of death from cancer globally, with 20 million men expected to be affected by 2024 thus considered as chronic illness which requires immediate attention. As an androgen-dependent illness that relies on the androgen receptor for development and progression, inhibition of the androgen receptor can lead to a therapeutic solution, hence serving as a vital therapeutic target. This study focused on the computational analysis of the inhibitory potentials of Vitis vinifera, a reported plant with anti-cancer properties, against androgen receptor employing molecular docking, ADMET studies, Binding energy study, pharmacophore modeling, and molecular dynamics simulation approaches. After the investigation, it was determined that 5 compounds: cis-piceid, cis-astrigin, gallocatechin, phlorizin, and trans-polydatin, might be possible androgen receptor inhibitors since they had higher docking scores and ADMET qualities than compared standards, with cis-piceid being the best-predicted inhibitor.
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Affiliation(s)
- Samuel O Olubode
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Mutolib O Bankole
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Precious A Akinnusi
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Olayinka S Adanlawo
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Kehinde I Ojubola
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Daniel O Nwankwo
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Onome E Edjebah
- Department of Pharmacology and Therapeutics, Delta State University, Delta State, Nigeria
| | - Ayomide O Adebesin
- Department of Biochemistry, Cancer Genomics Lab, Covenant University, Ota, Nigeria
| | - Abigail O Ayodele
- Center for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria
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Sur VP, Simonik O, Novotna M, Mazumdar A, Liska F, Vimberg V, Komrskova K. Dynamic study of small toxic hydrophobic proteins PepA1 and PepG1 of Staphylococcus aureus. Int J Biol Macromol 2022; 219:1360-1371. [PMID: 35932805 DOI: 10.1016/j.ijbiomac.2022.07.192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022]
Abstract
Toxin-antitoxin (TA) systems are small genetic elements which encode toxin proteins that interfere with vital cellular functions. PepA1 and PepG1 toxin proteins, known also as SprA1 and SprG1, are type I TA. In Staphylococcus aureus (S. aureus), their expression without the antitoxin counterparts (SprA1AS and SprF1), is lethal to the pathogen. Molecular Dynamics (MD) simulation was performed for PepA1 and PepG1 to understand their dynamic state, conformational changes, and their toxicity. The protein structures were constructed and used for MD simulation and the conformational changes, stability, flexibility, fluctuations, hydrophobicity, and role of their dynamic state on function prediction were studied extensively by GROMACS MD simulation analysis tools. In silico study indicated that the PepA1 and PepG1 proteins change their structural conformation from an open to closed state where PepA1 conformational changes were faster (10 ns) than PepG1 (20 ns) while PepG1 exerted more stability and flexibility than PepA1. According to SASA values, PepG1 is more hydrophobic than the PepA1 and forms fewer hydrogen bonds than PepA1. The in vivo study with PepA1 and PepG1 proteins provided evidence that both the conformation changes between the open and closed states and the amino acid sequence are crucial for peptide toxicity.
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Affiliation(s)
- Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Ondrej Simonik
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Michaela Novotna
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Aninda Mazumdar
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Frantisek Liska
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Vladimir Vimberg
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Katerina Komrskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic; Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic.
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Zamri MHB, Ujihara Y, Nakamura M, Mofrad MRK, Sugita S. Decoding the Effect of Hydrostatic Pressure on TRPV1 Lower-Gate Conformation by Molecular-Dynamics Simulation. Int J Mol Sci 2022; 23:ijms23137366. [PMID: 35806371 PMCID: PMC9266826 DOI: 10.3390/ijms23137366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/21/2022] [Accepted: 06/29/2022] [Indexed: 01/25/2023] Open
Abstract
In response to hydrostatic pressure, the cation channel transient receptor potential vanilloid 1 (TRPV1) is essential in signaling pathways linked to glaucoma. When activated, TRPV1 undergoes a gating transition from a closed to an open state that allows the influx of Ca2+ ions. However, the gating mechanism of TRPV1 in response to hydrostatic pressure at the molecular level is still lacking. To understand the effect of hydrostatic pressure on the activation of TRPV1, we conducted molecular-dynamics (MD) simulations on TRPV1 under different hydrostatic pressure configurations, with and without a cell membrane. The TRPV1 membrane-embedded model is more stable than the TPRV1-only model, indicating the importance of including the cell membrane in MD simulation. Under elevated pressure at 27.6 mmHg, we observed a more dynamic and outward motion of the TRPV1 domains in the lower-gate area than in the simulation under normal pressure at 12.6 mmHg. While a complete closed-to-open-gate transition was not evident in the limited course of our MD simulations, an increase in the channel radius at the lower gate was observed at 27.6 mmHg versus that at 12.6 mmHg. These findings provide novel information regarding the effect of hydrostatic pressure on TRPV1 channels.
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Affiliation(s)
- Muhammad Harith Bin Zamri
- Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, School of Engineering, Nagoya 466-8555, Japan; (M.H.B.Z.); (Y.U.); (M.N.)
| | - Yoshihiro Ujihara
- Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, School of Engineering, Nagoya 466-8555, Japan; (M.H.B.Z.); (Y.U.); (M.N.)
| | - Masanori Nakamura
- Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, School of Engineering, Nagoya 466-8555, Japan; (M.H.B.Z.); (Y.U.); (M.N.)
- Center of Biomedical Physics and Information Technology, Nagoya Institute of Technology, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Graduate School of Engineering, Nagoya 466-8555, Japan
| | - Mohammad R. K. Mofrad
- Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA;
| | - Shukei Sugita
- Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, School of Engineering, Nagoya 466-8555, Japan; (M.H.B.Z.); (Y.U.); (M.N.)
- Center of Biomedical Physics and Information Technology, Nagoya Institute of Technology, Nagoya 466-8555, Japan
- Correspondence: ; Tel.: +81-52-735-7125
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18
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Moharana M, Pattanayak SK, Khan F. Identification of phytochemicals from Eclipta alba and assess their potentiality against Hepatitis C virus envelope glycoprotein: virtual screening, docking, and molecular dynamics simulation study. J Biomol Struct Dyn 2022:1-17. [PMID: 35694813 DOI: 10.1080/07391102.2022.2085804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Hepatitis C virus has a major role in spreading chronic liver disease and hepatocellular carcinoma. Factors such as high costs, pharmacological side effects, and the development of drug resistance strains require the development of new and potentially effective antiviral to treat the various stages of Hepatitis C. Bioactive chemicals have been extracted from medicinal plants and are utilized by humans for the goal of maintaining a healthy lifestyle. The goal of this work is to recognize phytochemicals from Eclipta alba and assess their potentiality activity against the hepatitis C virus envelope glycoprotein using in silico approaches. Phytochemicals from Eclipta alba were virtually screened by Auto dock raccoon and 12 compounds were selected for molecular docking to probe the active binding site. The top two compounds based on the binding score like ecliptalbine and oleanolic acid with HCV E2 glycoprotein exhibit binding energy -8.88 and -8.02 kcal/mol, respectively. The chemicals' usefulness was reinforced by positive pharmacokinetic data. The phytocompounds were identified as potent HCV inhibitors based on the drug likeness and ADMET properties. Both ecliptalbine and oleanolic acid underwent molecular dynamics simulations to determine features such as RMSD, RMSF, SASA, hydrogen-bond number, and MM-PBSA-based binding free energy. From the molecular docking and molecular dynamics simulation study revealed that oleanolic acid obtained from Eclipta alba can be used as inhibitors against Hepatitis C. The identified inhibitor from our study will be study in vitro and in vivo studies to check their efficacy against Hepatitis C.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maheswata Moharana
- Department of Chemistry, National Institute of Technology, Raipur, India
| | | | - Fahmida Khan
- Department of Chemistry, National Institute of Technology, Raipur, India
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Baig MH, Yousuf M, Khan MI, Khan I, Ahmad I, Alshahrani MY, Hassan MI, Dong JJ. Investigating the Mechanism of Inhibition of Cyclin-Dependent Kinase 6 Inhibitory Potential by Selonsertib: Newer Insights Into Drug Repurposing. Front Oncol 2022; 12:865454. [PMID: 35720007 PMCID: PMC9204300 DOI: 10.3389/fonc.2022.865454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/06/2022] [Indexed: 12/23/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) play significant roles in numerous physiological, and are considered an attractive drug target for cancer, neurodegenerative, and inflammatory diseases. In the present study, we have aimed to investigate the binding affinity and inhibitory potential of selonsertib toward CDK6. Using the drug repurposing approach, we performed molecular docking of selonsertib with CDK6 and observed a significant binding affinity. To ascertain, we further performed essential dynamics analysis and free energy calculation, which suggested the formation of a stable selonsertib-CDK6 complex. The in-silico findings were further experimentally validated. The recombinant CDK6 was expressed, purified, and treated with selonsertib. The binding affinity of selonsertib to CDK6 was estimated by fluorescence binding studies and enzyme inhibition assay. The results indicated an appreciable binding of selonsertib against CDK6, which subsequently inhibits its activity with a commendable IC50 value (9.8 μM). We concluded that targeting CDK6 by selonsertib can be an efficient therapeutic approach to cancer and other CDK6-related diseases. These observations provide a promising opportunity to utilize selonsertib to address CDK6-related human pathologies.
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Affiliation(s)
- Mohammad Hassan Baig
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Mohd. Yousuf
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohd. Imran Khan
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Imran Khan
- Department of Molecular Biology, Beykoz Institute of Life Sciences and Biotechnology, BezmialemVakif University, Istanbul, Turkey
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Jae-June Dong
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
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Mahata S, Behera SK, Kumar S, Sahoo PK, Sarkar S, Fazil MHUT, Nasare VD. In-silico and in-vitro investigation of STAT3-PIM1 heterodimeric complex: Its mechanism and inhibition by curcumin for cancer therapeutics. Int J Biol Macromol 2022; 208:356-366. [DOI: 10.1016/j.ijbiomac.2022.03.137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 01/19/2023]
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21
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Sinyani A, Idowu K, Shunmugam L, Kumalo HM, Khan R. A molecular dynamics perspective into estrogen receptor inhibition by selective flavonoids as alternative therapeutic options. J Biomol Struct Dyn 2022; 41:4093-4105. [PMID: 35477414 DOI: 10.1080/07391102.2022.2062786] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Zearalenone is an estrogenic mycotoxin which is a common food contaminant and has been implicated in increasing the incidence of carcinogenesis and other reproductive health ailments through the estrogen receptor alpha (ERα) pathway. Competitive ERα blockers such as 4-Hydroxytamoxifen (OHT), are synthetic FDA approved drugs which, albeit being an effective anticancer agent, induces life altering side effects. For this reason, there is an increased interest in the use of naturally occurring medicinal plant products such as flavonoids. This study aimed to identity flavonoid ERα inhibitors and provide insights into the mechanism of inhibition using computational techniques. The Molecular Mechanics/Generalized Born Surface Area calculations revealed that quercetrin, hesperidin, epigallocatechin 3-gallate and kaempferol 7-O-glucoside out of 14 flavonoids had higher binding affinity for ERα than OHT. The structural analysis revealed that the binding of the compounds to the receptor lead to dynamic alterations, which induced conformational shift in the structure and orientation of the receptor resulting in stabilised, compact and low energy systems. The results of this study provide imperative information that supports the use of flavonoids in the inhibition of ERα to prevent or ameliorate the consequential adverse effects associated with zearalenone exposure.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Angela Sinyani
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kehinde Idowu
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP)/Genomics Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Letitia Shunmugam
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel Mathambo Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rene Khan
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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22
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Baig MH, Gupta P, Khan MI, Alajmi MF, Hussain A, Hassan MI, Dong JJ. Probing the interaction of Selonsertib with human serum albumin: In silico and in vitro approaches. Curr Top Med Chem 2022; 22:879-890. [PMID: 35352662 DOI: 10.2174/1568026622666220330012032] [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] [Received: 08/27/2021] [Revised: 12/30/2021] [Accepted: 01/18/2022] [Indexed: 11/22/2022]
Abstract
Introduction - Selonsertib, the most recently developed selective inhibitor of apoptosis signal-regulating kinase 1, was found to be highly productive in patients with stage 2 or 3 non-alcoholic steatohepatitis. We elucidated the binding characteristics, mechanism of interaction, and dynamic behaviors of selonsertib with human serum albumin (HSA), a major circulatory transport protein. Method- Different biophysical approaches (fluorescence quenching and isothermal titration calorimetry (ITC) were combined with various in silico techniques to examine the binding of selonsertib to HSA. Molecular docking results, analysis of molecular dynamics trajectories, and essential dynamics investigations indicated the stable binding of selonsertib to HSA. Further in vitro studies were performed to validate the observed interaction. Result- ITC results confirmed the robust binding and high affinity of selonsertib and HSA. Likewise, the fluorescence quenching results highlighted the binding affinity of selonsertib and HSA. Collectively, our findings offer deeper insight into the binding mechanism of selonsertib and HSA, emphasizing the selonsertib-mediated structural changes within HSA, along with a comprehensive rationale for the biological transport and accumulation of selonsertib in the blood plasma. Conclusion- Therefore, considering the bioavailability and effectiveness of selonsertib, assessing the interactions of this inhibitor with carrier proteins is crucial to elucidate its biological processes at the molecular level. This evidence carries the considerable scientific potential for future drug design.
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Affiliation(s)
- Mohammad Hassan Baig
- Department of Family Medicine, Yonsei University College of Medicine, Gangnam Severance Hospital, 211 Eonju-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi- 110025, INDIA
| | - Mohd Imran Khan
- Department of Internal Medicine, Yonsei University College of Medicine, Gangnam Severance Hospital, 211 Eonju-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi- 110025, INDIA
| | - Jae-June Dong
- Department of Family Medicine, Yonsei University College of Medicine, Gangnam Severance Hospital, 211 Eonju-ro, Gangnam-gu, Seoul, Republic of Korea
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Drug Discovery of Plausible Lead Natural Compounds That Target the Insulin Signaling Pathway: Bioinformatics Approaches. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2832889. [PMID: 35356248 PMCID: PMC8958086 DOI: 10.1155/2022/2832889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/16/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022]
Abstract
The growing smooth talk in the field of natural compounds is due to the ancient and current interest in herbal medicine and their potentially positive effects on health. Dozens of antidiabetic natural compounds were reported and tested in vivo, in silico, and in vitro. The role of these natural compounds, their actions on the insulin signaling pathway, and the stimulation of the glucose transporter-4 (GLUT4) insulin-responsive translocation to the plasma membrane (PM) are all crucial in the treatment of diabetes and insulin resistance. In this review, we collected and summarized a group of available in vivo and in vitro studies which targeted isolated phytochemicals with possible antidiabetic activity. Moreover, the in silico docking of natural compounds with some of the insulin signaling cascade key proteins is also summarized based on the current literature. In this review, hundreds of recent studies on pure natural compounds that alleviate type II diabetes mellitus (type II DM) were revised. We focused on natural compounds that could potentially regulate blood glucose and stimulate GLUT4 translocation through the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) pathway. On attempt to point out potential new natural antidiabetic compounds, this review also focuses on natural ingredients that were shown to interact with proteins in the insulin signaling pathway in silico, regardless of their in vitro/in vivo antidiabetic activity. We invite interested researchers to test these compounds as potential novel type II DM drugs and explore their therapeutic mechanisms.
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Sharma T, Baig MH, Khan MI, Alotaibi SS, Alorabi M, Dong JJ. Computational screening of camostat and related compounds against human TMPRSS2: A Potential Treatment of COVID-19. Saudi Pharm J 2022; 30:217-224. [PMID: 35095307 PMCID: PMC8787670 DOI: 10.1016/j.jsps.2022.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 01/07/2022] [Indexed: 02/06/2023] Open
Abstract
The global coronavirus pandemic has burdened the human population with mass fatalities and disastrous socio-economic consequences. The frequent occurrence of these new variants has fueled the already prevailing challenge. There is still a necessity for highly effective small molecular agents to prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Here, we targeted the human transmembrane surface protease TMPRSS2, which is essential for proteolytic activation of SARS-CoV-2. Camostat is a well-known inhibitor of serine proteases and an effective TMPRSS2 inhibitor. A virtual library of camostat-like compounds was computationally screened against the catalytic site of TMPRSS2. Following a sequential in-depth molecular docking and dynamics simulation, we report the compounds that exhibited promising efficacy against TMPRSS2. The molecular docking and MM/PBSA free energy calculation study indicates these compounds carry excellent binding affinity against TMPRSS2 and found them more effective than camostat. The study will open doors for the effective treatment of coronavirus disease 2019.
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Affiliation(s)
- Tanuj Sharma
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Republic of Korea
| | - Mohammad Hassan Baig
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Republic of Korea
- Corresponding authors.
| | - Mohd Imran Khan
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Republic of Korea
| | - Saqer S. Alotaibi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Mohammed Alorabi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Jae-June Dong
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Republic of Korea
- Corresponding authors.
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Islam MA, Rallabandi VPS, Mohammed S, Srinivasan S, Natarajan S, Dudekula DB, Park J. Screening of β1- and β2-Adrenergic Receptor Modulators through Advanced Pharmacoinformatics and Machine Learning Approaches. Int J Mol Sci 2021; 22:11191. [PMID: 34681845 PMCID: PMC8538848 DOI: 10.3390/ijms222011191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
Cardiovascular diseases (CDs) are a major concern in the human race and one of the leading causes of death worldwide. β-Adrenergic receptors (β1-AR and β2-AR) play a crucial role in the overall regulation of cardiac function. In the present study, structure-based virtual screening, machine learning (ML), and a ligand-based similarity search were conducted for the PubChem database against both β1- and β2-AR. Initially, all docked molecules were screened using the threshold binding energy value. Molecules with a better binding affinity were further used for segregation as active and inactive through ML. The pharmacokinetic assessment was carried out on molecules retained in the above step. Further, similarity searching of the ChEMBL and DrugBank databases was performed. From detailed analysis of the above data, four compounds for each of β1- and β2-AR were found to be promising in nature. A number of critical ligand-binding amino acids formed potential hydrogen bonds and hydrophobic interactions. Finally, a molecular dynamics (MD) simulation study of each molecule bound with the respective target was performed. A number of parameters obtained from the MD simulation trajectories were calculated and substantiated the stability between the protein-ligand complex. Hence, it can be postulated that the final molecules might be crucial for CDs subjected to experimental validation.
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Affiliation(s)
- Md Ataul Islam
- 3BIGS Omicscore Pvt. Ltd., 1, O Shaughnessy Rd, Langford Gardens, Bengaluru, Karnataka 560025, India; (M.A.I.); (V.P.S.R.); (S.M.); (S.S.); (D.B.D.)
| | - V. P. Subramanyam Rallabandi
- 3BIGS Omicscore Pvt. Ltd., 1, O Shaughnessy Rd, Langford Gardens, Bengaluru, Karnataka 560025, India; (M.A.I.); (V.P.S.R.); (S.M.); (S.S.); (D.B.D.)
| | - Sameer Mohammed
- 3BIGS Omicscore Pvt. Ltd., 1, O Shaughnessy Rd, Langford Gardens, Bengaluru, Karnataka 560025, India; (M.A.I.); (V.P.S.R.); (S.M.); (S.S.); (D.B.D.)
| | - Sridhar Srinivasan
- 3BIGS Omicscore Pvt. Ltd., 1, O Shaughnessy Rd, Langford Gardens, Bengaluru, Karnataka 560025, India; (M.A.I.); (V.P.S.R.); (S.M.); (S.S.); (D.B.D.)
| | | | - Dawood Babu Dudekula
- 3BIGS Omicscore Pvt. Ltd., 1, O Shaughnessy Rd, Langford Gardens, Bengaluru, Karnataka 560025, India; (M.A.I.); (V.P.S.R.); (S.M.); (S.S.); (D.B.D.)
| | - Junhyung Park
- 3BIGS Co., Ltd., 156, Gwanggyo-ro, Yeongtong-gu, Suwon-si 16506, Korea;
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Safavi A, Ghodousi ES, Ghavamizadeh M, Sabaghan M, Azadbakht O, veisi A, Babaei H, Nazeri Z, Darabi MK, Zarezade V. Computational investigation of novel farnesyltransferase inhibitors using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking and molecular dynamics simulation studies: A new insight into cancer treatment. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Samaranayake CP, Sastry SK. Molecular dynamics evidence for nonthermal effects of electric fields on pectin methylesterase activity. Phys Chem Chem Phys 2021; 23:14422-14432. [PMID: 34180917 DOI: 10.1039/d0cp05950a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Experimental studies relevant to the nonthermal effects of electric fields on biological systems are emerging. However, these effects are poorly understood at the molecular level. The present study investigates pectin methylesterase, a cell wall modifying enzyme in plants, exposed to various electric field strengths. Molecular dynamics (MD) of the enzyme were studied with and without (thermal-only) electric field applications. The measurements were interpreted on the basis of equivalent energy input to gain insights into the effect of electric field treatment time at a constant temperature (50 °C). Results reveal that electric fields exert nonthermal effects on both local and global protein structure. In 1 μs simulations, the results show significant (P ≤ 0.05) shrinkage of the catalytic domain and shortening of enzyme-water hydrogen bond lifetime by a 50 V cm-1 electric field. Unwinding of the helical segments, altered intra- and intermolecular hydrogen bond patterns, and increased hydration are also caused by the 50 V cm-1 electric field. This study serves to understand the electric field influence on the functional role of proteins.
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Affiliation(s)
- Chaminda P Samaranayake
- Department of Food, Agricultural and Biological Engineering, The Ohio State University, 590 Woody Hayes Drive, Columbus, Ohio 43210, USA.
| | - Sudhir K Sastry
- Department of Food, Agricultural and Biological Engineering, The Ohio State University, 590 Woody Hayes Drive, Columbus, Ohio 43210, USA.
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Sinha SK, Prasad SK, Islam MA, Gurav SS, Patil RB, AlFaris NA, Aldayel TS, AlKehayez NM, Wabaidur SM, Shakya A. Identification of bioactive compounds from Glycyrrhiza glabra as possible inhibitor of SARS-CoV-2 spike glycoprotein and non-structural protein-15: a pharmacoinformatics study. J Biomol Struct Dyn 2021; 39:4686-4700. [PMID: 32552462 PMCID: PMC7309308 DOI: 10.1080/07391102.2020.1779132] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022]
Abstract
At present, the world is facing a pandemic named as COVID-19, caused by SARS-CoV-2. Traditional Chinese medicine has recommended the use of liquorice (Glycyrrhiza species) in the treatment of infections caused by SARS-CoV-2. Therefore, the present investigation was carried out to identify the active molecule from the liquorice against different protein targets of COVID-19 using an in-silico approach. The molecular docking simulation study of 20 compounds along with two standard antiviral drugs (Lopinavir and Rivabirin) was carried out with the help of Autodock vina software using two protein targets from COVID-19 i.e. spike glycoprotein (PDB ID: 6VSB) and Non-structural Protein-15 (Nsp15) endoribonuclease (PDB ID: 6W01). From the observed binding energy and the binding interactions, glyasperin A showed high affinity towards Nsp15 endoribonuclease with uridine specificity, while glycyrrhizic acid was found to be best suited for the binding pocket of spike glycoprotein and also prohibited the entry of the virus into the host cell. Further, the dynamic behavior of the best-docked molecules inside the spike glycoprotein and Nsp15 endoribonuclease were explored through all-atoms molecular dynamics (MD) simulation study. Several parameters from the MD simulation have substantiated the stability of protein-ligand stability. The binding free energy of both glyasperin A and glycyrrhizic acid was calculated from the entire MD simulation trajectory through the MM-PBSA approach and found to high binding affinity towards the respective protein receptor cavity. Thus, glyasperin A and glycyrrhizic acid could be considered as the best molecule from liquorice, which could find useful against COVID-19. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saurabh K. Sinha
- Department of Pharmaceutical Sciences, Mohanlal Shukhadia University, Udaipur, India
| | - Satyendra K. Prasad
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, India
| | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- School of Health Sciences, University of Kwazulu-Natal, Durban, South Africa
| | - Shailendra S. Gurav
- Goa College of Pharmacy, Department of Pharmacognosy, Goa University, Panaji, India
| | - Rajesh B. Patil
- Sinhgad Technical Education Society’s, Smt. Kashibai Navale College of Pharmacy, Pune, India
| | - Nora Abdullah AlFaris
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Tahany Saleh Aldayel
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nora M. AlKehayez
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | - Anshul Shakya
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
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Purohit A, Singh G, Yadav SK. Chimeric bi-functional enzyme possessing xylanase and deacetylase activity for hydrolysis of agro-biomass rich in acetylated xylan. Colloids Surf B Biointerfaces 2021; 204:111832. [PMID: 33984614 DOI: 10.1016/j.colsurfb.2021.111832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Here, a chimeric bifunctional enzyme was developed for two activities xylanase and deacetylase. Chimeric enzyme was designed by combining the relevant amino acid stretches from two different parent sequences, such as polysaccharide/xylan deacetylase (ref id: MT682066) and xylanase (ref id WP_110897546.1). Five different hypothetical chimeras were developed and one of the best predicted chimeric protein GA_2(syn_SKYAP01) was synthesized. The GA_2(syn_SKYAP01) possessed the specific activity of 14.905 ± 0.8 U/mg for deacetylase and 100.87 ± 14.2 U/mg for xylanase. Optimum level of both the activities together was achieved at pH 5 and 60 °C. The chimeric protein was also found to be stable at higher temperature of 71°C. Functionality of the developed chimeric protein for both the activities was confirmed by the hydrolysis of commercial xylan into xylooligosaccharides and the release of acetic acid from glucose pentacetate and 7-amino cephalosporin. The designed bifunctional enzyme was found to be highly efficient.
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Affiliation(s)
- Anjali Purohit
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81 (Knowledge City), Mohali, 140306, PB, India
| | - Gurjant Singh
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81 (Knowledge City), Mohali, 140306, PB, India
| | - Sudesh Kumar Yadav
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81 (Knowledge City), Mohali, 140306, PB, India.
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Analysis of natural compounds against the activity of SARS-CoV-2 NSP15 protein towards an effective treatment against COVID-19: a theoretical and computational biology approach. J Mol Model 2021; 27:160. [PMID: 33963942 PMCID: PMC8105700 DOI: 10.1007/s00894-021-04750-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/15/2021] [Indexed: 12/26/2022]
Abstract
Coronavirus infectious disease 2019 (COVID-19), a viral infection caused by a novel coronavirus (nCoV), continues to emerge as a serious threat to public health. This pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) has infected globally with 1,550,000 plus deaths to date, representing a high risk to public health. No effective drug or vaccine is available to curb down this deadly virus. The expedition for searching for a potential drug or vaccine against COVID-19 is of massive potential and favour to the community. This study is focused on finding an effective natural compound that can be processed further into a potential inhibitor to check the activity of SARS-CoV-2 with minimal side effects targeting NSP15 protein, which belongs to the EndoU enzyme family. The natural screening suggested two efficient compounds (PubChem ID: 95372568 and 1776037) with dihydroxyphenyl region of the compound, found to be important in the interaction with the viral protein showing promising activity which may act as a potent lead inhibitory molecule against the virus. In combination with virtual screening, modelling, drug likeliness, molecular docking, and 500 ns cumulative molecular dynamics simulations (100 ns for each complex) along with the decomposition analysis to calculate and confirm the stability and fold, we propose 95372568 and 1776037 as novel compounds of natural origin capable of getting developed into potent lead molecules against SARS-CoV-2 target protein NSP15.
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Muthu Kumar T, Ramanathan K. Probiotic Polysaccharides as Toll-Like Receptor 4 Modulators—An In Silico Strategy. ADVANCES IN PROBIOTICS 2021:121-133. [DOI: 10.1016/b978-0-12-822909-5.00008-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. PLoS One 2020; 15:e0238344. [PMID: 32881907 PMCID: PMC7470274 DOI: 10.1371/journal.pone.0238344] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/14/2020] [Indexed: 12/20/2022] Open
Abstract
A novel severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causing COVID-19 pandemic in humans, recently emerged and has exported in more than 200 countries as a result of rapid spread. In this study, we have made an attempt to investigate the SARS-CoV-2 genome reported from 13 different countries, identification of mutations in major coronavirus proteins of these different SARS-CoV-2 genomes and compared with SARS-CoV. These thirteen complete genome sequences of SARS-CoV-2 showed high identity (>99%) to each other, while they shared 82% identity with SARS-CoV. Here, we performed a very systematic mutational analysis of SARS-CoV-2 genomes from different geographical locations, which enabled us to identify numerous unique features of this viral genome. This includes several important country-specific unique mutations in the major proteins of SARS-CoV-2 namely, replicase polyprotein, spike glycoprotein, envelope protein and nucleocapsid protein. Indian strain showed mutation in spike glycoprotein at R408I and in replicase polyprotein at I671T, P2144S and A2798V,. While the spike protein of Spain & South Korea carried F797C and S221W mutation, respectively. Likewise, several important country specific mutations were analyzed. The effect of mutations of these major proteins were also investigated using various in silico approaches. Main protease (Mpro), the therapeutic target protein of SARS with maximum reported inhibitors, was thoroughly investigated and the effect of mutation on the binding affinity and structural dynamics of Mpro was studied. It was found that the R60C mutation in Mpro affects the protein dynamics, thereby, affecting the binding of inhibitor within its active site. The implications of mutation on structural characteristics were determined. The information provided in this manuscript holds great potential in further scientific research towards the design of potential vaccine candidates/small molecular inhibitor against COVID19.
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Bhowmick S, AlFaris NA, ALTamimi JZ, ALOthman ZA, Aldayel TS, Wabaidur SM, Islam MA. Screening and analysis of bioactive food compounds for modulating the CDK2 protein for cell cycle arrest: Multi-cheminformatics approaches for anticancer therapeutics. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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34
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Ahmad SS, Sinha M, Ahmad K, Khalid M, Choi I. Study of Caspase 8 Inhibition for the Management of Alzheimer's Disease: A Molecular Docking and Dynamics Simulation. Molecules 2020; 25:molecules25092071. [PMID: 32365525 PMCID: PMC7249184 DOI: 10.3390/molecules25092071] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 01/13/2023] Open
Abstract
Alzheimer’s disease (AD) is the most common type of dementia and usually manifests as diminished episodic memory and cognitive functions. Caspases are crucial mediators of neuronal death in a number of neurodegenerative diseases, and caspase 8 is considered a major therapeutic target in the context of AD. In the present study, we performed a virtual screening of 200 natural compounds by molecular docking with respect to their abilities to bind with caspase 8. Among them, rutaecarpine was found to have the highest (negative) binding energy (−6.5 kcal/mol) and was further subjected to molecular dynamics (MD) simulation analysis. Caspase 8 was determined to interact with rutaecarpine through five amino acid residues, specifically Thr337, Lys353, Val354, Phe355, and Phe356, and two hydrogen bonds (ligand: H35-A: LYS353:O and A:PHE355: N-ligand: N5). Furthermore, a 50 ns MD simulation was conducted to optimize the interaction, to predict complex flexibility, and to investigate the stability of the caspase 8–rutaecarpine complex, which appeared to be quite stable. The obtained results propose that rutaecarpine could be a lead compound that bears remarkable anti-Alzheimer’s potential against caspase 8.
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Affiliation(s)
- Syed Sayeed Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.S.A.); (K.A.)
| | - Meetali Sinha
- Department of Bioengineering, Integral University, Lucknow 226026, India;
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.S.A.); (K.A.)
| | - Mohammad Khalid
- College of Pharmacy, Department of Pharmacognosy, Prince Sattam Bin Abdul Aziz University, Alkharj 16278, Riyadh, Saudi Arabia;
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (S.S.A.); (K.A.)
- Correspondence: ; Fax: +82-53-810-4769
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Hasnain MJU, Shoaib M, Qadri S, Afzal B, Anwar T, Abbas SH, Sarwar A, Talha Malik HM, Tariq Pervez M. Computational analysis of functional single nucleotide polymorphisms associated with SLC26A4 gene. PLoS One 2020; 15:e0225368. [PMID: 31971949 PMCID: PMC6977751 DOI: 10.1371/journal.pone.0225368] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 11/03/2019] [Indexed: 11/25/2022] Open
Abstract
Single Nucleotide Polymorphisms (SNPs) are the most common candidate mutations in human beings that play a vital role in the genetic basis of certain diseases. Previous studies revealed that Solute Carrier Family 26 Member 4 (SLC26A4) being an essential gene of the multi-faceted transporter family SLC26 facilitates reflexive movement of Iodide into follicular lumen through apical membrane of thyrocyte. SLC26A4 gene encodes Pendred protein, a membrane glycoprotein, highly hydrophobic in nature, present at the apical membrane of thyrocyte functioning as transporter of iodide for thyroid cells. A minor genetic variation in SLC26A4 can cause Pendred syndrome, a syndrome associated with thyroid glands and deafness. In this study, we performed in-silico analysis of 674 missense SNPs of SLC26A4 using different computational platforms. The bunch of tools including SNPNEXUS, SNAP-2, PhD-SNP, SNPs&GO, I-Mutant, ConSurf, and ModPred were used to predict 23 highly confident damaging and disease causing nsSNPs (G209V, G197R, L458P, S427P, Q101P, W472R, N392Y, V359E, R409C, Q235R, R409P, G139V, G497S, H723R, D87G, Y127H, F667C, G334A, G95R, S427C, R291W, Q383H and E384G) that could potentially alter the SLC26A4 gene. Moreover, protein structure prediction, protein-ligand docking and Molecular Dynamics simulation were performed to confirm the impact of two evident alterations (Y127H and G334A) on the protein structure and function.
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Affiliation(s)
| | - Muhammad Shoaib
- Department of Computer Science and Engineering, UET, Lahore, Pakistan
| | - Salman Qadri
- Department of CS & IT, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Bakhtawar Afzal
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Tehreem Anwar
- Department of Bioinformatics, Virtual University of Pakistan, Lahore, Pakistan
| | - Syed Hassan Abbas
- Department of Bioinformatics, Virtual University of Pakistan, Lahore, Pakistan
| | - Amina Sarwar
- Department of Bioinformatics, Virtual University of Pakistan, Lahore, Pakistan
| | | | - Muhammad Tariq Pervez
- Department of Bioinformatics, Virtual University of Pakistan, Lahore, Pakistan
- * E-mail:
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Shcherbinin D, Veselovsky A, Rubtsova M, Grigorenko V, Egorov A. The impact of long-distance mutations on the Ω-loop conformation in TEM type β-lactamases. J Biomol Struct Dyn 2019; 38:2369-2376. [PMID: 31241429 DOI: 10.1080/07391102.2019.1634642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
β-lactamases are hydrolytic enzymes primarily responsible for occurrence and abundance of bacteria resistant to β-lactam antibiotics. TEM type β-lactamases are formed by the parent enzyme TEM-1 and more than two hundred of its mutants. Positions for the known amino acid substitutions cover ∼30% of TEM type enzyme's sequence. These substitutions are divided into the key mutations that lead to changes in catalytic properties of β-lactamases, and the secondary ones, which role is poorly understood. In this study, Residue Interaction Networks were constructed from molecular dynamic trajectories of β-lactamase TEM-1 and its variants with two key substitutions, G238S and E240K, and their combinations with secondary ones (M182T and Q39K). Particular attention was paid to a detailed analysis of the interactions that affect conformation and mobility of the Ω-loop, representing a part of the β-lactamase active site. It was shown that key mutations weakened the stability of contact inside the Ω-loop thus increasing its mobility. Combination of three amino acid substitutions, including the 182 residue, leads to the release of R65 promoting its new contacts with N175 and D176. As a result, Ω-loop is fixed on the protein globule. The second distal mutation Q39K prevents changes in spatial position of R65, which lead to the weakening of the effect of M182T substitution and the recovery of the Ω-loop mobility. Thus, the distal secondary mutations are directed for recovering the mobility of enzyme disturbed by the key mutations responsible for expansion of substrate specificity. AbbreviationsESBLextended spectrum beta-lactamasesIRinhibitor resistant beta-lactamasesMDmolecular dynamicsRINresidue interaction networksRMSDroot mean square deviationRMSFroot mean square fluctuations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitrii Shcherbinin
- Institute of Biomedical Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Maya Rubtsova
- Chemistry Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vitaly Grigorenko
- Chemistry Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Egorov
- Chemistry Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
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Kashif M, Hira SK, Upadhyaya A, Gupta U, Singh R, Paladhi A, Khan FI, Rub A, Manna PP. In silico studies and evaluation of antiparasitic role of a novel pyruvate phosphate dikinase inhibitor in Leishmania donovani infected macrophages. Int J Antimicrob Agents 2019; 53:508-514. [DOI: 10.1016/j.ijantimicag.2018.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 12/10/2018] [Accepted: 12/22/2018] [Indexed: 01/08/2023]
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Rehan M, Bajouh OS. Virtual screening of naphthoquinone analogs for potent inhibitors against the cancer-signaling PI3K/AKT/mTOR pathway. J Cell Biochem 2019; 120:1328-1339. [PMID: 30298630 DOI: 10.1002/jcb.27100] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/26/2018] [Indexed: 01/24/2023]
Abstract
The PI3K/AKT/mTOR pathway is one of the most commonly disrupted signaling pathways that plays a role in the development and pathogenicity of multiple cancers. Therefore, the critical proteins of this pathway have been targeted for anticancer therapy. The scientific community has increasingly been realizing the anti-cancer therapeutic potential of naphthoquinone analogs. These compounds constitute a major class of diverse sets of plant metabolites, which include various natural products and synthetic compounds with proven anticancer activity. The current study involved structural computational biology approaches to explore compounds from a diverse pool of naphthoquinone analogs that can inhibit key cancer-signaling proteins phosphoinositide 3-kinase (PI3K), protein kinase B, PKB (AKT), and mammalian target of rapamycin (mTOR). The novel compound identified commonly among the top 10 dock score lists of PI3K, AKT, and mTOR was selected for further study and proposed as a potential inhibitor of the 3 cancer-signaling proteins and an anticancer agent. Further, to check the docking accuracy and potential of the compound, post docking analyses, namely, binding comparison with the native ligand, the role of the interacting residue role in binding, predicted binding energy and dissociation constant calculations, etc., were performed. All these measures showed good-quality binding, and thus provide weight to our prediction of the novel compound as a pan PI3K/AKT/mTOR inhibitor and an anticancer agent. Finally, to compare the binding and similarity in the active sites of the 3 protein kinases, a ligand-based active site alignment was performed and analyzed. Thus, the study proposed a novel naphthoquinone analog as a potential anticancer drug, and provided comparative structural insight into its binding to the 3 protein kinases.
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Affiliation(s)
- Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Osama S Bajouh
- Department of Obstetrics and Gynecology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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Sharma M, Jha P, Verma P, Chopra M. Combined comparative molecular field analysis, comparative molecular similarity indices analysis, molecular docking and molecular dynamics studies of histone deacetylase 6 inhibitors. Chem Biol Drug Des 2019; 93:910-925. [PMID: 30667160 DOI: 10.1111/cbdd.13488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/09/2019] [Accepted: 01/12/2019] [Indexed: 01/04/2023]
Abstract
Human histone deacetylase isoform 6 (HDAC6) has been shown to have an immense role in cell motility and aggresome formation and is being an attractive selective target for the treatment of multiple tumour types and neurodegenerative conditions. The discovery of selective HDAC6 inhibitors with new chemical functionalities is therefore of utmost interest to researchers. In order to examine the structural requirements for HDAC6-specific inhibitors and to derive predictive model which can be used for designing new selective HDAC6 inhibitors, a three-dimensional quantitative structure-activity relationship study was carried out on a diverse set of ligands using common feature-based pharmacophore alignment followed by employing comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques. The models displayed high correlation of 0.978 and 0.991 for best CoMFA and CoMSIA models, respectively, and a good statistical significance. The model could be used for predicting activities of the test set compounds as well as for deriving useful information regarding steric, electrostatic, hydrophobic properties of the molecules used in this study. Further, the training and test set molecules were docked into the HDAC6 binding site and molecular dynamics was carried out to suggest structural requirements for design of new inhibitors.
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Affiliation(s)
- Monika Sharma
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Prakash Jha
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Priyanka Verma
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
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Pereira R, Rabelo VWH, Sibajev A, Abreu PA, Castro HC. Class A β-lactamases and inhibitors: In silico analysis of the binding mode and the relationship with resistance. J Biotechnol 2018; 279:37-46. [PMID: 29753682 DOI: 10.1016/j.jbiotec.2018.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/22/2018] [Accepted: 05/03/2018] [Indexed: 02/01/2023]
Abstract
β-lactams are one of the most common antimicrobials used to treat bacterial infections. However, bacterial resistance has compromised their efficacy, mainly due to the β-lactamase enzyme production. To overcome this resistance, β-lactamase inhibitors can be used in association with these antimicrobials. Herein, we analyzed the structural characteristics of β-lactamases and their interactions with classical inhibitors, such as clavulanic acid (CA), sulbactam (SB) and tazobactam (TZ) to gain insights into resistance. The homology models of five class A β-lactamases, namely CARB-3, IMI-1, SFO-1, SHV-5 and TEM-10, were constructed and validated and revealed an overall 3D structural conservation, but with significant differences in the electrostatic potential maps, especially at important regions in the catalytic site. Molecular dockings of CA, SB and TZ with these enzymes revealed a covalent bond with the S70 in all complexes, except Carb-3 which is in agreement with experimental data reported so far. This is likely related to the less voluminous active site of Carb-3 model. Although few specific contacts were observed in the β-lactamase-inhibitor complexes, all compounds interacted with the residues in positions 73, 130, 132, 236 and 237. Therefore, this study provides new perspectives for the design of innovative compounds with broad-spectrum inhibitory profiles against β-lactamases.
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Affiliation(s)
- Rebeca Pereira
- Programa de Pós-graduação em Ciências e Biotecnologia - Instituto de Biologia, Universidade Federal Fluminense, Campus do Valonguinho, Niterói, RJ, CEP 24210-130, Brazil
| | - Vitor Won-Held Rabelo
- Programa de Pós-graduação em Ciências e Biotecnologia - Instituto de Biologia, Universidade Federal Fluminense, Campus do Valonguinho, Niterói, RJ, CEP 24210-130, Brazil; Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro, Campus Macaé, RJ, CEP 27965-045, Brazil
| | - Alexander Sibajev
- Centro de Ciências da Saúde - Curso de Medicina, Universidade Federal de Roraima, Campus do Paricarana, Boa Vista, RR, CEP 69304-000, Brazil
| | - Paula Alvarez Abreu
- Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro, Campus Macaé, RJ, CEP 27965-045, Brazil.
| | - Helena Carla Castro
- Programa de Pós-graduação em Ciências e Biotecnologia - Instituto de Biologia, Universidade Federal Fluminense, Campus do Valonguinho, Niterói, RJ, CEP 24210-130, Brazil.
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Peptide based therapeutics and their use for the treatment of neurodegenerative and other diseases. Biomed Pharmacother 2018; 103:574-581. [PMID: 29677544 DOI: 10.1016/j.biopha.2018.04.025] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/21/2018] [Accepted: 04/03/2018] [Indexed: 12/16/2022] Open
Abstract
Bioactive peptides are actively involved in different biological functions and importantly contribute to human health, and the use of peptides as therapeutics has a long successful history in disease management. A number of peptides have wide-ranging therapeutic effects, such as antioxidant, antimicrobial, and antithrombotic effects. Neurodegenerative diseases are typically caused by abnormal aggregations of proteins or peptides, and the depositions of these aggregates in or on neurons, disrupt signaling and eventually kill neurons. During recent years, research on short peptides has advanced tremendously. This review offers a brief introduction to peptide based therapeutics and their application in disease management and provides an overview of peptide vaccines, and toxicity related issues. In addition, the importance of peptides in the management of different neurodegenerative diseases and their therapeutic applications is discussed. The present review provides an understanding of peptides and their applications for the management of different diseases, but with focus on neurodegenerative diseases. The role of peptides as anti-cancer, antimicrobial and antidiabetic agents has also been discussed.
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Kashif M, Tabrez S, Husein A, Arish M, Kalaiarasan P, Manna PP, Subbarao N, Akhter Y, Rub A. Identification of novel inhibitors against UDP‐galactopyranose mutase to combat leishmaniasis. J Cell Biochem 2017; 119:2653-2665. [DOI: 10.1002/jcb.26433] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/18/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Mohammad Kashif
- Infection and Immunity Lab, Department of BiotechnologyJamia Millia Islamia (A Central University)New DelhiIndia
- Immunobiology Laboratory, Department of ZoologyInstitute of Science, Banaras Hindu UniversityVaranasiIndia
| | - Shams Tabrez
- Infection and Immunity Lab, Department of BiotechnologyJamia Millia Islamia (A Central University)New DelhiIndia
| | - Atahar Husein
- Infection and Immunity Lab, Department of BiotechnologyJamia Millia Islamia (A Central University)New DelhiIndia
| | - Mohd Arish
- Infection and Immunity Lab, Department of BiotechnologyJamia Millia Islamia (A Central University)New DelhiIndia
| | - Ponnusamy Kalaiarasan
- School of Computational and Integrative SciencesJawaharlal Nehru UniversityNew DelhiIndia
| | - Partha P. Manna
- Immunobiology Laboratory, Department of ZoologyInstitute of Science, Banaras Hindu UniversityVaranasiIndia
| | - Naidu Subbarao
- School of Computational and Integrative SciencesJawaharlal Nehru UniversityNew DelhiIndia
| | - Yusuf Akhter
- School of Life Sciences, Central University of Himachal PradeshTemporary Academic BlockShahpurKangra (H.P.)India
| | - Abdur Rub
- Infection and Immunity Lab, Department of BiotechnologyJamia Millia Islamia (A Central University)New DelhiIndia
- Department of Medical Laboratory Sciences, College of Applied Medical ScienceMajmaah UniversityAl MajmaahKSA
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Srinivasan E, Rajasekaran R. Deciphering the loss of metal binding due to mutation D83G of human SOD1 protein causing FALS disease. Int J Biol Macromol 2017; 107:521-529. [PMID: 28899654 DOI: 10.1016/j.ijbiomac.2017.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 01/23/2023]
Abstract
Mutations in Cu/Zn superoxide dismutase 1 (SOD1) protein are found to be the causative factor, behind the majority of familial amyotrophic later sclerosis (FALS) cases. The mutations particularly on the metal (Zn) binding residues are found to increase the disease onset in the individuals suffering from FALS, while the presence of the metal ion (Zn) is essential for the catalytic activity and retaining the protein stability. Thus in our study, we focused on one such metal binding mutant (D83G) and assessed the impact of the mutation on protein structure and function. The influence of mutation was examined dynamically, using discrete molecular dynamics on both the native and mutant SOD1 protein respectively. Accordingly, the variation in conformational stability, residual flexibility and protein compactness along with the change in conformational free energy were monitored over the entire dynamic period. Moreover, the motion of native and mutant SOD1 was also observed via the essential dynamics. Besides, the disparity in Zn ion binding was inspected through distance analysis and steered molecular dynamics, correspondingly. Therefore, the study provides a better understanding over the profound effect of mutation on SOD1, both structurally and functionally, using computational approaches.
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Affiliation(s)
- E Srinivasan
- Bioinformatics lab, Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore - 632014, Tamil Nadu, India
| | - R Rajasekaran
- Bioinformatics lab, Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore - 632014, Tamil Nadu, India.
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Shcherbinin DS, Rubtsova MY, Grigorenko VG, Uporov IV, Veselovsky AV, Egorov AM. The study of the role of mutations M182T and Q39K in the TEM-72 β-lactamase structure by the molecular dynamics method. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2017. [DOI: 10.1134/s1990750817020056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Shcherbinin DS, Rubtsova MY, Grigorenko VG, Uporov IV, Veselovsky AV, Egorov AM. [Investigation the role of mutations M182T and Q39K in structure of beta-lactamase TEM-72 by molecular dynamics method]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 62:527-534. [PMID: 27797327 DOI: 10.18097/pbmc20166205527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Synthesis of b-lactamases is one of the common mechanisms of bacterial resistance to b-lactam antibiotics including penicillins and cephalosporins. The widespread use of antibiotics results in appearance of numerous extended-spectrum b-lactamase variants or resistance to inhibitors. Mutations of 92 residues of TEM type were found. Several mutations are the key mutations that determine the extension of spectrum of substrates. However, roles of the most associated mutations, located far from active site, remain unknown. We have investigated the role of associated mutations in structure of b-lactamase TEM-72, which contain two key mutation (G238S, E240K) and two associated mutations (Q39K, M182T) by means of simulation of molecular dynamics. The key mutation lead to destabilization of the protein globule, characterized by increased mobility of amino acid residues at high temperature of modelling. Mutation M182T lead to stabilization protein, whereas mutation Q39K is destabilizing mutation. It seems that the last mutation serves for optimization of conformational mobility of b-lactamase and may influence on enzyme activity.
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Affiliation(s)
| | - M Yu Rubtsova
- Lomonosov Moscow State University, Chemical Department, Moscow, Russia
| | - V G Grigorenko
- Lomonosov Moscow State University, Chemical Department, Moscow, Russia
| | - I V Uporov
- Lomonosov Moscow State University, Chemical Department, Moscow, Russia
| | | | - A M Egorov
- Lomonosov Moscow State University, Chemical Department, Moscow, Russia
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Rehman A, Akhtar S, Siddiqui MH, Sayeed U, Ahmad SS, Arif JM, Khan MKA. Identification of potential leads against 4-hydroxytetrahydrodipicolinate synthase from Mycobacterium tuberculosis. Bioinformation 2016; 12:400-407. [PMID: 28293071 PMCID: PMC5320922 DOI: 10.6026/97320630012400] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 11/19/2016] [Indexed: 11/23/2022] Open
Abstract
4-hydroxy-tetrahydrodipicolinate synthase (DHDPS) is an important enzyme needed for the biosynthesis of lysine and many more key metabolites in Mycobacterium tuberculosis (Mtb). Inhibition of DHDPS is supposed to a promising therapeutic target due to its specific role in sporulation, cross-linking of the peptidiglycan polymers and biosynthesis of amino acids. In this work, a known inhibitor-based similarity search was carried out against a natural products database (Super Natural II) towards identification of more potent phyto-inhibitors. Molecular interaction studies were accomplished using three different tools to understand and establish the participation of active site residues as the key players in stabilizing the binding mode of ligands and target protein. The best phyto-compound deduced on the basis of binding affinity was further used as a template to make similarity scan across the PubChem Compound database (score > = 80 %) to get more divesred leads. In this search 5098 hits were obtained that further reduced to 262 after drug-likeness filtration. These phytochemicallike compounds were docked at the active site of DHDPS.Then, those hits selected from docking analysis that showing stronger binding and forming maximum H-bonds with the active site residues (Thr54, Thr55, Tyr143, Arg148 and Lys171). Finally, we predicted one phytochemical compound (SN00003544), two PubChem-compounds (CID41032023, CID54025334) akin to phytochemical molecule showing better interactions in comaprison of known inhibitors of target protein.These findings might be further useful to gain the structural insight into the designing of novel leads against DapA family.
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Affiliation(s)
- Ajijur Rehman
- Department of Biosciences, Faculty of Applied Sciences, Integral University Lucknow, Uttar Pradesh, India-226026
| | - Salman Akhtar
- Department of Bioengineering, Faculty of Engineering, Integral University Lucknow, Uttar Pradesh, India-226026
| | - Mohd Haris Siddiqui
- Department of Bioengineering, Faculty of Engineering, Integral University Lucknow, Uttar Pradesh, India-226026
| | - Usman Sayeed
- Department of Bioengineering, Faculty of Engineering, Integral University Lucknow, Uttar Pradesh, India-226026
| | - Syed Sayeed Ahmad
- Department of Bioengineering, Faculty of Engineering, Integral University Lucknow, Uttar Pradesh, India-226026
| | - Jamal M. Arif
- Department of Biosciences, Faculty of Applied Sciences, Integral University Lucknow, Uttar Pradesh, India-226026
| | - M. Kalim A. Khan
- Department of Bioengineering, Faculty of Engineering, Integral University Lucknow, Uttar Pradesh, India-226026
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