51
|
Phospholipids and Hyaluronan: From Molecular Interactions to Nano- and Macroscale Friction. COLLOIDS AND INTERFACES 2022. [DOI: 10.3390/colloids6030038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Phospholipids and hyaluronan are two key biomolecules that contribute to the excellent lubrication of articular joints. Phospholipids alone and in combination with hyaluronan have also displayed low friction forces on smooth surfaces in micro- and nanosized tribological contacts. In an effort to develop aqueous-based lubrication systems, it is highly relevant to explore if these types of molecules also are able to provide efficient lubrication of macroscopic tribological contacts involving surfaces with roughness larger than the thickness of the lubricating layer. To this end, we investigated the lubrication performance of hyaluronan, the phospholipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and mixtures of these two components using glass surfaces in a mini-traction machine. We compared our data with those obtained using flat silica surfaces in previous atomic force microscopy studies, and we also highlighted insights on hyaluronan–phospholipid interactions gained from recent simulations. Our data demonstrate that hyaluronan alone does not provide any lubricating benefit, but DPPC alone and in mixtures with hyaluronan reduces the friction force by an order of magnitude.
Collapse
|
52
|
Song MT, Wang WZ, Lu Y, Han RM, Skibsted LH, Zhang JP. Double-Site Binding and Anti-/Pro-oxidation of Luteolin on Bovine Serum Albumin Mediated by Copper(II) Coordination. ACS OMEGA 2022; 7:19521-19534. [PMID: 35721975 PMCID: PMC9202249 DOI: 10.1021/acsomega.2c01226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
The interactions of luteolin (Lut) with bovine serum albumin (BSA) mediated by Cu(II) were investigated by spectroscopic, calorimetric, and molecular dynamic (MD) methods. Fluorescence studies showed that the binding of Lut to BSA was significantly enhanced by Cu(II) coordination with the number of binding sites and binding constant increasing from n = 1 and K a = 3.2 × 105 L·mol-1 for Lut to n = 2 and K a = 7.1 × 105 L·mol-1 for a 1:1 Cu(II)-luteolin complex, in agreement with the results from isothermal titration calorimetry (ITC). Site-specific experiments with warfarin and ibuprofen and MD confirmed that two binding sites of BSA were sequentially occupied by two Cu(II)-luteolin complexes. Cu(II) coordination increased the antioxidant activity of luteolin by 60% in the inhibition of carbonyl formation from the oxidation of amino groups in the side chain of BSA induced by the peroxyl radical ROO•; however, it counteracted the antioxidant effects of luteolin and played pro-oxidative roles in BSA aggregation induced by •OH.
Collapse
Affiliation(s)
- Meng-Ting Song
- Key
Laboratory of Advanced Light Conversion Materials and Biophotonics,
Department of Chemistry, Renmin University
of China, Beijing 100872, China
| | - Wen-Zhu Wang
- Key
Laboratory of Advanced Light Conversion Materials and Biophotonics,
Department of Chemistry, Renmin University
of China, Beijing 100872, China
| | - Yao Lu
- Key
Laboratory of Advanced Light Conversion Materials and Biophotonics,
Department of Chemistry, Renmin University
of China, Beijing 100872, China
| | - Rui-Min Han
- Key
Laboratory of Advanced Light Conversion Materials and Biophotonics,
Department of Chemistry, Renmin University
of China, Beijing 100872, China
| | - Leif H. Skibsted
- Department
of Food Science, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark
| | - Jian-Ping Zhang
- Key
Laboratory of Advanced Light Conversion Materials and Biophotonics,
Department of Chemistry, Renmin University
of China, Beijing 100872, China
| |
Collapse
|
53
|
Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface. ENTROPY 2022; 24:e24060811. [PMID: 35741532 PMCID: PMC9222412 DOI: 10.3390/e24060811] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/24/2022]
Abstract
Albumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions on human serum albumin–hyaluronan/chondroitin-6-sulfate interactions examined using molecular docking followed by molecular dynamics simulations. We analyze chosen glycosaminoglycans binding by employing a conformational entropy approach. In addition, several protein–polymer complexes have been studied to check how the binding site and presence of ions influence affinity. The presence of divalent cations contributes to the decrease of conformational entropy near carboxyl and sulfate groups. This observation can indicate the higher affinity between glycosaminoglycans and albumin. Moreover, domains IIIA and IIIB of albumin have the highest affinity as those are two domains that show a positive net charge that allows for binding with negatively charged glycosaminoglycans. Finally, in discussion, we suggest some research path to find particular features that would carry information about the dynamics of the particular type of polymers or ions.
Collapse
|
54
|
Dash R, Munni YA, Mitra S, Choi HJ, Jahan SI, Chowdhury A, Jang TJ, Moon IS. Dynamic insights into the effects of nonsynonymous polymorphisms (nsSNPs) on loss of TREM2 function. Sci Rep 2022; 12:9378. [PMID: 35672339 PMCID: PMC9174165 DOI: 10.1038/s41598-022-13120-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
Single nucleotide variations in Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) are associated with many neurodegenerative diseases, including Nasu-Hakola disease (NHD), frontotemporal dementia (FTD), and late-onset Alzheimer's disease because they disrupt ligand binding to the extracellular domain of TREM2. However, the effects of nonsynonymous single nucleotide polymorphisms (nsSNPs) in TREM2 on disease progression remain unknown. In this study, we identified several high-risk nsSNPs in the TREM2 gene using various deleterious SNP predicting algorithms and analyzed their destabilizing effects on the ligand recognizing region of the TREM2 immunoglobulin (Ig) domain by molecular dynamics (MD) simulation. Cumulative prediction by all tools employed suggested the three most deleterious nsSNPs involved in loss of TREM2 function are rs549402254 (W50S), rs749358844 (R52C), and rs1409131974 (D104G). MD simulation showed that these three variants cause substantial structural alterations and conformational remodeling of the apical loops of the TREM2 Ig domain, which is responsible for ligand recognition. Detailed analysis revealed that these variants substantially increased distances between apical loops and induced conformation remodeling by changing inter-loop nonbonded contacts. Moreover, all nsSNPs changed the electrostatic potentials near the putative ligand-interacting region (PLIR), which suggested they might reduce specificity or loss of binding affinity for TREM2 ligands. Overall, this study identifies three potential high-risk nsSNPs in the TREM2 gene. We propose further studies on the molecular mechanisms responsible for loss of TREM2 function and the associations between TREM2 nsSNPs and neurodegenerative diseases.
Collapse
Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Sarmistha Mitra
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Ho Jin Choi
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Sultana Israt Jahan
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Apusi Chowdhury
- Department of Pharmaceutical Science, North-South University, Dhaka, 1229, Bangladesh
| | - Tae Jung Jang
- Department of Pathology, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
| |
Collapse
|
55
|
Parihar A, Sonia ZF, Akter F, Ali MA, Hakim FT, Hossain MS. Phytochemicals-based targeting RdRp and main protease of SARS-CoV-2 using docking and steered molecular dynamic simulation: A promising therapeutic approach for Tackling COVID-19. Comput Biol Med 2022; 145:105468. [PMID: 35390745 PMCID: PMC8964014 DOI: 10.1016/j.compbiomed.2022.105468] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/27/2022] [Accepted: 03/27/2022] [Indexed: 02/05/2023]
Abstract
The ongoing COVID-19 pandemic has affected millions of people worldwide and caused substantial socio-economic losses. Few successful vaccine candidates have been approved against SARS-CoV-2; however, their therapeutic efficacy against the mutated strains of the virus remains questionable. Furthermore, the limited supply of vaccines and promising antiviral drugs have created havoc in the present scenario. Plant-based phytochemicals (bioactive molecules) are promising because of their low side effects and high therapeutic value. In this study, we aimed to screen for suitable phytochemicals with higher therapeutic value using the two most crucial proteins of SARS-CoV-2, the RNA-dependent RNA polymerase (RdRp) and main protease (Mpro). We used computational tools such as molecular docking and steered molecular dynamics simulations to gain insights into the different types of interactions and estimated the relative binding forces between the phytochemicals and their respective targets. To the best of our knowledge, this is the first report that not only involves a search for a therapeutic bioactive molecule but also sheds light on the mechanisms underlying target inhibition in terms of calculations of force and work needed to extractthe ligand from the pocket of its target. The complexes showing higher binding forces were subjected to 200 ns molecular dynamic simulations to check the stability of the ligand inside the binding pocket. Our results suggested that isoskimmiwallin and terflavin A are potential inhibitors of RdRp, whereas isoquercitrin and isoorientin are the lead molecules against Mpro. Collectively, our findings could potentially aid in the development of novel therapeutics against COVID-19.
Collapse
Affiliation(s)
- Arpana Parihar
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, 462026, MP, India,Corresponding author
| | - Zannatul Ferdous Sonia
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Farjana Akter
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Fuad Taufiqul Hakim
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Md Shahadat Hossain
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| |
Collapse
|
56
|
Yadav J, Singh H, Pal SK, Das S, Srivastava VK, Jyoti A, Sharma V, Kumar S, Kaushik S. Exploring the molecular interaction of Pheniramine with Enterococcus faecalis Homoserine Kinase: In-silico and in vitro studies. J Mol Recognit 2022; 35:e2979. [PMID: 35642097 DOI: 10.1002/jmr.2979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 05/03/2022] [Accepted: 05/26/2022] [Indexed: 11/07/2022]
Abstract
Infections caused by the bacteria Enterococcus faecalis (also known as E. faecalis) are common in hospitals. This bacterium is resistant to a wide range of medicines and causes a variety of nosocomial infections. An increase in the number of infections caused by multidrug-resistant (MDR) bacteria is causing substantial economic and health issues around the world. Consequently, new therapeutic techniques to tackle the growing threat of E. faecalis infections must be developed as soon as possible. In this regard, we have targeted a protein that is regarded to be critical for the survival of bacteria in this experiment. Homoserine kinase (HSK) is a threonine metabolism enzyme that belongs to the GHMP kinase superfamily. It is a crucial enzyme in threonine metabolism. This enzyme is responsible for a critical step in the threonine biosynthesis pathway. Given the important function that E. faecalis Homoserine Kinase (ESK) plays in bacterial metabolism, we proposed that E. faecalis HSK be cloned, overexpressed, purified, and subjected to structural analyses using homology modelling. In addition, we have reported on the model's molecular docking and Molecular Dynamic Stimulation (MD Stimulation) investigations to validate the results of the docking experiments. The results were promising. In silico investigations came up with the conclusion: pheniramine has good binding affinity for the E. faecalis HSK.
Collapse
Affiliation(s)
- Jyoti Yadav
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Harpreet Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sudhir Kumar Pal
- Centre for Bioseparation Technology, VIT University, Vellore, India
| | - Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | | | - Anupam Jyoti
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Chandigarh, India
| | - Vinay Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanjit Kumar
- Centre for Bioseparation Technology, VIT University, Vellore, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| |
Collapse
|
57
|
Jukič M, Auger R, Folcher V, Proj M, Barreteau H, Gobec S, Touzé T. Towards discovery of inhibitors of the undecaprenyl-pyrophosphate phosphatase BacA by virtual high-throughput screening. Comput Struct Biotechnol J 2022; 20:2360-2371. [PMID: 35664230 PMCID: PMC9127117 DOI: 10.1016/j.csbj.2022.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/01/2022] Open
Abstract
BacA is an important conserved bacterial protein and a promising drug target. We identified the first small molecule inhibitors of BacA via ensemble docking. Novel inhibitors possess 5-sulfamoyl-2-thenoic acid scaffold. Hit compounds display IC50s from 42 to 374 μM and antibacterial activity on E. coli. Reported compounds are a valuable starting point for new antibacterial drug design.
Increasing resistance to common antibiotics is becoming a major challenge that requires the development of new antibacterial agents. Peptidoglycan is an essential heteropolymer of the bacterial envelope that ensures the integrity and shape of all bacteria and is also an important target for antibiotics. The biosynthesis of peptidoglycan depends on a lipid carrier, undecaprenyl phosphate. As a byproduct of peptidoglycan polymerization, the lipid carrier is released as undecaprenyl pyrophosphate, which must be recycled to allow new polymerization cycles. To this end, it undergoes a dephosphorylation process catalyzed by the membrane phosphatase BacA, which is specific and highly conserved in bacteria. In the present study, we identified small molecules displaying inhibitory potency towards BacA. We began by preparing a commercial compound library, followed by high-throughput virtual screening by ensemble docking using the 3D structure of BacA and molecular dynamics snapshots to account for the flexibility of the protein. Of 83 compounds computationally selected and tested in a biochemical assay, one sulfamoylthiophene molecule showed significant inhibition of the undecaprenyl pyrophosphate dephosphorylation activity catalyzed by BacA. Subsequently, an additional 33 scaffold analogs were selected and acquired, of which 6 compounds exhibited BacA inhibition. The IC50 values of these compounds ranged from 42 to 366 μM. In addition, significant antibacterial activity against Escherichia coli was observed in TolC/PAP2-depleted strains. We believe that the overall strategy followed in this study and the identified class of inhibitors provide a solid foundation for the further development of potent BacA-targeted inhibitors and the discovery of novel antibacterial compounds.
Collapse
|
58
|
In vitro antioxidant and cytotoxicity activities and in silico anticancer property of methanolic leaf extract of Leucas indica. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
59
|
Raj V, Lee JH, Shim JJ, Lee J. Antiviral activities of 4H-chromen-4-one scaffold-containing flavonoids against SARS-CoV-2 using computational and in vitro approaches. J Mol Liq 2022; 353:118775. [PMID: 35194277 PMCID: PMC8849861 DOI: 10.1016/j.molliq.2022.118775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 10/14/2021] [Accepted: 02/15/2022] [Indexed: 12/19/2022]
Abstract
The widespread outbreak of the novel coronavirus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused the main health challenge worldwide. This pandemic has attracted the attention of the research communities in various fields, prompting efforts to discover rapid drug molecules for the treatment of the life-threatening COVID-19 disease. This study is aimed at investigating 4H-chromen-4-one scaffold-containing flavonoids that combat the SARS-CoV-2 virus using computational and in vitro approaches. Virtual screening studies of the molecule's library for 4H-chromen-4-one scaffold were performed with the recently reported coronavirus main protease (Mpro, also called 3CLpro) because it plays an essential role in the maturation and processing of the viral polyprotein. Based on the virtual screening, the top hit molecules such as isoginkgetin and afzelin molecules were selected for further estimating in vitro antiviral efficacies against SARS-CoV-2 in Vero cells. Additionally, these molecules were also docked with RNA-dependent RNA Polymerase (RdRp) to reveal the ligands-protein molecular interaction. In the in vitro study, isoginkgetin showed remarkable inhibition potency against the SARS-CoV-2 virus, with an IC50 value of 22.81 μM, compared to remdesivir, chloroquine, and lopinavir with IC50 values of 7.18, 11.63, and 11.49 μM, respectively. Furthermore, the complex stability of isoginkgetin with an active binding pocket of the SARS-CoV-2 Mpro and RdRp supports its inhibitory potency against the SARS-CoV-2. Thus, isoginkgetin is a potent leading drug candidate and needs to be used in in vivo trials for the treatment of SARS-CoV-2 infected patients.
Collapse
|
60
|
Discovery of a new generation of angiotensin receptor blocking drugs: receptor mechanisms and in silico binding to enzymes relevant to covid-19. Comput Struct Biotechnol J 2022; 20:2091-2111. [PMID: 35432786 PMCID: PMC8994259 DOI: 10.1016/j.csbj.2022.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 12/14/2022] Open
Abstract
The discovery and facile synthesis of a new class of sartan-like arterial antihypertensive drugs (angiotensin receptor blockers [ARBs]), subsequently referred to as “bisartans” is reported. In vivo results and complementary molecular modelling presented in this communication indicate bisartans may be beneficial for the treatment of not only heart disease, diabetes, renal dysfunction, and related illnesses, but possibly COVID-19. Bisartans are novel bis-alkylated imidazole sartan derivatives bearing dual symmetric anionic biphenyl tetrazole moieties. In silico docking and molecular dynamics studies revealed bisartans exhibited higher binding affinities for the ACE2/spike protein complex (PDB 6LZG) compared to all other known sartans. They also underwent stable docking to the Zn2+ domain of the ACE2 catalytic site as well as the critical interfacial region between ACE2 and the SARS-CoV-2 receptor binding domain. Additionally, semi-stable docking of bisartans at the arginine-rich furin-cleavage site of the SARS-CoV-2 spike protein (residues 681–686) required for virus entry into host cells, suggest bisartans may inhibit furin action thereby retarding viral entry into host cells. Bisartan tetrazole groups surpass nitrile, the pharmacophoric “warhead” of PF-07321332, in its ability to disrupt the cysteine charge relay system of 3CLpro. However, despite the apparent targeting of multifunctional sites, bisartans do not inhibit SARS-CoV-2 infection in bioassays as effectively as PF-07321332 (Paxlovid).
Collapse
|
61
|
Rafaee A, Kashani-Amin E, Meybodi AM, Ebrahim-Habibi A, Sabbaghian M. Structural modeling of human AKAP3 protein and in silico analysis of single nucleotide polymorphisms associated with sperm motility. Sci Rep 2022; 12:3656. [PMID: 35256641 PMCID: PMC8901789 DOI: 10.1038/s41598-022-07513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/28/2022] [Indexed: 11/20/2022] Open
Abstract
AKAP3 is a member of the A-kinase anchoring proteins and it is a constituent of the sperm fibrous sheath. AKAP3 is needed for the formation of sperm flagellum structure, sperm motility, and male fertility. This study aims to model the AKAP3 tertiary structure and identify the probable impact of four mutations characterized in infertile men on the AKAP3 structure. The T464S, I500T, E525K, and I661T substitutions were analyzed using in silico methods. The secondary structure and three-dimensional model of AKAP3 were determined using PSI-BLAST based secondary structure prediction and Robetta servers. The TM-score was used to quantitatively measure the structural similarities between native and mutated models. All of the desired substitutions were classified as benign. I-Mutant results showed all of the substitutions decreased AKAP3 stability; however, the I500T and I661T were more effective. Superposition and secondary structure comparisons between native and mutants showed no dramatic deviations. Our study provided an appropriate model for AKAP3. Destabilization of AKAP3 caused by these substitutions did not appear to induce structural disturbances. As AKAP3 is involved in male infertility, providing more structural insights and the impact of mutations that cause protein functional diversity could elucidate the etiology of male fertility problems at molecular level.
Collapse
Affiliation(s)
- Alemeh Rafaee
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Elaheh Kashani-Amin
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Anahita Mohseni Meybodi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Marjan Sabbaghian
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| |
Collapse
|
62
|
Gadgoli UB, Y C SK, Kumar D, Pai MM, Pulya S, Ghosh B, Kulkarni OP. Estrogenic Activity of Tetrazole Derivatives Bearing Bisphenol Structures: Computational Studies, Synthesis, and In Vitro Assessment. J Chem Inf Model 2022; 62:854-873. [PMID: 35143200 DOI: 10.1021/acs.jcim.1c01077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The classification of bisphenol A (BPA) as an industrial endocrine disruptor has led to a ban of this ubiquitous critical starting material from food and medical applications. Thus, scientists worldwide are researching to develop non-ER binding starting compounds to fulfill unmet market needs. In line with this trending research topic, the current paper highlights the development of tetrazole derivatives bearing a bisphenol structure (TbB) as a novel weak binder or potential inactive to the estrogen receptor (ER) and androgen receptor (AR). The structure and ligand-based approach supported by binding affinity analysis, electrostatic complementarity, ADMET prediction, and in silico studies identified TbBs as privileged substitutes for BPA. Five TbB ligands were successfully synthesized and subjected to biological testing comprising radioligand competitive binding and functional cellular assays. The measured IC50 value for BPA was found to be 0.24 μM, whereas all the inhibitions were less than 15% for the two TbB ligands, 223-2 and 223-3. As these TbB ligands did not meet the established acceptance criteria of 50% inhibition, they are considered as extremely weak binders to ERα. Steric clashes, the desolvation effect, and the increased total polar surface area (TPSA) of TbB ligands in the hydrophobic binding site are hypothesized to be possible reasons for low binding. Modeling studies complemented by bioassays highlight TbB compounds as privileged prospective BPA replacements. However, more research on TbB ligand toxicity is needed to understand and substantiate that the adverse effects on the hormonal system, for example, via metabolic activation, are not elicited.
Collapse
Affiliation(s)
- Umesh B Gadgoli
- Department of Chemistry, M.S. Ramaiah University of Applied Sciences, Bengaluru, Karnataka 560054, India
| | - Sunil Kumar Y C
- Department of Chemistry, M.S. Ramaiah University of Applied Sciences, Bengaluru, Karnataka 560054, India
| | - Deepak Kumar
- Department of Chemistry, M.S. Ramaiah University of Applied Sciences, Bengaluru, Karnataka 560054, India
| | - Ms Maya Pai
- Department of Chemistry, M.S. Ramaiah University of Applied Sciences, Bengaluru, Karnataka 560054, India
| | - Sravani Pulya
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Medchal, Hyderabad 500078, India
| | - Balaram Ghosh
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Medchal, Hyderabad 500078, India
| | - Onkar Prakash Kulkarni
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Medchal, Hyderabad 500078, India
| |
Collapse
|
63
|
Bhatt DP, Mills CA, Anderson KA, Henriques BJ, Lucas TG, Francisco S, Liu J, Ilkayeva OR, Adams AE, Kulkarni SR, Backos DS, Major MB, Grimsrud PA, Gomes CM, Hirschey MD. Deglutarylation of glutaryl-CoA dehydrogenase by deacylating enzyme SIRT5 promotes lysine oxidation in mice. J Biol Chem 2022; 298:101723. [PMID: 35157847 PMCID: PMC8969154 DOI: 10.1016/j.jbc.2022.101723] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022] Open
Abstract
A wide range of protein acyl modifications has been identified on enzymes across various metabolic processes; however, the impact of these modifications remains poorly understood. Protein glutarylation is a recently identified modification that can be nonenzymatically driven by glutaryl-CoA. In mammalian systems, this unique metabolite is only produced in the lysine and tryptophan oxidative pathways. To better understand the biology of protein glutarylation, we studied the relationship between enzymes within the lysine/tryptophan catabolic pathways, protein glutarylation, and regulation by the deglutarylating enzyme sirtuin 5 (SIRT5). Here, we identify glutarylation on the lysine oxidation pathway enzyme glutaryl-CoA dehydrogenase (GCDH) and show increased GCDH glutarylation when glutaryl-CoA production is stimulated by lysine catabolism. Our data reveal that glutarylation of GCDH impacts its function, ultimately decreasing lysine oxidation. We also demonstrate the ability of SIRT5 to deglutarylate GCDH, restoring its enzymatic activity. Finally, metabolomic and bioinformatic analyses indicate an expanded role for SIRT5 in regulating amino acid metabolism. Together, these data support a feedback loop model within the lysine/tryptophan oxidation pathway in which glutaryl-CoA is produced, in turn inhibiting GCDH function via glutaryl modification of GCDH lysine residues and can be relieved by SIRT5 deacylation activity.
Collapse
|
64
|
Niederquell A, Stoyanov E, Kuentz M. Hydroxypropyl Cellulose for Drug Precipitation Inhibition: From the Potential of Molecular Interactions to Performance Considering Microrheology. Mol Pharm 2022; 19:690-703. [PMID: 35005970 DOI: 10.1021/acs.molpharmaceut.1c00832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
There has been recent interest in using hydroxypropyl cellulose (HPC) for supersaturating drug formulations. This study investigated the potential for molecular HPC interactions with the model drug celecoxib by integrating novel approaches in the field of drug supersaturation analysis. Following an initial polymer characterization study, quantum-chemical calculations and molecular dynamics simulations were complemented with results of inverse gas chromatography and broadband diffusing wave spectroscopy. HPC performance was studied regarding drug solubilization and kinetics of desupersaturation using different grades (i.e., HPC-UL, SSL, SL, and L). The results suggested that the potential contribution of dispersive interactions and hydrogen bonding depended strongly on the absence or presence of the aqueous phase. It was proposed that aggregation of HPC polymer chains provided a complex heterogeneity of molecular environments with more or less excluded water for drug interaction. In precipitation experiments at a low aqueous polymer concentration (i.e., 0.01%, w/w), grades L and SL appeared to sustain drug supersaturation better than SSL and UL. However, UL was particularly effective in drug solubilization at pH 6.8. Thus, a better understanding of drug-polymer interactions is important for formulation development, and polymer blends may be used to harness the combined advantages of individual polymer grades.
Collapse
Affiliation(s)
- Andreas Niederquell
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz CH 4132, Switzerland
| | - Edmont Stoyanov
- Nisso Chemical, Europe, Berliner Allee 42, Düsseldorf 40212, Germany
| | - Martin Kuentz
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz CH 4132, Switzerland
| |
Collapse
|
65
|
Bełdowski P, Przybyłek M, Sionkowska A, Cysewski P, Gadomska M, Musiał K, Gadomski A. Effect of Chitosan Deacetylation on Its Affinity to Type III Collagen: A Molecular Dynamics Study. MATERIALS (BASEL, SWITZERLAND) 2022; 15:463. [PMID: 35057179 PMCID: PMC8781747 DOI: 10.3390/ma15020463] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 02/04/2023]
Abstract
The ability to form strong intermolecular interactions by linear glucosamine polysaccharides with collagen is strictly related to their nonlinear dynamic behavior and hence bio-lubricating features. Type III collagen plays a crucial role in tissue regeneration, and its presence in the articular cartilage affects its bio-technical features. In this study, the molecular dynamics methodology was applied to evaluate the effect of deacetylation degree on the chitosan affinity to type III collagen. The computational procedure employed docking and geometry optimizations of different chitosan structures characterized by randomly distributed deacetylated groups. The eight different degrees of deacetylation from 12.5% to 100% were taken into account. We found an increasing linear trend (R2 = 0.97) between deacetylation degree and the collagen-chitosan interaction energy. This can be explained by replacing weak hydrophobic contacts with more stable hydrogen bonds involving amino groups in N-deacetylated chitosan moieties. In this study, the properties of chitosan were compared with hyaluronic acid, which is a natural component of synovial fluid and cartilage. As we found, when the degree of deacetylation of chitosan was greater than 0.4, it exhibited a higher affinity for collagen than in the case of hyaluronic acid.
Collapse
Affiliation(s)
- Piotr Bełdowski
- Institute of Mathematics & Physics, Bydgoszcz University of Science & Technology, 85-796 Bydgoszcz, Poland;
| | - Maciej Przybyłek
- Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950 Bydgoszcz, Poland; (M.P.); (P.C.)
| | - Alina Sionkowska
- Department of Biomaterials and Cosmetics Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarin 7, 87-100 Toruń, Poland; (A.S.); (M.G.); (K.M.)
| | - Piotr Cysewski
- Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950 Bydgoszcz, Poland; (M.P.); (P.C.)
| | - Magdalena Gadomska
- Department of Biomaterials and Cosmetics Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarin 7, 87-100 Toruń, Poland; (A.S.); (M.G.); (K.M.)
| | - Katarzyna Musiał
- Department of Biomaterials and Cosmetics Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarin 7, 87-100 Toruń, Poland; (A.S.); (M.G.); (K.M.)
| | - Adam Gadomski
- Institute of Mathematics & Physics, Bydgoszcz University of Science & Technology, 85-796 Bydgoszcz, Poland;
| |
Collapse
|
66
|
Mitrović A, Senjor E, Jukić M, Bolčina L, Prunk M, Proj M, Nanut MP, Gobec S, Kos J. New inhibitors of cathepsin V impair tumor cell proliferation and elastin degradation and increase immune cell cytotoxicity. Comput Struct Biotechnol J 2022; 20:4667-4687. [PMID: 36147668 PMCID: PMC9459403 DOI: 10.1016/j.csbj.2022.08.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 11/26/2022] Open
Abstract
Identification of novel potent inhibitors of lysosomal cysteine peptidase cathepsin V. New inhibitors of cathepsin V demonstrated antitumor activity. They impair tumor cell proliferation and elastase degradation and increase immune cell cytotoxicity. Cathepsin V inhibitor impaired conversion of immunosuppressive factor cystatin F to its active monomeric form.
Cathepsin V is a human lysosomal cysteine peptidase with specific functions during pathological processes and is as such a promising therapeutic target. Peptidase inhibitors represent powerful pharmacological tools for regulating excessive proteolytic activity in various diseases. Cathepsin V is highly related to cathepsin L but differs in tissue distribution, binding site morphology, substrate specificity, and function. To validate its therapeutic potential and extend the number of potent and selective cathepsin V inhibitors, we used virtual high-throughput screening of commercially available compound libraries followed by an evaluation of kinetic properties to identify novel potent and selective cathepsin V inhibitors. We identified the ureido methylpiperidine carboxylate derivative, compound 7, as a reversible, selective, and potent inhibitor of cathepsin V. It also exhibited the most preferable characteristics for further evaluation with in vitro functional assays that simulate the processes in which cathepsin V is known to play an important role. Compound 7 exerted significant effects on cell proliferation, elastin degradation, and immune cell cytotoxicity. The latter was increased because compound 7 impaired conversion of immunosuppressive factor cystatin F to its active monomeric form. Taken together, our results present novel potent inhibitors of cathepsin V and provide new hit compounds for detailed development and optimization. Further, we demonstrate that cathepsin V is a potential target for new approaches to cancer therapy.
Collapse
Affiliation(s)
- Ana Mitrović
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
- Corresponding author at: Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.
| | - Emanuela Senjor
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Marko Jukić
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lara Bolčina
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Mateja Prunk
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Matic Proj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Milica Perišić Nanut
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janko Kos
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| |
Collapse
|
67
|
Zanfirescu A, Nitulescu G, Mihai DP, Nitulescu GM. Identifying FAAH Inhibitors as New Therapeutic Options for the Treatment of Chronic Pain through Drug Repurposing. Pharmaceuticals (Basel) 2021; 15:38. [PMID: 35056095 PMCID: PMC8781999 DOI: 10.3390/ph15010038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 01/29/2023] Open
Abstract
Chronic pain determines a substantial burden on individuals, employers, healthcare systems, and society. Most of the affected patients report dissatisfaction with currently available treatments. There are only a few and poor therapeutic options-some therapeutic agents are an outgrowth of drugs targeting acute pain, while others have several serious side effects. One of the primary degradative enzymes for endocannabinoids, fatty acid amide hydrolase (FAAH) attracted attention as a significant molecular target for developing new therapies for neuropsychiatric and neurological diseases, including chronic pain. Using chemical graph mining, quantitative structure-activity relationship (QSAR) modeling, and molecular docking techniques we developed a multi-step screening protocol to identify repurposable drugs as FAAH inhibitors. After screening the DrugBank database using our protocol, 273 structures were selected, with five already approved drugs, montelukast, repaglinide, revefenacin, raloxifene, and buclizine emerging as the most promising repurposable agents for treating chronic pain. Molecular docking studies indicated that the selected compounds interact with the enzyme mostly non-covalently (except for revefenacin) through shape complementarity to the large substrate-binding pocket in the active site. A molecular dynamics simulation was employed for montelukast and revealed stable interactions with the enzyme. The biological activity of the selected compounds should be further confirmed by employing in vitro and in vivo studies.
Collapse
Affiliation(s)
- Anca Zanfirescu
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania
| | - Georgiana Nitulescu
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania
| | - Dragos Paul Mihai
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania
| | - George Mihai Nitulescu
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania
| |
Collapse
|
68
|
Sultana MUC, Uddin MG, Hossain MB, Ali MA, Sonia ZF, Kamal S, Halim MA. Molecular dynamics investigation of ivermectin bound to importin alpha/beta heterodimer. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.2015066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Mossammad U. C. Sultana
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md. Giash Uddin
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
- Department of Pharmacy, University of Chittagong, Chittagong, Bangladesh
| | - Md. Billal Hossain
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Zannatul Ferdous Sonia
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Suprio Kamal
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| |
Collapse
|
69
|
Sami SA, Marma KKS, Mahmud S, Khan MAN, Albogami S, El-Shehawi AM, Rakib A, Chakraborty A, Mohiuddin M, Dhama K, Uddin MMN, Hossain MK, Tallei TE, Emran TB. Designing of a Multi-epitope Vaccine against the Structural Proteins of Marburg Virus Exploiting the Immunoinformatics Approach. ACS OMEGA 2021; 6:32043-32071. [PMID: 34870027 PMCID: PMC8638006 DOI: 10.1021/acsomega.1c04817] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 05/08/2023]
Abstract
Marburg virus disease (MVD) caused by the Marburg virus (MARV) generally appears with flu-like symptoms and leads to severe hemorrhagic fever. It spreads via direct contact with infected individuals or animals. Despite being considered to be less threatening in terms of appearances and the number of infected patients, the high fatality rate of this pathogenic virus is a major concern. Until now, no vaccine has been developed to combat this deadly virus. Therefore, vaccination for this virus is necessary to reduce its mortality. Our current investigation focuses on the design and formulation of a multi-epitope vaccine based on the structural proteins of MARV employing immunoinformatics approaches. The screening of potential T-cell and B-cell epitopes from the seven structural proteins of MARV was carried out through specific selection parameters. Afterward, we compiled the shortlisted epitopes by attaching them to an appropriate adjuvant and linkers. Population coverage analysis, conservancy analysis, and MHC cluster analysis of the shortlisted epitopes were satisfactory. Importantly, physicochemical characteristics, human homology assessment, and structure validation of the vaccine construct delineated convenient outcomes. We implemented disulfide bond engineering to stabilize the tertiary or quaternary interactions. Furthermore, stability and physical movements of the vaccine protein were explored using normal-mode analysis. The immune simulation study of the vaccine complexes also exhibited significant results. Additionally, the protein-protein docking and molecular dynamics simulation of the final construct exhibited a higher affinity toward toll-like receptor-4 (TLR4). From simulation trajectories, multiple descriptors, namely, root mean square deviations (rmsd), radius of gyration (Rg), root mean square fluctuations (RMSF), solvent-accessible surface area (SASA), and hydrogen bonds, have been taken into account to demonstrate the inflexible and rigid nature of receptor molecules and the constructed vaccine. Inclusively, our findings suggested the vaccine constructs' ability to regulate promising immune responses against MARV pathogenesis.
Collapse
Affiliation(s)
- Saad Ahmed Sami
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Kay Kay Shain Marma
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Shafi Mahmud
- Microbiology
Laboratory, Bioinformatics Division, Department of Genetic Engineering
and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Asif Nadim Khan
- Department of Biochemistry and Molecular
Biology, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh
| | - Sarah Albogami
- Department
of Biotechnology, College of Science, Taif
University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed M. El-Shehawi
- Department
of Biotechnology, College of Science, Taif
University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Rakib
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Agnila Chakraborty
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Mostafah Mohiuddin
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary
Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Mir Muhammad Nasir Uddin
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Mohammed Kamrul Hossain
- Department of Pharmacy,
Faculty of Biological Sciences, University
of Chittagong, Chittagong 4331, Bangladesh
| | - Trina Ekawati Tallei
- Department of Biology,
Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi 95115, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| |
Collapse
|
70
|
Shakil S. Molecular interaction of inhibitors with human brain butyrylcholinesterase. EXCLI JOURNAL 2021; 20:1597-1607. [PMID: 35024017 PMCID: PMC8743831 DOI: 10.17179/excli2021-4418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/16/2021] [Indexed: 11/17/2022]
Abstract
Alzheimer's disease is a topic of deep research interest across the global scientific community. Butyrylcholinesterase (BuChE) is an important enzyme, and an interesting anti-Alzheimer's target. Identification or fresh design of promising BuChE-inhibitors is warranted. Virtual screening supported by molecular dynamics simulations has emerged as a key component of present drug-discovery cascades. The research piece aimed at identification of a putative BuChE-inhibitor as a fresh molecular frame that might aid drug design in the context of Alzheimer's disease. The study utilized 'MCULE' to screen a set of 5 million ligands to test their ability to bind to human BuChE. Pharmacokinetic profiling was achieved by the 'SWISS ADME' program. Toxicities were duly assessed. YASARA STRUCTURE version 20.10.4.W.64 was employed to run 133 ns molecular dynamics (MD) simulation for the complex of 'the top screened out inhibitor' and 'the human BuChE enzyme'. The simulation was executed for approx. 4 days (~93 hrs) on an HP ZR30w workstation. YANACONDA, a special language contained in YASARA STRUCTURE was employed to perform complex tasks. Fine resolution figures (notably the RMSD vs time plot) were created. Snapshots were extracted at every 250 ps. The selected ligand, (3-Bromophenyl)[5-(4-chlorophenyl)-5-hydroxy-3-(trifluoromethyl)-4,5-dihydro-1H-pyrazol-1-yl]methanone, exhibited the best overall binding with human BuChE. It interacted with human BuChE through 19 residues. Markedly, 9 of the 19 residues were confirmed to be matching to those of the reference complex (PDB ID 5DYW). Trajectory analysis returned 533 snapshots. The RMSD versus time plot indicated that around 22 ns, equilibrium was achieved and, from then on, the 'BuChE-Top inhibitor' complex remained predominantly stable. From 22 ns and onwards till 133 ns, the backbone RMSD fluctuations were observed to remain limited within a range of 1.2-1.9 Å. The molecule, (3-Bromophenyl)[5-(4-chlorophenyl)-5-hydroxy-3-(trifluoromethyl)-4,5-dihydro-1H-pyrazol-1-yl]methanone, satisfied ADMET requirements. Additionally, the feasibility of the proposed enzyme-inhibitor complex was supported by an adequately extended MD simulation of 133 ns. Hence, the proposed molecule could be a likely lead for designing inhibitor(s) against human BuChE. Scope remains for validatory wet laboratory investigation.
Collapse
Affiliation(s)
- Shazi Shakil
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia,*To whom correspondence should be addressed: Shazi Shakil, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia, E-mail: ,
| |
Collapse
|
71
|
Ramírez-Palacios C, Wijma HJ, Thallmair S, Marrink SJ, Janssen DB. Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:5569-5580. [PMID: 34653331 PMCID: PMC8611723 DOI: 10.1021/acs.jcim.1c00617] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ω-Transaminases (ω-TAs) catalyze the conversion of ketones to chiral amines, often with high enantioselectivity and specificity, which makes them attractive for industrial production of chiral amines. Tailoring ω-TAs to accept non-natural substrates is necessary because of their limited substrate range. We present a computational protocol for predicting the enantioselectivity and catalytic selectivity of an ω-TA from Vibrio fluvialis with different substrates and benchmark it against 62 compounds gathered from the literature. Rosetta-generated complexes containing an external aldimine intermediate of the transamination reaction are used as starting conformations for multiple short independent molecular dynamics (MD) simulations. The combination of molecular docking and MD simulations ensures sufficient and accurate sampling of the relevant conformational space. Based on the frequency of near-attack conformations observed during the MD trajectories, enantioselectivities can be quantitatively predicted. The predicted enantioselectivities are in agreement with a benchmark dataset of experimentally determined ee% values. The substrate-range predictions can be based on the docking score of the external aldimine intermediate. The low computational cost required to run the presented framework makes it feasible for use in enzyme design to screen thousands of enzyme variants.
Collapse
Affiliation(s)
- Carlos Ramírez-Palacios
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sebastian Thallmair
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.,Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany
| | - Siewert J Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
72
|
Akter S, Hossain S, Ali MA, Hosen MI, Shekhar HU. Comprehensive Characterization of the Coding and Non-Coding Single Nucleotide Polymorphisms in the Tumor Protein p63 (TP63) Gene Using In Silico Tools. Biomolecules 2021; 11:1733. [PMID: 34827731 PMCID: PMC8637305 DOI: 10.3390/biom11111733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/08/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) help to understand the phenotypic variations in humans. Genome-wide association studies (GWAS) have identified SNPs located in the tumor protein 63 (TP63) locus to be associated with the genetic susceptibility of cancers. However, there is a lack of in-depth characterization of the structural and functional impacts of the SNPs located at the TP63 gene. The current study was designed for the comprehensive characterization of the coding and non-coding SNPs in the human TP63 gene for their functional and structural significance. The functional and structural effects of the SNPs were investigated using a wide variety of computational tools and approaches, including molecular dynamics (MD) simulation. The deleterious impact of eight nonsynonymous SNPs (nsSNPs) affecting protein stability, structure, and functions was measured by using 13 bioinformatics tools. These eight nsSNPs are in highly conserved positions in protein and were predicted to decrease protein stability and have a deleterious impact on the TP63 protein function. Molecular docking analysis showed five nsSNPs to reduce the binding affinity of TP63 protein to DNA with significant results for three SNPs (R319H, G349E, and C347F). Further, MD simulations revealed the possible disruption of TP63 and DNA binding, hampering the essential protein function. PolymiRTS study found five non-coding SNPs in miRNA binding sites, and the GTEx portal recognized five eQTLs SNPs in single tissue of the lung, heart (LV), and cerebral hemisphere (brain). Characterized nsSNPs and non-coding SNPs will help researchers to focus on TP63 gene loci and ascertain their association with certain diseases.
Collapse
Affiliation(s)
- Shamima Akter
- Department of Bioinformatics and Computational Biology, George Mason University, Fairfax, VA 22030, USA;
| | - Shafaat Hossain
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh; (S.H.); (M.I.H.)
| | - Md. Ackas Ali
- Division of Computer Aided Drug-Design, The Red-Green Research Center, 16, Tejkunipara, Tejgaon, Dhaka 1215, Bangladesh;
| | - Md. Ismail Hosen
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh; (S.H.); (M.I.H.)
| | - Hossain Uddin Shekhar
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh; (S.H.); (M.I.H.)
| |
Collapse
|
73
|
Eckert T, von Cosel J, Kamps B, Siebert HC, Zhang R, Zhang N, Gousias K, Petridis AK, Kanakis D, Falahati K. Evidence for Quantum Chemical Effects in Receptor-Ligand Binding Between Integrin and Collagen Fragments - A Computational Investigation With an Impact on Tissue Repair, Neurooncolgy and Glycobiology. Front Mol Biosci 2021; 8:756701. [PMID: 34869589 PMCID: PMC8637888 DOI: 10.3389/fmolb.2021.756701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/22/2021] [Indexed: 11/23/2022] Open
Abstract
The collagen-integrin interactions are mediated by the doubly charged Mg2+ cation. In nature this cation seems to have the optimal binding strength to stabilize this complex. It is essential that the binding is not too weak so that the complex becomes unstable, however, it is also of importance that the ligand-receptor binding is still labile enough so that the ligand can separate from the receptor in a suited environment. In the case of crystal growing for experimentally useful integrin-collagen fragment complexes it turned out that Co2+ cations are ideal mediators to form stable complexes for such experiments. Although, one can argue that Co2+ is in this context an artificial cation, however, it is now of special interest to test the impact of this cation in cell-culture experiments focusing on integrin-ligand interactions. In order to examine, in particular, the role cobalt ions we have studied a Co2+ based model system using quantum chemical calculations. Thereby, we have shown that hybrid and long-range corrected functional, which are approximations provide already a sufficient level of accuracy. It is of interest to study a potential impact of cations on the binding of collagen-fragments including collagens from various species because different integrins have numerous biological functions (e.g. Integrin - NCAM (Neural cell adhesion molecule) interactions) and are triggered by intact and degraded collagen fragments. Since integrin-carbohydrate interactions play a key role when bio-medical problems such as tumor cell adhesion and virus-host cell infections have to be addressed on a sub-molecular level it is essential to understand the interactions with heavy-metal ions also at the sub-atomic level. Our findings open new routes, especially, in the fields of tissue repair and neuro-oncology for example for cell-culture experiments with different ions. Since Co2+ ions seem to bind stronger to integrin than Mg2+ ions it should be feasible to exchange these cations in suited tumor tissues although different cations are present in other metalloproteins which are active in such tissues. Various staining methods can be applied to document the interactions of integrins with carbohydrate chains and other target structures. Thereby, it is possible to study a potential impact of these interactions on biological functions. It was therefore necessary to figure out first which histological-glycobiological experimental settings of tumor cells are suited for our purpose. Since the interactions of several metalloproteins (integrin, ADAM12) with polysialic acid and the HNK-1 epitope play a crucial role in tumor tissues selected staining methods are proper tools to obtain essential information about the impact of the metal ions under study.
Collapse
Affiliation(s)
- Thomas Eckert
- RISCC Research Institute for Scientific Computing and Consulting, Heuchelheim, Germany
- Institut für Veterinärphysiologie und Biochemie, Fachbereich Veterinärmedizin, Justus-Liebig- Universität Gießen, Gießen, Germany
- Fachbereich Biologie und Chemie, Hochschule Fresenius University of Applied Sciences, Idstein, Germany
| | - Jan von Cosel
- RISCC Research Institute for Scientific Computing and Consulting, Heuchelheim, Germany
| | - Benedict Kamps
- RISCC Research Institute for Scientific Computing and Consulting, Heuchelheim, Germany
- Fachbereich Biologie und Chemie, Hochschule Fresenius University of Applied Sciences, Idstein, Germany
| | | | - Ruiyan Zhang
- RI-B-NT Research Institute of Bioinformatics and Nanotechnology, Kiel, Germany
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng, China
| | - Ning Zhang
- RI-B-NT Research Institute of Bioinformatics and Nanotechnology, Kiel, Germany
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng, China
| | - Konstantinos Gousias
- Klinik für Neurochirurgie, Klinikum Lünen, St.-Marien-Hospital, Akad. Lehrkrankenhaus der Westf. Wilhelms-Universität Münster, Lünen, Germany
| | | | - Dimitrios Kanakis
- Institute of Pathology, University of Nicosia Medical School, Nicosia, Cyprus
| | - Konstantin Falahati
- RISCC Research Institute for Scientific Computing and Consulting, Heuchelheim, Germany
| |
Collapse
|
74
|
Bełdowski P, Przybyłek M, Raczyński P, Dedinaite A, Górny K, Wieland F, Dendzik Z, Sionkowska A, Claesson PM. Albumin-Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics. Int J Mol Sci 2021; 22:ijms222212360. [PMID: 34830249 PMCID: PMC8625520 DOI: 10.3390/ijms222212360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/28/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
The lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin is one of the major components in synovial fluid. Its electrostatic properties, including the ability to form molecular complexes, are closely related to pH, solvation, and the presence of ions. In the context of synovial fluid, it is relevant to describe the possible interactions between albumin and hyaluronate, taking into account solution composition effects. In this study, the influence of Na+, Mg2+, and Ca2+ ions on human serum albumin–hyaluronan interactions were examined using molecular dynamics tools. It was established that the presence of divalent cations, and especially Ca2+, contributes mostly to the increase of the affinity between hyaluronan and albumin, which is associated with charge compensation in negatively charged hyaluronan and albumin. Furthermore, the most probable binding sites were structurally and energetically characterized. The indicated moieties exhibit a locally positive charge which enables hyaluronate binding (direct and water mediated).
Collapse
Affiliation(s)
- Piotr Bełdowski
- Faculty of Chemical Technology and Engineering, Institute of Mathematics & Physics, Bydgoszcz University of Science & Technology, 85-796 Bydgoszcz, Poland
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Engineering Pedagogics, SE-100 44 Stockholm, Sweden;
- Correspondence:
| | - Maciej Przybyłek
- Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950 Bydgoszcz, Poland;
| | - Przemysław Raczyński
- Faculty of Science and Technology, University of Silesia in Katowice, 75 Pułku Piechoty 1A, 41-500 Chorzow, Poland; (P.R.); (K.G.); (Z.D.)
| | - Andra Dedinaite
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Engineering Pedagogics, SE-100 44 Stockholm, Sweden;
- Division of Bioscience and Materials, RISE Research Institutes of Sweden, SE-114 86 Stockholm, Sweden
| | - Krzysztof Górny
- Faculty of Science and Technology, University of Silesia in Katowice, 75 Pułku Piechoty 1A, 41-500 Chorzow, Poland; (P.R.); (K.G.); (Z.D.)
| | - Florian Wieland
- Helmholtz-Zentrum Hereon: Institute for metallic Biomaterials, Max-Planck-Straße 1, 21502 Geesthacht, Germany;
| | - Zbigniew Dendzik
- Faculty of Science and Technology, University of Silesia in Katowice, 75 Pułku Piechoty 1A, 41-500 Chorzow, Poland; (P.R.); (K.G.); (Z.D.)
| | - Alina Sionkowska
- Department of Biomaterials and Cosmetics Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarin 7, 87-100 Torun, Poland;
| | - Per M. Claesson
- KTH Royal Institute of Technology, Department of Chemistry, Surface and Corrosion Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, SE-100 44 Stockholm, Sweden;
| |
Collapse
|
75
|
Paul GK, Mahmud S, Hasan MM, Zaman S, Uddin MS, Saleh MA. Biochemical and in silico study of leaf and bark extracts from Aphanamixis polystachya against common pathogenic bacteria. Saudi J Biol Sci 2021; 28:6592-6605. [PMID: 34764775 PMCID: PMC8568816 DOI: 10.1016/j.sjbs.2021.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Aphanamixis polystachya may be a natural, renewable resource against antibiotic-resistant bacterial infections. The antibacterial activity of A. polystachya leaf and bark extracts was investigated against three antibiotic-resistant bacterial species and one fungus. Methanolic leaf extract showed only limited antibacterial activity but both methanolic and aqueous bark extract showed high antimicrobial activity. In an antioxidant activity test, leaf and bark extracts exhibited 50% free radical scavenging at a concentration of 107.14 ± 3.14 μg/mL and 97.13 ± 3.05 μg/mL, respectively, indicating that bark extracts offer more antioxidative activity than leaf extracts. Bark extracts also showed lower toxicity than leaf extracts. This suggests that bark extracts may offer greater development potential than leaf extracts. The molecular dynamics were also investigated through the simulated exploration of multiple potential interactions to understand the interaction dynamics (root-mean-square deviation, solvent-accessible surface area, radius of gyration, and the hydrogen bonding of chosen compounds to protein targets) and possible mechanisms of inhibition. This molecular modeling of compounds derived from A. polystachya revealed that inhibition may occur by binding to the active sites of the target proteins of the tested bacterial strains. A. polystachya bark extract may be used as a natural source of drugs to control antibiotic-resistant bacteria.
Collapse
Affiliation(s)
| | | | - Md. Mehedi Hasan
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| |
Collapse
|
76
|
Jukič M, Janežič D, Bren U. Potential Novel Thioether-Amide or Guanidine-Linker Class of SARS-CoV-2 Virus RNA-Dependent RNA Polymerase Inhibitors Identified by High-Throughput Virtual Screening Coupled to Free-Energy Calculations. Int J Mol Sci 2021; 22:11143. [PMID: 34681802 PMCID: PMC8540652 DOI: 10.3390/ijms222011143] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new pathogen from the family of Coronaviridae that caused a global pandemic of COVID-19 disease. In the absence of effective antiviral drugs, research of novel therapeutic targets such as SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) becomes essential. This viral protein is without a human counterpart and thus represents a unique prospective drug target. However, in vitro biological evaluation testing on RdRp remains difficult and is not widely available. Therefore, we prepared a database of commercial small-molecule compounds and performed an in silico high-throughput virtual screening on the active site of the SARS-CoV-2 RdRp using ensemble docking. We identified a novel thioether-amide or guanidine-linker class of potential RdRp inhibitors and calculated favorable binding free energies of representative hits by molecular dynamics simulations coupled with Linear Interaction Energy calculations. This innovative procedure maximized the respective phase-space sampling and yielded non-covalent inhibitors representing small optimizable molecules that are synthetically readily accessible, commercially available as well as suitable for further biological evaluation and mode of action studies.
Collapse
Affiliation(s)
- Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia;
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Dušanka Janežič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia;
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
| |
Collapse
|
77
|
Identifying the Most Potent Dual-Targeting Compound(s) against 3CLprotease and NSP15exonuclease of SARS-CoV-2 from Nigella sativa: Virtual Screening via Physicochemical Properties, Docking and Dynamic Simulation Analysis. Processes (Basel) 2021. [DOI: 10.3390/pr9101814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background: The outbreak of the coronavirus (SARS-CoV-2) has drastically affected the human population and caused enormous economic deprivation. It belongs to the β-coronavirus family and causes various problems such as acute respiratory distress syndrome and has resulted in a global pandemic. Though various medications have been under trial for combating COVID-19, specific medicine for treating COVID-19 is unavailable. Thus, the current situation urgently requires effective treatment modalities. Nigella sativa, a natural herb with reported antiviral activity and various pharmacological properties, has been selected in the present study to identify a therapeutic possibility for treating COVID-19. Methods: The present work aimed to virtually screen the bioactive compounds of N. sativa based on the physicochemical properties and docking approach against two SARS-CoV-2 enzymes responsible for crucial functions: 3CLpro (Main protease) and NSP15 (Nonstructural protein 15 or exonuclease). However, simulation trajectory analyses for 100 ns were accomplished by using the YASARA STRUCTURE tool based on the AMBER14 force field with 400 snapshots every 250 ps. RMSD and RMSF plots were successfully obtained for each target. Results: The results of molecular docking have shown higher binding energy of dithymoquinone (DTQ), a compound of N. sativa against 3CLpro and Nsp15, i.e., −8.56 kcal/mol and −8.31 kcal/mol, respectively. Further, the dynamic simulation has shown good stability of DTQ against both the targeted enzymes. In addition, physicochemical evaluation and toxicity assessment also revealed that DTQ obeyed the Lipinski rule and did not have any toxic side effects. Importantly, DTQ was much better in every aspect among the 13 N. sativa compounds and 2 control compounds tested. Conclusions: The results predicted that DTQ is a potent therapeutic molecule that could dual-target both 3CLpro and NSP15 for anti-COVID therapy.
Collapse
|
78
|
Moussaoui O, Byadi S, Eddine Hachim M, Sghyar R, Bahsis L, Moslova K, Aboulmouhajir A, Rodi YK, Podlipnik Č, Hadrami EMEL, Chakroune S. Selective synthesis of novel quinolones-amino esters as potential antibacterial and antifungal agents: Experimental, mechanistic study, docking and molecular dynamic simulations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
79
|
Cabezas-Pérusse Y, Daligault F, Ferrières V, Tasseau O, Tranchimand S. Modulation of the Activity and Regioselectivity of a Glycosidase: Development of a Convenient Tool for the Synthesis of Specific Disaccharides. Molecules 2021; 26:5445. [PMID: 34576917 PMCID: PMC8468180 DOI: 10.3390/molecules26185445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/24/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
The synthesis of disaccharides, particularly those containing hexofuranoside rings, requires a large number of steps by classical chemical means. The use of glycosidases can be an alternative to limit the number of steps, as they catalyze the formation of controlled glycosidic bonds starting from simple and easy to access building blocks; the main drawbacks are the yields, due to the balance between the hydrolysis and transglycosylation of these enzymes, and the enzyme-dependent regioselectivity. To improve the yield of the synthesis of β-d-galactofuranosyl-(1→X)-d-mannopyranosides catalyzed by an arabinofuranosidase, in this study we developed a strategy to mutate, then screen the catalyst, followed by a tailored molecular modeling methodology to rationalize the effects of the identified mutations. Two mutants with a 2.3 to 3.8-fold increase in transglycosylation yield were obtained, and in addition their accumulated regioisomer kinetic profiles were very different from the wild-type enzyme. Those differences were studied in silico by docking and molecular dynamics, and the methodology revealed a good predictive quality in regards with the regioisomer profiles, which is in good agreement with the experimental transglycosylation kinetics. So, by engineering CtAraf51, new biocatalysts were enabled to obtain the attractive central motif from the Leishmania lipophosphoglycan core with a higher yield and regioselectivity.
Collapse
Affiliation(s)
- Yari Cabezas-Pérusse
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, Université de Rennes, F-35000 Rennes, France; (Y.C.-P.); (V.F.); (O.T.)
| | - Franck Daligault
- CNRS, UFIP (Unité de Fonctionnalité et Ingénierie des Protéines)—UMR 6286, Université de Nantes, F-44000 Nantes, France;
| | - Vincent Ferrières
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, Université de Rennes, F-35000 Rennes, France; (Y.C.-P.); (V.F.); (O.T.)
| | - Olivier Tasseau
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, Université de Rennes, F-35000 Rennes, France; (Y.C.-P.); (V.F.); (O.T.)
| | - Sylvain Tranchimand
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, Université de Rennes, F-35000 Rennes, France; (Y.C.-P.); (V.F.); (O.T.)
| |
Collapse
|
80
|
Meng Q, Ramírez-Palacios C, Capra N, Hooghwinkel ME, Thallmair S, Rozeboom HJ, Thunnissen AMWH, Wijma HJ, Marrink SJ, Janssen DB. Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines. ACS Catal 2021; 11:10733-10747. [PMID: 34504735 PMCID: PMC8419838 DOI: 10.1021/acscatal.1c02053] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/26/2021] [Indexed: 01/19/2023]
Abstract
![]()
ω-Transaminases
(ω-TA) are attractive biocatalysts
for the production of chiral amines from prochiral ketones via asymmetric synthesis. However, the substrate scope of
ω-TAs is usually limited due to steric hindrance at the active
site pockets. We explored a protein engineering strategy using computational
design to expand the substrate scope of an (S)-selective
ω-TA from Pseudomonas jessenii (PjTA-R6) toward the production of bulky amines. PjTA-R6 is attractive for use in applied biocatalysis due
to its thermostability, tolerance to organic solvents, and acceptance
of high concentrations of isopropylamine as amino donor. PjTA-R6 showed no detectable activity for the synthesis of six bicyclic
or bulky amines targeted in this study. Six small libraries composed
of 7–18 variants each were separately designed via computational methods and tested in the laboratory for ketone to
amine conversion. In each library, the vast majority of the variants
displayed the desired activity, and of the 40 different designs, 38
produced the target amine in good yield with >99% enantiomeric
excess.
This shows that the substrate scope and enantioselectivity of PjTA mutants could be predicted in silico with high accuracy. The single mutant W58G showed the best performance
in the synthesis of five structurally similar bulky amines containing
the indan and tetralin moieties. The best variant for the other bulky
amine, 1-phenylbutylamine, was the triple mutant W58M + F86L + R417L,
indicating that Trp58 is a key residue in the large binding pocket
for PjTA-R6 redesign. Crystal structures of the two
best variants confirmed the computationally predicted structures.
The results show that computational design can be an efficient approach
to rapidly expand the substrate scope of ω-TAs to produce enantiopure
bulky amines.
Collapse
Affiliation(s)
- Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Carlos Ramírez-Palacios
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, AG Groningen 9747, Groningen, The Netherlands
| | - Nikolas Capra
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Mattijs E. Hooghwinkel
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Sebastian Thallmair
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, AG Groningen 9747, Groningen, The Netherlands
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, Frankfurt am Main 60438, Germany
| | - Henriëtte J. Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Hein J. Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Siewert J. Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, AG Groningen 9747, Groningen, The Netherlands
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| |
Collapse
|
81
|
Khadke SK, Lee JH, Kim YG, Raj V, Lee J. Assessment of Antibiofilm Potencies of Nervonic and Oleic Acid against Acinetobacter baumannii Using In Vitro and Computational Approaches. Biomedicines 2021; 9:biomedicines9091133. [PMID: 34572317 PMCID: PMC8466663 DOI: 10.3390/biomedicines9091133] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/25/2021] [Accepted: 08/29/2021] [Indexed: 12/24/2022] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen, and its biofilms are tolerant to desiccation, nutrient starvation, and antimicrobial treatment on biotic and abiotic surfaces, tissues, and medical devices. Biofilm formation by A. baumannii is triggered by a quorum sensing cascade, and we hypothesized that fatty acids might inhibit its biofilm formation by interfering with quorum sensing. Initially, we investigated the antibiofilm activities of 24 fatty acids against A. baumannii ATCC 17978 and two clinical isolates. Among these fatty acids, two unsaturated fatty acids, nervonic and oleic acid, at 20 μg/mL significantly inhibited A. baumannii biofilm formation without affecting its planktonic cell growth (MICs were >500 μg/mL) and markedly decreased the motility of A. baumannii but had no toxic effect on the nematode Caenorhabditis elegans. Interestingly, molecular dynamic simulations showed that both fatty acids bind to the quorum sensing acyl homoserine lactone synthase (AbaI), and decent conformational stabilities of interactions between the fatty acids and AbaI were exhibited. Our results demonstrate that nervonic and oleic acid inhibit biofilm formation by A. baumannii strains and may be used as lead molecules for the control of persistent A. baumannii infections.
Collapse
Affiliation(s)
| | | | | | | | - Jintae Lee
- Correspondence: ; Tel.: +82-53-810-2533; Fax: +82-53-810-4631
| |
Collapse
|
82
|
Fallica A, Barbaraci C, Amata E, Pasquinucci L, Turnaturi R, Dichiara M, Intagliata S, Gariboldi MB, Marras E, Orlandi VT, Ferroni C, Martini C, Rescifina A, Gentile D, Varchi G, Marrazzo A. Nitric Oxide Photo-Donor Hybrids of Ciprofloxacin and Norfloxacin: A Shift in Activity from Antimicrobial to Anticancer Agents. J Med Chem 2021; 64:11597-11613. [PMID: 34319100 PMCID: PMC8389907 DOI: 10.1021/acs.jmedchem.1c00917] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Indexed: 12/11/2022]
Abstract
The potential anticancer effect of fluoroquinolone antibiotics has been recently unveiled and related to their ability to interfere with DNA topoisomerase II. We herein envisioned the design and synthesis of novel Ciprofloxacin and Norfloxacin nitric oxide (NO) photo-donor hybrids to explore the potential synergistic antitumor effect exerted by the fluoroquinolone scaffold and NO eventually produced upon light irradiation. Anticancer activity, evaluated on a panel of tumor cell lines, showed encouraging results with IC50 values in the low micromolar range. Some compounds displayed intense antiproliferative activity on triple-negative and doxorubicin-resistant breast cancer cell lines, paving the way for their potential use to treat aggressive, refractory and multidrug-resistant breast cancer. No significant additive effect was observed on PC3 and DU145 cells following NO release. Conversely, antimicrobial photodynamic experiments on both Gram-negative and Gram-positive microorganisms displayed a significant killing rate in Staphylococcus aureus, accounting for their potential effectiveness as selective antimicrobial photosensitizers.
Collapse
Affiliation(s)
- Antonino
Nicolò Fallica
- Department
of Drug and Health Sciences (DSFS), University
of Catania, Viale A. Doria, 6, 95125 Catania, Italy
| | - Carla Barbaraci
- Department
of Drug and Health Sciences (DSFS), University
of Catania, Viale A. Doria, 6, 95125 Catania, Italy
| | - Emanuele Amata
- Department
of Drug and Health Sciences (DSFS), University
of Catania, Viale A. Doria, 6, 95125 Catania, Italy
| | - Lorella Pasquinucci
- Department
of Drug and Health Sciences (DSFS), University
of Catania, Viale A. Doria, 6, 95125 Catania, Italy
| | - Rita Turnaturi
- Department
of Drug and Health Sciences (DSFS), University
of Catania, Viale A. Doria, 6, 95125 Catania, Italy
| | - Maria Dichiara
- Department
of Drug and Health Sciences (DSFS), University
of Catania, Viale A. Doria, 6, 95125 Catania, Italy
| | - Sebastiano Intagliata
- Department
of Drug and Health Sciences (DSFS), University
of Catania, Viale A. Doria, 6, 95125 Catania, Italy
| | - Marzia Bruna Gariboldi
- Department
of Biotechnology and Life Sciences (DBSV), University of Insubria, Via JH Dunant 3, 21100 Varese, Italy
| | - Emanuela Marras
- Department
of Biotechnology and Life Sciences (DBSV), University of Insubria, Via JH Dunant 3, 21100 Varese, Italy
| | - Viviana Teresa Orlandi
- Department
of Biotechnology and Life Sciences (DBSV), University of Insubria, Via JH Dunant 3, 21100 Varese, Italy
| | - Claudia Ferroni
- Institute
for the Organic Synthesis and Photoreactivity − ISOF, Via Piero Gobetti, 101, 40129 Bologna, Italy
| | - Cecilia Martini
- Institute
for the Organic Synthesis and Photoreactivity − ISOF, Via Piero Gobetti, 101, 40129 Bologna, Italy
| | - Antonio Rescifina
- Department
of Drug and Health Sciences (DSFS), University
of Catania, Viale A. Doria, 6, 95125 Catania, Italy
| | - Davide Gentile
- Department
of Drug and Health Sciences (DSFS), University
of Catania, Viale A. Doria, 6, 95125 Catania, Italy
| | - Greta Varchi
- Institute
for the Organic Synthesis and Photoreactivity − ISOF, Via Piero Gobetti, 101, 40129 Bologna, Italy
| | - Agostino Marrazzo
- Department
of Drug and Health Sciences (DSFS), University
of Catania, Viale A. Doria, 6, 95125 Catania, Italy
| |
Collapse
|
83
|
Dash R, Mitra S, Munni YA, Choi HJ, Ali MC, Barua L, Jang TJ, Moon IS. Computational Insights into the Deleterious Impacts of Missense Variants on N-Acetyl-d-glucosamine Kinase Structure and Function. Int J Mol Sci 2021; 22:8048. [PMID: 34360815 PMCID: PMC8347710 DOI: 10.3390/ijms22158048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/05/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022] Open
Abstract
An enzyme of the mammalian amino-sugar metabolism pathway, N-acetylglucosamine kinase (NAGK), that synthesizes N-acetylglucosamine (GlcNAc)-6-phosphate, is reported to promote dynein functions during mitosis, axonal and dendritic growth, cell migration, and selective autophagy, which all are unrelated to its enzyme activity. As non-enzymatic structural functions can be altered by genetic variation, we made an effort in this study aimed at deciphering the pathological effect of nonsynonymous single-nucleotide polymorphisms (nsSNPs) in NAGK gene. An integrated computational approach, including molecular dynamics (MD) simulation and protein-protein docking simulation, was used to identify the damaging nsSNPs and their detailed structural and functional consequences. The analysis revealed the four most damaging variants (G11R, G32R, G120E, and A156D), which are highly conserved and functional, positioned in both small (G11R and G32R) and large (G120E and A156D) domains of NAGK. G11R is located in the ATP binding region, while variants present in the large domain (G120E and A156D) were found to induce substantial alterations in the structural organizations of both domains, including the ATP and substrate binding sites. Furthermore, all variants were found to reduce binding energy between NAGK and dynein subunit DYNLRB1, as revealed by protein-protein docking and MM-GBSA binding energy calculation supporting their deleteriousness on non-canonical function. We hope these findings will direct future studies to gain more insight into the role of these variants in the loss of NAGK function and their role in neurodevelopmental disorders.
Collapse
Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Sarmistha Mitra
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Ho Jin Choi
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| | - Md. Chayan Ali
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh;
| | - Largess Barua
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
| | - Tae Jung Jang
- Department of Pathology, Dongguk University College of Medicine, Gyeongju 38066, Korea;
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; (R.D.); (S.M.); (Y.A.M.); (H.J.C.)
| |
Collapse
|
84
|
Liu X, Wang H, Zhao X, Luo Q, Wang Q, Tan K, Wang Z, Jiang J, Cui J, Du E, Xia L, Du W, Chen D, Xia L, Xiao S. Arginine methylation of METTL14 promotes RNA N 6-methyladenosine modification and endoderm differentiation of mouse embryonic stem cells. Nat Commun 2021; 12:3780. [PMID: 34145242 PMCID: PMC8213825 DOI: 10.1038/s41467-021-24035-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/28/2021] [Indexed: 11/08/2022] Open
Abstract
RNA N6-methyladenosine (m6A), the most abundant internal modification of mRNAs, plays key roles in human development and health. Post-translational methylation of proteins is often critical for the dynamic regulation of enzymatic activity. However, the role of methylation of the core methyltransferase METTL3/METTL14 in m6A regulation remains elusive. We find by mass spectrometry that METTL14 arginine 255 (R255) is methylated (R255me). Global mRNA m6A levels are greatly decreased in METTL14 R255K mutant mouse embryonic stem cells (mESCs). We further find that R255me greatly enhances the interaction of METTL3/METTL14 with WTAP and promotes the binding of the complex to substrate RNA. We show that protein arginine N-methyltransferases 1 (PRMT1) interacts with and methylates METTL14 at R255, and consistent with this, loss of PRMT1 reduces mRNA m6A modification globally. Lastly, we find that loss of R255me preferentially affects endoderm differentiation in mESCs. Collectively, our findings show that arginine methylation of METTL14 stabilizes the binding of the m6A methyltransferase complex to its substrate RNA, thereby promoting global m6A modification and mESC endoderm differentiation. This work highlights the crosstalk between protein methylation and RNA methylation in gene expression.
Collapse
Affiliation(s)
- Xiaona Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, P.R. China
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hailong Wang
- Kingmed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, P.R. China
| | - Xueya Zhao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Qizhi Luo
- Department of Forensic Toxicology, School of Forensic Medicine, Southern Medical University, Guangzhou, P.R. China
| | - Qingwen Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Kaifen Tan
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Zihan Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Jia Jiang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Jinru Cui
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Enhui Du
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Linjian Xia
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Wenyi Du
- Sichuan MoDe Technology Co., Ltd, Chengdu, P. R. China
| | - Dahua Chen
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Institute of Biomedical Research, Yunnan University, Kunming, P.R. China.
| | - Laixin Xia
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China.
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, P.R. China.
| | - Shan Xiao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China.
| |
Collapse
|
85
|
Islam R, Parves MR, Paul AS, Uddin N, Rahman MS, Mamun AA, Hossain MN, Ali MA, Halim MA. A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2. J Biomol Struct Dyn 2021; 39:3213-3224. [PMID: 32340562 PMCID: PMC7232885 DOI: 10.1080/07391102.2020.1761883] [Citation(s) in RCA: 171] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 04/23/2020] [Indexed: 12/23/2022]
Abstract
The main protease of SARS-CoV-2 is one of the important targets to design and develop antiviral drugs. In this study, we have selected 40 antiviral phytochemicals to find out the best candidates which can act as potent inhibitors against the main protease. Molecular docking is performed using AutoDock Vina and GOLD suite to determine the binding affinities and interactions between the phytochemicals and the main protease. The selected candidates strongly interact with the key Cys145 and His41 residues. To validate the docking interactions, 100 ns molecular dynamics (MD) simulations on the five top-ranked inhibitors including hypericin, cyanidin 3-glucoside, baicalin, glabridin, and α-ketoamide-11r are performed. Principal component analysis (PCA) on the MD simulation discloses that baicalin, cyanidin 3-glucoside, and α-ketoamide-11r have structural similarity with the apo-form of the main protease. These findings are also strongly supported by root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), and solvent accessible surface area (SASA) investigations. PCA is also used to find out the quantitative structure-activity relationship (QSAR) for pattern recognition of the best ligands. Multiple linear regression (MLR) of QSAR reveals the R2 value of 0.842 for the training set and 0.753 for the test set. Our proposed MLR model can predict the favorable binding energy compared with the binding energy detected from molecular docking. ADMET analysis demonstrates that these candidates appear to be safer inhibitors. Our comprehensive computational and statistical analysis show that these selected phytochemicals can be used as potential inhibitors against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Rajib Islam
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md. Rimon Parves
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Archi Sundar Paul
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Nizam Uddin
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD, USA
| | - Md. Sajjadur Rahman
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD, USA
| | - Abdulla Al Mamun
- Key Laboratory of Soft Chemistry and Functional Materials of MOE, School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Md. Nayeem Hossain
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md. Ackas Ali
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, AR, USA
| |
Collapse
|
86
|
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: 7] [Impact Index Per Article: 2.3] [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.
Collapse
|
87
|
Shakil S, Rizvi SMD, Greig NH. High Throughput Virtual Screening and Molecular Dynamics Simulation for Identifying a Putative Inhibitor of Bacterial CTX-M-15. Antibiotics (Basel) 2021; 10:antibiotics10050474. [PMID: 33919115 PMCID: PMC8143117 DOI: 10.3390/antibiotics10050474] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 11/28/2022] Open
Abstract
Background: Multidrug resistant bacteria are a major therapeutic challenge. CTX-M-type enzymes are an important group of class A extended-spectrum β-lactamases (ESBLs). ESBLs are the enzymes that arm bacterial pathogens with drug resistance to an array of antibiotics, notably the advanced-generation cephalosporins. The current need for an effective CTX-M-inhibitor is high. Objective: The aim of the current study was to identify a promising anti-CTX-M-15 ligand whose chemical skeleton could be used as a ‘seed-molecule’ for future drug design against resistant bacteria. Methods: Virtual screening of 5,000,000 test molecules was performed by ‘MCULE Drug Discovery Platform’. ‘ADME analyses’ was performed by ‘SWISS ADME’. TOXICITY CHECKER of MCULE was employed to predict the safety profile of the test molecules. The complex of the ‘Top inhibitor’ with the ‘bacterial CTX-M-15 enzyme’ was subjected to 102.25 ns molecular dynamics simulation. This simulation was run for 3 days on a HP ZR30w workstation. Trajectory analyses were performed by employing the macro ‘md_analyze.mcr’ of YASARA STRUCTURE version 20.12.24.W.64 using AMBER14 force field. YANACONDA macro language was used for complex tasks. Figures, including RMSD and RMSF plots, were generated. Snapshots were acquired after every 250 ps. Finally, two short videos of ‘41 s’ and ‘1 min and 22 s’ duration were recorded. Results: 5-Amino-1-(2H-[1,2,4]triazino[5,6-b]indol-3-yl)-1H-pyrazole-4-carbonitrile, denoted by the MCULE-1352214421-0-56, displayed the most efficient binding with bacterial CTX-M-15 enzyme. This screened molecule significantly interacted with CTX-M-15 via 13 amino acid residues. Notably, nine amino acid residues were found common to avibactam binding (the reference ligand). Trajectory analysis yielded 410 snapshots. The RMSD plot revealed that around 26 ns, equilibrium was achieved and, thereafter, the complex remained reasonably stable. After a duration of 26 ns and onwards until 102.25 ns, the backbone RMSD fluctuations were found to be confined within a range of 0.8–1.4 Å. Conclusion: 5-Amino-1-(2H-[1,2,4]triazino[5,6-b]indol-3-yl)-1H-pyrazole-4-carbonitrile could emerge as a promising seed molecule for CTX-M-15-inhibitor design. It satisfied ADMET features and displayed encouraging ‘simulation results’. Advanced plots obtained by trajectory analyses predicted the stability of the proposed protein-ligand complex. ‘Hands on’ wet laboratory validation is warranted.
Collapse
Affiliation(s)
- Shazi Shakil
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence:
| | - Syed M. Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81481, Saudi Arabia;
| | - Nigel H. Greig
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA;
| |
Collapse
|
88
|
Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor. Int J Mol Sci 2021; 22:ijms22073595. [PMID: 33808384 PMCID: PMC8038099 DOI: 10.3390/ijms22073595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 12/04/2022] Open
Abstract
A molecular docking approach was employed to evaluate the binding affinity of six triterpenes, namely epifriedelanol, friedelin, α-amyrin, α-amyrin acetate, β-amyrin acetate, and bauerenyl acetate, towards the cannabinoid type 1 receptor (CB1). Molecular docking studies showed that friedelin, α-amyrin, and epifriedelanol had the strongest binding affinity towards CB1. Molecular dynamics simulation studies revealed that friedelin and α-amyrin engaged in stable non-bonding interactions by binding to a pocket close to the active site on the surface of the CB1 target protein. The studied triterpenes showed a good capacity to penetrate the blood–brain barrier. These results help to provide some evidence to justify, at least in part, the previously reported antinociceptive and sedative properties of Vernonia patula.
Collapse
|
89
|
Detzel MS, Schmalohr BF, Steinbock F, Hopp MT, Ramoji A, Paul George AA, Neugebauer U, Imhof D. Revisiting the interaction of heme with hemopexin. Biol Chem 2021; 402:675-691. [PMID: 33581700 DOI: 10.1515/hsz-2020-0347] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/06/2021] [Indexed: 12/23/2022]
Abstract
In hemolytic disorders, erythrocyte lysis results in massive release of hemoglobin and, subsequently, toxic heme. Hemopexin is the major protective factor against heme toxicity in human blood and currently considered for therapeutic use. It has been widely accepted that hemopexin binds heme with extraordinarily high affinity of <1 pM in a 1:1 ratio. However, several lines of evidence point to a higher stoichiometry and lower affinity than determined 50 years ago. Here, we re-analyzed these data. SPR and UV/Vis spectroscopy were used to monitor the interaction of heme with the human protein. The heme-binding sites of hemopexin were characterized using hemopexin-derived peptide models and competitive displacement assays. We obtained a K D value of 0.32 ± 0.04 nM and the ratio for the interaction was determined to be 1:1 at low heme concentrations and at least 2:1 (heme:hemopexin) at high concentrations. We were able to identify two yet unknown potential heme-binding sites on hemopexin. Furthermore, molecular modelling with a newly created homology model of human hemopexin suggested a possible recruiting mechanism by which heme could consecutively bind several histidine residues on its way into the binding pocket. Our findings have direct implications for the potential administration of hemopexin in hemolytic disorders.
Collapse
Affiliation(s)
- Milena Sophie Detzel
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121Bonn, Germany
| | - Benjamin Franz Schmalohr
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121Bonn, Germany
| | - Francèl Steinbock
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121Bonn, Germany
| | - Marie-Thérèse Hopp
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121Bonn, Germany
| | - Anuradha Ramoji
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, D-07747Jena, Germany.,Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, D-07745Jena, Germany
| | - Ajay Abisheck Paul George
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121Bonn, Germany
| | - Ute Neugebauer
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, D-07747Jena, Germany.,Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, D-07745Jena, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121Bonn, Germany
| |
Collapse
|
90
|
Ezaj MMA, Junaid M, Akter Y, Nahrin A, Siddika A, Afrose SS, Nayeem SMA, Haque MS, Moni MA, Hosen SMZ. Whole proteome screening and identification of potential epitopes of SARS-CoV-2 for vaccine design-an immunoinformatic, molecular docking and molecular dynamics simulation accelerated robust strategy. J Biomol Struct Dyn 2021; 40:6477-6502. [PMID: 33586620 DOI: 10.1080/07391102.2021.1886171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the most cryptic pandemic outbreak of the 21st century, has gripped more than 1.8 million people to death and infected almost eighty six million. As it is a new variant of SARS, there is no approved drug or vaccine available against this virus. This study aims to predict some promising cytotoxic T lymphocyte epitopes in the SARS-CoV-2 proteome utilizing immunoinformatic approaches. Firstly, we identified 21 epitopes from 7 different proteins of SARS-CoV-2 inducing immune response and checked for allergenicity and conservancy. Based on these factors, we selected the top three epitopes, namely KAYNVTQAF, ATSRTLSYY, and LTALRLCAY showing functional interactions with the maximum number of MHC alleles and no allergenicity. Secondly, the 3D model of selected epitopes and HLA-A*29:02 were built and Molecular Docking simulation was performed. Most interestingly, the best two epitopes predicted by docking are part of two different structural proteins of SARS-CoV-2, namely Membrane Glycoprotein (ATSRTLSYY) and Nucleocapsid Phosphoprotein (KAYNVTQAF), which are generally target of choice for vaccine designing. Upon Molecular Docking, interactions between selected epitopes and HLA-A*29:02 were further validated by 50 ns Molecular Dynamics (MD) simulation. Analysis of RMSD, Rg, SASA, number of hydrogen bonds, RMSF, MM-PBSA, PCA, and DCCM from MD suggested that ATSRTLSYY is the most stable and promising epitope than KAYNVTQAF epitope. Moreover, we also identified B-cell epitopes for each of the antigenic proteins of SARS CoV-2. Findings of our work will be a good resource for wet lab experiments and will lessen the timeline for vaccine construction.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Md Muzahid Ahmed Ezaj
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.,Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh
| | - Md Junaid
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh
| | - Yeasmin Akter
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Biotechnology & Genetic Engineering, Noakhali Science & Technology University, Noakhali, Bangladesh
| | - Afsana Nahrin
- Department of Pharmacy, University of Science and Technology Chittagong, Chattogram, Bangladesh
| | - Aysha Siddika
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Syeda Samira Afrose
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - S M Abdul Nayeem
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Md Sajedul Haque
- Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - S M Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh.,Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for Applied Medical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
91
|
Raj V, Park JG, Cho KH, Choi P, Kim T, Ham J, Lee J. Assessment of antiviral potencies of cannabinoids against SARS-CoV-2 using computational and in vitro approaches. Int J Biol Macromol 2021; 168:474-485. [PMID: 33290767 PMCID: PMC7836687 DOI: 10.1016/j.ijbiomac.2020.12.020] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
Effective treatment choices to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are limited because of the absence of effective target-based therapeutics. The main object of the current research was to estimate the antiviral activity of cannabinoids (CBDs) against the human coronavirus SARS-CoV-2. In the presented research work, we performed in silico and in vitro experiments to aid the sighting of lead CBDs for treating the viral infections of SARS-CoV-2. Virtual screening was carried out for interactions between 32 CBDs and the SARS-CoV-2 Mpro enzyme. Afterward, in vitro antiviral activity was carried out of five CBDs molecules against SARS-CoV-2. Interestingly, among them, two CBDs molecules namely Δ9 -tetrahydrocannabinol (IC50 = 10.25 μM) and cannabidiol (IC50 = 7.91 μM) were observed to be more potent antiviral molecules against SARS-CoV-2 compared to the reference drugs lopinavir, chloroquine, and remdesivir (IC50 ranges of 8.16-13.15 μM). These molecules were found to have stable conformations with the active binding pocket of the SARS-CoV-2 Mpro by molecular dynamic simulation and density functional theory. Our findings suggest cannabidiol and Δ9 -tetrahydrocannabinol are possible drugs against human coronavirus that might be used in combination or with other drug molecules to treat COVID-19 patients.
Collapse
Affiliation(s)
- Vinit Raj
- School of Chemical Engineering, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jae Gyu Park
- Advanced Bio Convergence Center, Pohang Technopark Foundation, Pohang, Republic of Korea
| | - Kiu-Hyung Cho
- Gyeongbuk Institute for Bio industry, Andong, Republic of Korea
| | - Pilju Choi
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Taejung Kim
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Jungyeob Ham
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology (UST), Seoul, Republic of Korea.
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan, Republic of Korea.
| |
Collapse
|
92
|
Dhar L, Hossain S, Rahman MS, Quraishi SB, Saha K, Rahman F, Rahman MT. Adsorption Mechanism of Methylene Blue by Graphene Oxide-Shielded Mg-Al-Layered Double Hydroxide From Synthetic Wastewater. J Phys Chem A 2021; 125:954-965. [PMID: 33480691 DOI: 10.1021/acs.jpca.0c09124] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pollution of water resources by various pollutants is a global environmental issue, particularly, dye pollution has a major contribution to it. From various studies, it is confirmed that adsorption is an excellent remediation technique compared to others. Mg-Al-layered double hydroxides (LDHs) intercalated with NO3- ions act as an effective adsorbent-removing ionic species like heavy metal and dyes. Another popular nanomaterial is graphene oxide (GO), which is successfully used as an adsorbent for different pollutants like dye and heavy metal ions. It is prepared based on the modified Hummers method. In this study, GO was introduced on the surface of LDH to improve its adsorption capacity. The adsorption process is well described by the Freundlich model. The maximum adsorption capacity was obtained at around 0.5 and 0.85 mmol of methylene blue (MB) per gram of Mg-Al LDH and modified Mg-Al LDH with GO, respectively. The reaction kinetics of MB with both adsorbents is determined to be the pseudo-second-order. To get more insights of the mechanism, molecular dynamics (MD) simulation was conducted among the modified Mg-Al LDH with GO and MB molecules at both low- and high-concentration environments, which demonstrated that the developed composite adsorbs MB molecules predominantly onto its GO surface and then the MB molecules are adsorbed by the LDH surface. C-H···O (2.49-3.04 Å) and pi-donor···H-O (2.45-3.05 Å) are the major driving forces behind the strong adsorbability. Besides, S···H-O, S···O,N···O-H, pi···lone pair, pi···sigma, pi···cation, and alkyl···hydrophobic interactions play important roles in stabilizing the MB molecules onto the surface of the composite.
Collapse
Affiliation(s)
- Loknath Dhar
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Saddam Hossain
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Sajjadur Rahman
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota 57007, United States
| | - Shamshad B Quraishi
- Chemistry Division, Atomic Energy Center, Bangladesh Atomic Energy Commission, Dhaka 1207, Bangladesh
| | - Koushik Saha
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Farzana Rahman
- Department of General Educational Development, Daffodil International University, Dhaka 1207, Bangladesh
| | - Mir Tamzid Rahman
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| |
Collapse
|
93
|
An Integrated Pharmacophore/Docking/3D-QSAR Approach to Screening a Large Library of Products in Search of Future Botulinum Neurotoxin A Inhibitors. Int J Mol Sci 2020; 21:ijms21249470. [PMID: 33322848 PMCID: PMC7764241 DOI: 10.3390/ijms21249470] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 12/19/2022] Open
Abstract
Botulinum toxins are neurotoxins produced by Clostridium botulinum. This toxin can be lethal for humans as a cause of botulism; however, in small doses, the same toxin is used to treat different conditions. Even if the therapeutic doses are effective and safe, the adverse reactions could be local and could unmask a subclinical impairment of neuromuscular transmissions. There are not many cases of adverse events in the literature; however, it is possible that sometimes they do not occur as they are transient and, if they do occur, there is no possibility of a cure other than to wait for the pharmacological effect to end. Inhibition of botulinum neurotoxin type A (BoNT/A) effects is a strategy for treating botulism as it can provide an effective post-exposure remedy. In this paper, 13,592,287 compounds were screened through a pharmacophore filter, a 3D-QSAR model, and a virtual screening; then, the compounds with the best affinity were selected. Molecular dynamics simulation studies on the first four compounds predicted to be the most active were conducted to verify that the poses foreseen by the docking were stable. This approach allowed us to identify compounds with a calculated inhibitory activity in the range of 316–500 nM.
Collapse
|
94
|
Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CL pro) Non-Covalent Small-Molecule Inhibitors. Molecules 2020; 25:molecules25245808. [PMID: 33316996 PMCID: PMC7763084 DOI: 10.3390/molecules25245808] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new strain of Coronaviridae. In the closing 2019 to early 2020 months, the virus caused a global pandemic of COVID-19 disease. We performed a virtual screening study in order to identify potential inhibitors of the SARS-CoV-2 main viral protease (3CLpro or Mpro). For this purpose, we developed a novel approach using ensemble docking high-throughput virtual screening directly coupled with subsequent Linear Interaction Energy (LIE) calculations to maximize the conformational space sampling and to assess the binding affinity of identified inhibitors. A large database of small commercial compounds was prepared, and top-scoring hits were identified with two compounds singled out, namely 1-[(R)-2-(1,3-benzimidazol-2-yl)-1-pyrrolidinyl]-2-(4-methyl-1,4-diazepan-1-yl)-1-ethanone and [({(S)-1-[(1H-indol-2-yl)methyl]-3-pyrrolidinyl}methyl)amino](5-methyl-2H-pyrazol-3-yl)formaldehyde. Moreover, we obtained a favorable binding free energy of the identified compounds, and using contact analysis we confirmed their stable binding modes in the 3CLpro active site. These compounds will facilitate further 3CLpro inhibitor design.
Collapse
|
95
|
Kruszewska N, Domino K, Drelich R, Urbaniak W, Petelska AD. Interactions between Beta-2-Glycoprotein-1 and Phospholipid Bilayer-A Molecular Dynamic Study. MEMBRANES 2020; 10:membranes10120396. [PMID: 33291449 PMCID: PMC7762114 DOI: 10.3390/membranes10120396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 11/16/2022]
Abstract
This study aims to investigate the interactions appearing when the beta-2-glycoprotein-1 binds to a lipid bilayer. The inter- and intra-molecular forces acting between the two macromolecular systems have been investigated using a molecular dynamics simulation method. The importance of water bridges has also been addressed. Additionally, the viscoelastic response of the bilayer has been studied. In detail, the (saturated-chain) 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and (unsaturated-chain) 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) bilayers have been chosen to test their behavior near the protein. Both of the lipids have a polar head but different chemical structures and are similar to the main phospholipids present in the synovial fluid. This study is meaningful for further explaining the worsening friction properties in articular cartilage, as the inactivation of phospholipid bilayers by beta-2-glycoprotein-1 is believed to be a cause of the destruction of cartilage in most rheumatic diseases and osteoarthritis. It was found that the protein binds stronger to the DPPC bilayer than to the POPE, but in both cases, it has the potential to change the local bilayer stability. Nevertheless, the binding forces are placed within a small area (only a few lipids contribute to the binding, creating many interactions). However, together, they are not stronger than the covalent bonds between C-O, thus, potentially, it is possible to push the lipids into the bilayer but detaching the lipids' heads from the tail is not possible. Additionally, the protein causes water displacement from the vicinity of the bilayer, and this may be a contributor to the instability of the bilayer (disrupting the water bridges needed for the stabilization of the bilayer, especially in the case of DPPC where the heads are not so well stabilized by H-bonds as they are in POPE). Moreover, it was found that the diffusivity of lipids in the DPPC bilayer bound to the protein is significantly different from the diffusivity of the ones which are not in contact with the protein. The POPE bilayer is stiffer due to intramolecular interactions, which are stronger than in the DPPC; thus, the viscous to elastic effects in the POPE case are more significant than in the case of the DPPC. It is, therefore, harder to destabilize the POPE bilayer than the DPPC one.
Collapse
Affiliation(s)
- Natalia Kruszewska
- Institute of Mathematics and Physics, UTP University of Science and Technology, Kaliskiego 7, 85-796 Bydgoszcz, Poland
- Correspondence: (N.K.); (A.D.P.)
| | - Krzysztof Domino
- Institute of Theoretical and Applied Informatics, Polish Academy of Sciences, Bałtycka 5, 44-100 Gliwice, Poland;
| | - Radosław Drelich
- Faculty of Mathematics, Physics and Technical Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-867 Bydgoszcz, Poland; (R.D.); (W.U.)
| | - Wiesław Urbaniak
- Faculty of Mathematics, Physics and Technical Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-867 Bydgoszcz, Poland; (R.D.); (W.U.)
| | - Aneta D. Petelska
- Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-425 Bialystok, Poland
- Correspondence: (N.K.); (A.D.P.)
| |
Collapse
|
96
|
Samson JM, Ravindran Menon D, Vaddi PK, Kalani Williams N, Domenico J, Zhai Z, Backos DS, Fujita M. Computational Modeling of NLRP3 Identifies Enhanced ATP Binding and Multimerization in Cryopyrin-Associated Periodic Syndromes. Front Immunol 2020; 11:584364. [PMID: 33329557 PMCID: PMC7711157 DOI: 10.3389/fimmu.2020.584364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/20/2020] [Indexed: 11/13/2022] Open
Abstract
Cyropyrin-associated periodic syndromes (CAPS) are clinically distinct syndromes that encompass a phenotypic spectrum yet are caused by alterations in the same gene, NLRP3. Many CAPS cases and other NLRP3-autoinflammatory diseases (NLRP3-AIDs) are directly attributed to protein-coding alterations in NLRP3 and the subsequent dysregulation of the NLRP3 inflammasome leading to IL-1β-mediated inflammatory states. Here, we used bioinformatics tools, computational modeling, and computational assessments to explore the proteomic consequences of NLRP3 mutations, which potentially drive NLRP3 inflammasome dysregulation. We analyzed 177 mutations derived from familial cold autoinflammatory syndrome (FCAS), Muckle-Wells Syndrome (MWS), and the non-hereditary chronic infantile neurologic cutaneous and articular syndrome, also known as neonatal-onset multisystem inflammatory disease (CINCA/NOMID), as well as other NLRP3-AIDs. We found an inverse relationship between clinical severity and the severity of predicted structure changes resulting from mutations in NLRP3. Bioinformatics tools and computational modeling revealed that NLRP3 mutations that are predicted to be structurally severely-disruptive localize around the ATP binding pocket and that specific proteo-structural changes to the ATP binding pocket lead to enhanced ATP binding affinity by altering hydrogen-bond and charge interactions. Furthermore, we demonstrated that NLRP3 mutations that are predicted to be structurally mildly- or moderately-disruptive affect protein-protein interactions, such as NLRP3-ASC binding and NLRP3-NLRP3 multimerization, enhancing inflammasome formation and complex stability. Taken together, we provide evidence that proteo-structural mechanisms can explain multiple mechanisms of inflammasome activation in NLRP3-AID.
Collapse
Affiliation(s)
- Jenny Mae Samson
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Dinoop Ravindran Menon
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Prasanna K Vaddi
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nazanin Kalani Williams
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Joanne Domenico
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Zili Zhai
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Donald S Backos
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Mayumi Fujita
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Denver VA Medical Center, Aurora, CO, United States
| |
Collapse
|
97
|
Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter. Int J Mol Sci 2020; 21:ijms21207606. [PMID: 33066695 PMCID: PMC7589834 DOI: 10.3390/ijms21207606] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
The ATP-binding cassette transporter A1 (ABCA1) is a membrane-bound exporter protein involved in regulating serum HDL level by exporting cholesterol and phospholipids to load up in lipid-poor ApoA-I and ApoE, which allows the formation of nascent HDL. Mutations in the ABCA1 gene, when presents in both alleles, disrupt the canonical function of ABCA1, which associates with many disorders related to lipid transport. Although many studies have reported the phenotypic effects of a large number of ABCA1 variants, the pathological effect of non-synonymous polymorphisms (nsSNPs) in ABCA1 remains elusive. Therefore, aiming at exploring the structural and functional consequences of nsSNPs in ABCA1, in this study, we employed an integrated computational approach consisting of nine well-known in silico tools to identify damaging SNPs and molecular dynamics (MD) simulation to get insights into the magnitudes of the damaging effects. In silico tools revealed four nsSNPs as being most deleterious, where the two SNPs (G1050V and S1067C) are identified as the highly conserved and functional disrupting mutations located in the NBD1 domain. MD simulation suggested that both SNPs, G1050V and S1067C, changed the overall structural flexibility and dynamics of NBD1, and induced substantial alteration in the structural organization of ATP binding site. Taken together, these findings direct future studies to get more insights into the role of these variants in the loss of the ABCA1 function.
Collapse
|
98
|
Plant Nitrilase Homologues in Fungi: Phylogenetic and Functional Analysis with Focus on Nitrilases in Trametes versicolor and Agaricus bisporus. Molecules 2020; 25:molecules25173861. [PMID: 32854275 PMCID: PMC7503981 DOI: 10.3390/molecules25173861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/15/2020] [Accepted: 08/16/2020] [Indexed: 11/17/2022] Open
Abstract
Fungi contain many plant-nitrilase (NLase) homologues according to database searches. In this study, enzymes NitTv1 from Trametes versicolor and NitAb from Agaricus bisporus were purified and characterized as the representatives of this type of fungal NLase. Both enzymes were slightly more similar to NIT4 type than to NIT1/NIT2/NIT3 type of plant NLases in terms of their amino acid sequences. Expression of the synthetic genes in Escherichia coli Origami B (DE3) was induced with 0.02 mM isopropyl β-D-1-thiogalactopyranoside at 20 °C. Purification of NitTv1 and NitAb by cobalt affinity chromatography gave ca. 6.6 mg and 9.6 mg of protein per 100 mL of culture medium, respectively. Their activities were determined with 25 mM of nitriles in 50 mM Tris/HCl buffer, pH 8.0, at 30 °C. NitTv1 and NitAb transformed β-cyano-L-alanine (β-CA) with the highest specific activities (ca. 132 and 40 U mg−1, respectively) similar to plant NLase NIT4. β-CA was transformed into Asn and Asp as in NIT4 but at lower Asn:Asp ratios. The fungal NLases also exhibited significant activities for (aryl)aliphatic nitriles such as 3-phenylpropionitrile, cinnamonitrile and fumaronitrile (substrates of NLase NIT1). NitTv1 was more stable than NitAb (at pH 5–9 vs. pH 5–7). These NLases may participate in plant–fungus interactions by detoxifying plant nitriles and/or producing plant hormones. Their homology models elucidated the molecular interactions with various nitriles in their active sites.
Collapse
|
99
|
Ripon MKH, Lee H, Dash R, Choi HJ, Oktaviani DF, Moon IS, Haque MN. N-acetyl-D-glucosamine kinase binds dynein light chain roadblock 1 and promotes protein aggregate clearance. Cell Death Dis 2020; 11:619. [PMID: 32796833 PMCID: PMC7427805 DOI: 10.1038/s41419-020-02862-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022]
Abstract
Emerging evidence indicates that neurodegenerative diseases (NDs) result from a failure to clear toxic protein aggregates rather than from their generation. We previously showed N-acetylglucosamine kinase (NAGK) promotes dynein functionality and suggested this might promote aggregate removal and effectively address proteinopathies. Here, we report NAGK interacts with dynein light chain roadblock type 1 (DYNLRB1) and efficiently suppresses mutant huntingtin (mHtt) (Q74) and α-synuclein (α-syn) A53T aggregation in mouse brain cells. A kinase-inactive NAGKD107A also efficiently cleared Q74 aggregates. Yeast two-hybrid selection and in silico protein-protein docking analysis showed the small domain of NAGK (NAGK-DS) binds to the C-terminal of DYNLRB1. Furthermore, a small peptide derived from NAGK-DS interfered with Q74 clearance. We propose binding of NAGK-DS to DYNLRB1 'pushes up' the tail of dynein light chain and confers momentum for inactive phi- to active open-dynein transition.
Collapse
Affiliation(s)
- Md Kamal Hossain Ripon
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - HyunSook Lee
- Section of Neuroscience, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Raju Dash
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Ho Jin Choi
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Diyah Fatimah Oktaviani
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
| | - Il Soo Moon
- Department of Anatomy, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
- Section of Neuroscience, Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
| | - Md Nazmul Haque
- Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea
- Department of Fisheries Biology and Genetics, Patuakhali Science and Technology University, Patuakhali, 8602, Bangladesh
| |
Collapse
|
100
|
Gentile D, Fuochi V, Rescifina A, Furneri PM. New Anti SARS-Cov-2 Targets for Quinoline Derivatives Chloroquine and Hydroxychloroquine. Int J Mol Sci 2020; 21:E5856. [PMID: 32824072 PMCID: PMC7461590 DOI: 10.3390/ijms21165856] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/01/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022] Open
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a severe global health crisis. In this paper, we used docking and simulation methods to identify potential targets and the mechanism of action of chloroquine (CQ) and hydroxychloroquine (HCQ) against SARS-CoV-2. Our results showed that both CQ and HCQ influenced the functionality of the envelope (E) protein, necessary in the maturation processes of the virus, due to interactions that modify the flexibility of the protein structure. Furthermore, CQ and HCQ also influenced the proofreading and capping of viral RNA in SARS-CoV-2, performed by nsp10/nsp14 and nsp10/nsp16. In particular, HCQ demonstrated a better energy binding with the examined targets compared to CQ, probably due to the hydrogen bonding of the hydroxyl group of HCQ with polar amino acid residues.
Collapse
Affiliation(s)
- Davide Gentile
- Dipartimento di Scienze del Farmaco, University of Catania, 95125 Catania, Italy;
| | - Virginia Fuochi
- Dipartimento di Scienze Biomediche e Biotecnologiche, University of Catania, 95125 Catania, Italy;
| | - Antonio Rescifina
- Dipartimento di Scienze del Farmaco, University of Catania, 95125 Catania, Italy;
| | - Pio Maria Furneri
- Dipartimento di Scienze Biomediche e Biotecnologiche, University of Catania, 95125 Catania, Italy;
| |
Collapse
|