1
|
Zajaček D, Dunárová A, Bucinsky L, Štekláč M. Compromise in Docking Power of Liganded Crystal Structures of M pro SARS-CoV-2 Surpasses 90% Success Rate. J Chem Inf Model 2024; 64:1628-1643. [PMID: 38408033 DOI: 10.1021/acs.jcim.3c01552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Herein, we present the capacity of three different molecular docking programs (AutoDock, AutoDock Vina, and PLANTS) to identify and reproduce the binding modes of ligands present in 247 covalent and 169 noncovalent complex crystal structures of the severe acute respiratory syndrome coronavirus 2 main protease (Mpro). The compromise in docking power is evaluated with respect to their ability to generate poses similar to the crystal structure binding mode (heavy atoms' root-mean-square deviation < 2 Å) and their ability to recognize the native binding mode with an included compensation for the scoring function error. Noncovalently bound inhibitors are best modeled by AutoDock Vina (90.6% success rate in the active site), while the most relevant results for covalently bound inhibitors are produced by PLANTS (93.0%). AutoDock shows acceptable performance for both types of ligands, 81.1 and 76.4% for noncovalent and covalent complexes, respectively. All three programs manifest worse performance when reproducing surface-bound ligands. Comparison with other works illustrates the importance of crystal structure processing (12% of noncovalent and 26% of covalent ligands had to be manually corrected), proper sampling protocol settings, and inclusion of root-mean-square deviation (RMSD)/scoring function error compensations in crystal structure pose identification. Results are analyzed with respect to a clustering scheme of the noncovalently bound ligands and the chemical reaction type of the covalent ligand bound to the Cys145 residue. A comparison of screening power based on the docking scores of noncovalent ligands from the crystal structures with a "Directory of Useful Decoys, Enhanced" set of known decoys (6562 compounds) and ZINC15 in vivo subset (60,394 compounds) is provided. Ligand and protein input files are provided for future benchmarking purposes.
Collapse
Affiliation(s)
- Dávid Zajaček
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, SK-81237 Bratislava, Slovakia
| | - Adriána Dunárová
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, SK-81237 Bratislava, Slovakia
| | - Lukas Bucinsky
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, SK-81237 Bratislava, Slovakia
| | - Marek Štekláč
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, SK-81237 Bratislava, Slovakia
- Computing Center, Centre of Operations of the Slovak Academy of Sciences, Dúbravská cesta č. 9, SK-84535 Bratislava, Slovakia
| |
Collapse
|
2
|
Lee D, Jung HG, Park D, Bang J, Cheong DY, Jang JW, Kim Y, Lee S, Lee SW, Lee G, Kim YH, Hong JH, Hwang KS, Lee JH, Yoon DS. Bioengineered amyloid peptide for rapid screening of inhibitors against main protease of SARS-CoV-2. Nat Commun 2024; 15:2108. [PMID: 38453923 PMCID: PMC10920794 DOI: 10.1038/s41467-024-46296-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evoked a worldwide pandemic. As the emergence of variants has hampered the neutralization capacity of currently available vaccines, developing effective antiviral therapeutics against SARS-CoV-2 and its variants becomes a significant challenge. The main protease (Mpro) of SARS-CoV-2 has received increased attention as an attractive pharmaceutical target because of its pivotal role in viral replication and proliferation. Here, we generated a de novo Mpro-inhibitor screening platform to evaluate the efficacies of Mpro inhibitors based on Mpro cleavage site-embedded amyloid peptide (MCAP)-coated gold nanoparticles (MCAP-AuNPs). We fabricated MCAPs comprising an amyloid-forming sequence and Mpro-cleavage sequence, mimicking in vivo viral replication process mediated by Mpro. By measuring the proteolytic activity of Mpro and the inhibitory efficacies of various drugs, we confirmed that the MCAP-AuNP-based platform was suitable for rapid screening potential of Mpro inhibitors. These results demonstrated that our MCAP-AuNP-based platform has great potential for discovering Mpro inhibitors and may accelerate the development of therapeutics against COVID-19.
Collapse
Affiliation(s)
- Dongtak Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Hyo Gi Jung
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Dongsung Park
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, South Korea
| | - Junho Bang
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, South Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, South Korea
| | - Jae Won Jang
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Yonghwan Kim
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Seungmin Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, South Korea
| | - Sang Won Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA, 90064, USA
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, South Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, South Korea
| | - Yeon Ho Kim
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Ji Hye Hong
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, South Korea
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, South Korea.
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, South Korea.
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea.
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea.
- Astrion Inc, Seoul, 02841, South Korea.
| |
Collapse
|
3
|
Alhazmi AY, Khan FR, Rehman ZU, Hazazi A, Alotaibi BS, Alharthi NS, Alhuthali HM, Aba Alkhayl FF, Alshehri FF, Alkhoshaiban A, Al-Otaibi F. Structural and energetic analysis of NS5 protein inhibition by small molecules in Japanese encephalitis virus using machine learning and steered molecular dynamics approach. J Biomol Struct Dyn 2024:1-18. [PMID: 38407246 DOI: 10.1080/07391102.2024.2316767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
One of the viral diseases that affect millions of people around the world, particularly in developing countries, is Japanese encephalitis (JE). In this study, the conserved protein of this virus, that is, non-structural protein 5 (NS5), was used as a target protein for this study, and a compound library of 749 antiviral molecules was screened against NS5. The current study employed machine learning-based virtual screening combined with molecular docking. Here, three hits (24360, 123519051 and 213039) had lower binding energies (< -8 kcal/mol) than the control, S-Adenosyl-L-homocysteine (SAH). All the compounds showed significant H-bond interactions with functional residues, which were also observed by the control. Molecular dynamics simulation, MM/GBSA for binding free energy analysis, principal component analysis and free energy landscape were also performed to study the stability of the complex formation. All three compounds had similar root mean square deviation trends, which were comparable to the control, SAH. Post-MD, the 123519051-receptor complex had the highest number of H-bonds (4 to 5) after the control, out of which three exhibited the highest percentage occupancy (50%, 24% and 79%). Both docking and MD, 123519051 showed an H-bond with the residue Gly111, which was also found for the control-protein complex. 123519051 showed the lowest binding free energy with ΔGbind of -89 kJ/mol. Steered molecular dynamics depicted that 123519051 had the maximum magnitude of dissociation (1436.43 kJ/mol/nm), which was more than the control, validating its stable complex formation. This study concluded that 123519051 is a binder and could inhibit the protein NS5 of JE.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abdulfattah Y Alhazmi
- Pharmaceutical Practices Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences - AlQuwayiyah, Shaqra University, Saudi Arabia
| | - Zia Ur Rehman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences - AlQuwayiyah, Shaqra University, Saudi Arabia
| | - Nahed S Alharthi
- Department of Medical Laboratory. College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudia Arabia
| | - Hayaa M Alhuthali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Faris F Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faez Falah Alshehri
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | | | - Faisal Al-Otaibi
- Department of Pharmacy Practice, College of Pharmacy, Shaqra University, Saudi Arabia
| |
Collapse
|
4
|
Pathak A, Singh SP, Singh DB, Anjaria P, Tiwari A. Computational exploration of microsomal cytochrome P450 3A1 enzyme modulation by phytochemicals of Cichorium intybus L.: Insights into drug metabolism. Biopharm Drug Dispos 2024; 45:15-29. [PMID: 38243990 DOI: 10.1002/bdd.2380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/29/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
Drug metabolism plays a crucial role in drug fate, including therapeutic inactivation or activation, as well as the formation of toxic compounds. This underscores the importance of understanding drug metabolism in drug discovery and development. Considering the substantial costs associated with traditional drug development methods, computational approaches have emerged as valuable tools for predicting the metabolic fate of drug candidates. With this in mind, the present study aimed to investigate the potential mechanisms underlying the modulation of microsomal cytochrome P450 3A1 (CYP3A1) enzyme activity by various phytochemicals found in Cichorium intybus L., commonly known as chicory. To achieve this goal, several in silico methods, including molecular docking and molecular dynamics (MD) simulation, were employed to explore computationally the microsomal CYP3A1 enzyme. Schrodinger software was utilized for the molecular docking study, which involved the interaction analysis between CYP3A1 and 28 phytoconstituents of Cichorium intybus. Virtual screening of 28 compounds from chicory led to the identification of the top five ranked compounds. These compounds were evaluated for drug-likeness properties, pharmacokinetic profiles, and predicted binding affinities to CYP3A1. Caffeoylshikimic acid and cichoric acid emerged as promising candidates due to their favorable characteristics, including good oral bioavailability and high binding affinities to CYP3A1. Molecular dynamics simulations were conducted to assess the stability of caffeoylshikimic acid within the CYP3A1 binding pocket. The results demonstrated that caffeoylshikimic acid maintained stable interactions with the enzyme throughout the simulation, suggesting its potential as an effective modulator of CYP3A1 activity. The findings of this study have the potential to provide valuable insights into the complex molecular mechanisms by which Cichorium intybus L. acts on hepatocytes and modulates CYP3A1 enzyme expression or activity. By elucidating the impact of these phytochemicals on drug metabolism, this research contributes to our understanding of how chicory may interact with drugs and influence their efficacy and safety profiles.
Collapse
Affiliation(s)
- Abhishek Pathak
- Department of Veterinary Pharmacology & Toxicology, College of Veterinary and Animal Science, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India
| | - Satya Pal Singh
- Department of Veterinary Pharmacology & Toxicology, College of Veterinary and Animal Science, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India
| | - Dev Bukhsh Singh
- Department of Biotechnology, Siddharth University, Kapilvastu, Siddharth Nagar, India
| | - Pranav Anjaria
- College of Veterinary Science & Animal Husbandry, Kamdhenu University, Anand, Gujarat, India
| | - Apoorv Tiwari
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India
| |
Collapse
|
5
|
Singh SK, Sasmal S, Kumar Y. Therapeutic Potential of HMF and Its Derivatives: a Computational Study. Appl Biochem Biotechnol 2024; 196:841-877. [PMID: 37223872 PMCID: PMC10206368 DOI: 10.1007/s12010-023-04547-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2023] [Indexed: 05/25/2023]
Abstract
Over the past century, chemicals and energy have increasingly been derived from non-renewable resources. The growing demand for essential chemicals and shrinking inventory make reliable, sustainable sources essential. Carbohydrates offer by far the greatest carbon supply. Furan compounds, a particular family of dehydration products, are believed to offer high chemical potential. Here, we analyze 5-HMF (5, hydroxymethylfurfural) and some of its derivatives in particular, a furan-type platform chemical. To analyze the therapeutic potential of HMF and its derivatives, this study utilized cutting-edge technologies such as computer-aided drug design, virtual screening, molecular docking, and molecular dynamic simulation. We conducted 189 docking simulations and examined some of the most promising dock poses using the molecular dynamic simulator. As for the receptors for our compounds, the leading candidates are human acetylcholinesterase, beta-lactamases, P. aeruginosa LasR, and S. aureus tyrosyl-tRNA synthetases. Out of all derivatives considered in this study, 2,5-furandicarboxylic acid (FCA) performed best.
Collapse
Affiliation(s)
- Shashank Kumar Singh
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology, Dwarka Sector-3, New Delhi, 110078, India
| | - Soumya Sasmal
- Department of Biotechnology, Visva Bharati, Santiniketan, West Bengal, 731235, India
| | - Yatender Kumar
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology, Dwarka Sector-3, New Delhi, 110078, India.
| |
Collapse
|
6
|
Kumar P, Kayastha A, Singh VK, Kayastha AM. In Silico Structural and Functional Insight into the Binding Interactions of the Modeled Structure of Watermelon Urease with Urea. ACS Omega 2024; 9:2272-2285. [PMID: 38250402 PMCID: PMC10795036 DOI: 10.1021/acsomega.3c05993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Urease (EC 3.5.1.5) is an amidohydrolase. This nickel-dependent metalloenzyme converts urea into NH3 and CO2. Despite their vital role in plants, the structure and function of watermelon (Citrullus lanatus) urease are unknown. We used third- and fourth-generation gene prediction algorithms to annotate the C. lanatus urease sequence in this investigation. The solved urease structure from Canavalia ensiformis (PDB ID: 4GY7) was utilized as a template model to identify the target 3-D model structure of the unknown C. lanatus urease for the first time. Cluretox, the C. lanatus urease intrinsic disordered area identical to Jaburetox, was also found. The C. lanatus urease structure was docked with urea to study atom interaction, amino acid interactions, and binding analyses in the urease-urea complex at 3.5 Å. This study found that amino acids His517, Gly548, Asp631, Ala634, Thr569, His543, Met635, His407, His490, and Ala438 of C. lanatus urease bind urea. To study the molecular basis and mode of action of C. lanatus urease, molecular dynamics simulation was performed and RMSD, RMSF, Rg, SAS, and H-bond analyses were done. The calculated binding free energy (ΔG) for the urea-urease complex at 100 ns using the MM/PBSA method is -7.61 kJ/mol. Understanding its catalytic principles helps scientists construct more efficient enzymes, tailor fertilization to boost agricultural output, and create sustainable waste management solutions.
Collapse
Affiliation(s)
- Prince Kumar
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Arpan Kayastha
- Department
of Biosciences and Bioengineering, IIT Roorkee, Roorkee 247667, India
| | - Vinay Kumar Singh
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Arvind M. Kayastha
- School
of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| |
Collapse
|
7
|
Tuo H, Li W, Zhao W, Zhao J, Li D, Jin L. Shikonin alleviates doxorubicin-induced cardiotoxicity via Mst1/Nrf2 pathway in mice. Sci Rep 2024; 14:924. [PMID: 38195835 PMCID: PMC10776756 DOI: 10.1038/s41598-024-51675-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/08/2024] [Indexed: 01/11/2024] Open
Abstract
Doxorubicin (DOX) is a popular and potent anticancer drug, but its cardiotoxicity limits its clinical application. Shikonin has a wide range of biological functions, including antioxidant and anti-inflammatory effects. The aim of this study was to investigate the effects of shikonin on DOX-induced cardiac injury and to identify the underlying mechanisms. Mice receiving shikonin showed reduced cardiac injury response and enhanced cardiac function after DOX administration. Shikonin significantly attenuated DOX-induced oxidative damage, inflammation accumulation and cardiomyocyte apoptosis. Shikonin protects against DOX-induced cardiac injury by inhibiting Mammalian sterile 20-like kinase 1 (Mst1) and oxidative stress and activating the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway. In conclusion, shikonin alleviates DOX-induced cardiotoxicity by inhibiting Mst1 and activating Nrf2. Shikonin may be used to treat DOX-induced cardiac injury.
Collapse
Affiliation(s)
- Hu Tuo
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenjing Li
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wei Zhao
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Juan Zhao
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Danni Li
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lin Jin
- Department of Orthopedics, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuhan, 430060, China.
| |
Collapse
|
8
|
Hafeez S, Zafar Paracha R, Adnan F. Designing of fragment based inhibitors with improved activity against E. coli AmpC β-lactamase compared to the conventional antibiotics. Saudi J Biol Sci 2024; 31:103884. [PMID: 38125736 PMCID: PMC10730856 DOI: 10.1016/j.sjbs.2023.103884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
One of the most common primary resistance mechanism of multi-drug resistant (MDR) Gram negative pathogenic bacteria to combat β-lactam antibiotics, such as penicillins, cephalosporins and carbapenems is the generation of β- lactamases. The uropathogenic E. coli is mostly getting multi-drug resistance due to the synthesis of AmpC β-lactamases and therefore new antibiotics and inhibitors are needed to treat the evolving infections. The current study was designed for targetting AmpC β-lactamase of E. coli using molecular docking based virtual screening, linking fragments for designing novel compounds and binding mode analysis using molecular dynamic simulation with target protein. The FCH group all-purpose fragment library consisting of 9388 fragments has been screened against AmpC β-lactamase protein of E. coli and the antibiotics and anti-infectives used in treatment of Urinary tract Infections (UTIs) were also screened with AmpC β-lactamase protein. Among the 9388 fragments, 339 fragment candidates were selected and linked with cefepime antibiotic having maximum binding affinity for AmpC target protein. Computational analysis of interactions as well as molecular dynamics (MD) simulations were also conducted for identifying the most promising ligand-pocket complexes from docking investigations to comprehend their thermodynamic properties and verify the docking outcomes as well. Overall, the linked complexes (LCs) showed good binding interactions with AmpC β-lactamase. Interestingly, our fragment-based LCs remained relatively stable in comparison with cefepime antibiotic. Moreover, S12 fragment linked complex remained the most stable during 50 ns with remarkable number of interactions indicating it as promising candidate in novel lead discovery against MDR E. coli infections.
Collapse
Affiliation(s)
- Sidrah Hafeez
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Rehan Zafar Paracha
- School of Interdisciplinary Engineering and Sciences (SINES), National University of Science and Technology (NUST), Islamabad 44000, Pakistan
| | - Fazal Adnan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| |
Collapse
|
9
|
Rabaan AA, Halwani MA, Garout M, Alotaibi J, AlShehail BM, Alotaibi N, Almuthree SA, Alshehri AA, Alshahrani MA, Othman B, Alqahtani A, Alissa M. Exploration of phytochemical compounds against Marburg virus using QSAR, molecular dynamics, and free energy landscape. Mol Divers 2023:10.1007/s11030-023-10753-0. [PMID: 37925643 DOI: 10.1007/s11030-023-10753-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 10/21/2023] [Indexed: 11/07/2023]
Abstract
Marburg virus disease (MVD) is caused by the Marburg virus, a one-of-a-kind zoonotic RNA virus from the genus Filovirus. Thus, this current study employed AI-based QSAR and molecular docking-based virtual screening for identifying potential binders against the target protein (nucleoprotein (NP)) of the Marburg virus. A total of 2727 phytochemicals were used for screening, out of which the top three compounds (74977521, 90470472, and 11953909) were identified based on their predicted bioactivity (pIC50) and binding score (< - 7.4 kcal/mol). Later, MD simulation in triplicates and trajectory analysis were performed which showed that 11953909 and 74977521 had the most stable and consistent complex formations and had the most significant interactions with the highest number of hydrogen bonds. PCA (principal component analysis) and FEL (free energy landscape) analysis indicated that these compounds had favourable energy states for most of the conformations. The total binding free energy of the compounds using the MM/GBSA technique showed that 11953909 (ΔGTOTAL = - 30.78 kcal/mol) and 74977521 (ΔGTOTAL = - 30 kcal/mol) had the highest binding affinity with the protein. Overall, this in silico pipeline proposed that the phytochemicals 11953909 and 74977521 could be the possible binders of NP. This study aimed to find phytochemicals inhibiting the protein's function and potentially treating MVD.
Collapse
Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia.
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia.
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan.
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, 4781, Al Baha, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Jawaher Alotaibi
- Infectious diseases Unit, Department of Medicine, King Faisal Specialist Hospital and Research Center, 11564, Riyadh, Saudi Arabia
| | - Bashayer M AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Nouf Alotaibi
- Clinical pharmacy Department, College of Pharmacy, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Souad A Almuthree
- Department of Infectious Disease, King Abdullah Medical City, 43442, Makkah, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 61441, Najran, Saudi Arabia
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 61441, Najran, Saudi Arabia
| | - Basim Othman
- Department of Public Health, Faculty of Applied Medical Sciences, Al Baha University, 65779, Al Baha, Saudi Arabia
| | - Abdulaziz Alqahtani
- Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, 61321, Abha, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia.
| |
Collapse
|
10
|
Tewari D, Rawat K, Bisht A, Almoyad MAA, Wahab S, Chandra S, Pande V. Screening of potential inhibitors of Leishmania major N-myristoyltransferase from Azadirachta indica phytochemicals for leishmaniasis drug discovery by molecular docking, molecular dynamics simulation and density functional theory methods. J Biomol Struct Dyn 2023:1-18. [PMID: 37922151 DOI: 10.1080/07391102.2023.2279281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/30/2023] [Indexed: 11/05/2023]
Abstract
Leishmaniasis is one of the most neglected parasitic diseases worldwide. The toxicity of current drugs used for its treatment is a major obstacle to their effectiveness, necessitating the discovery and development of new therapeutic agents for better disease control. In Leishmania parasites, N-Myristoyltransferase (NMT) has been identified as a promising target for drug development. Thus, exploring well-known medicinal plants such as Azadirachta indica and their phytochemicals can offer a diverse range of treatment options, potentially leading to disease prevention and control. To assess the therapeutic potential of these compounds, their ADMET prediction and drug-likeness properties were analyzed. The top 4 compounds were selected which had better and significantly low binding energy than the reference molecule QMI. Based on the binding energy score of the top compounds, the results show that Isonimocinolide has the highest binding affinity (-9.8 kcal/mol). In addition, a 100 ns MD simulation of the four best compounds showed that Isonimocinolide and Nimbolide have good stability with LmNMT. These compounds were then subjected to MMPBSA (last 30 ns) calculation to analyze protein-ligand stability and dynamic behavior. Nimbolide and Meldenin showed lowest binding free energy i.e. -84.301 kJ/mol and -91.937 kJ/mol respectively. DFT was employed to calculate the HOMO-LUMO energy gap, global reactivity parameters, and molecular electrostatic potential of all hit molecules. The promising results obtained from MD simulations and MMPBSA analyses provide compelling evidence for the potential use of these compounds in future drug development efforts for the treatment of leishmaniasis.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Disha Tewari
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Kalpana Rawat
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Amisha Bisht
- Department of Botany, P.G. College Bageshwar, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Mohammad Ali Abdullah Almoyad
- Department of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Khamis Mushyt, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| |
Collapse
|
11
|
Ngema SS, Khumalo SH, Ojo MC, Pooe OJ, Malilehe TS, Basson AK, Madoroba E. Evaluation of Antimicrobial Activity by Marine Nocardiopsis dassonvillei against Foodborne Listeria monocytogenes and Shiga Toxin-Producing Escherichia coli. Microorganisms 2023; 11:2539. [PMID: 37894198 PMCID: PMC10609338 DOI: 10.3390/microorganisms11102539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/12/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
The emergence of multidrug-resistant pathogens creates public health challenges, prompting a continuous search for effective novel antimicrobials. This study aimed to isolate marine actinomycetes from South Africa, evaluate their in vitro antimicrobial activity against Listeria monocytogenes and Shiga toxin-producing Escherichia coli, and characterize their mechanisms of action. Marine actinomycetes were isolated and identified by 16S rRNA sequencing. Gas chromatography-mass spectrometry (GC-MS) was used to identify the chemical constituents of bioactive actinomycetes' secondary metabolites. Antibacterial activity of the secondary metabolites was assessed by the broth microdilution method, and their mode of actions were predicted using computational docking. While five strains showed antibacterial activity during primary screening, only Nocardiopsis dassonvillei strain SOD(B)ST2SA2 exhibited activity during secondary screening for antibacterial activity. GC-MS identified five major bioactive compounds: 1-octadecene, diethyl phthalate, pentadecanoic acid, 6-octadecenoic acid, and trifluoroacetoxy hexadecane. SOD(B)ST2SA2's extract demonstrated minimum inhibitory concentration and minimum bactericidal concentration, ranging from 0.78-25 mg/mL and 3.13 to > 25 mg/mL, respectively. Diethyl phthalate displayed the lowest bacterial protein-binding energies (kcal/mol): -7.2, dihydrofolate reductase; -6.0, DNA gyrase B; and -5.8, D-alanine:D-alanine ligase. Thus, marine N. dassonvillei SOD(B)ST2SA2 is a potentially good source of antibacterial compounds that can be used to control STEC and Listeria monocytogenes.
Collapse
Affiliation(s)
- Siyanda S. Ngema
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Solomuzi H. Khumalo
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Michael C. Ojo
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Ofentse J. Pooe
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa;
| | - Tsolanku S. Malilehe
- Department of Water and Sanitation, University of Limpopo, Private Bag X1106, Polokwane 0727, South Africa;
| | - Albertus K. Basson
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Evelyn Madoroba
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| |
Collapse
|
12
|
Singh AK, Prajapati KS, Kumar S. Hesperidin potentially interacts with the catalytic site of gamma-secretase and modifies notch sensitive genes and cancer stemness marker expression in colon cancer cells and colonosphere. J Biomol Struct Dyn 2023; 41:8432-8444. [PMID: 36239003 DOI: 10.1080/07391102.2022.2134213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/03/2022] [Indexed: 10/17/2022]
Abstract
Gamma secretase (GS) produces Notch Intracellular Domain (NICD) by trans-membrane cleavage of notch receptor. The NICD enters the nucleus and activates the notch signaling pathway (NSP) by activating notch-responsive gene transcription. Hyperactivation of NSP is related to cancer aggressiveness, therapy resistance, and poor therapy outcome, and decreased overall disease-free survival in patients. Till date, none of the GS inhibitors (GSI) has been clinically approved due to their toxicity in patients. Thus in the present study, we explored the GS catalytic site binding potential of hesperidin (natural flavone glycoside) and its effect on notch responsive gene expression in HCT-116 cells. Molecular docking, MM-GBSA binding energy calculations, and molecular dynamics (MD) simulation experiments were performed to study the GS catalytic site binding potential of hesperidin. The compound showed better GS catalytic site binding potential at the active site compared to experimentally validated GSI, N-N-(3, 5-Difluorophenacetyl)-L-alanyl-S-phenylglycine t-butyl ester (DAPT) in molecular docking and MM-GBSA experiments. MD simulation results showed that hesperidin forms stable and energetically favorable complex with gamma secretase in comparison to standard inhibitor (DAPT)-GS complex. Further, in vitro experiments showed that hesperidin inhibited cell growth and sphere formation potential in HCT-116 cells. Further, hesperidin treatment altered notch responsive genes (Hes1, Hey1, and E-cad) and cancer stemness/self-renewal markers expression at transcription levels. In conclusion, hesperidin produces toxicity in HCT-116 cells and decreases colonosphere formation by inhibiting transcription of notch signaling pathway target genes and stemness markers.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Kumari Sunita Prajapati
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| |
Collapse
|
13
|
El Khatabi K, Kumar S, El-Mernissi R, Singh AK, Ajana MA, Lakhlifi T, Bouachrine M. Novel Eubacterium rectale inhibitor from Coriandrum sativum L. for possible prevention of colorectal cancer: a computational approach. J Biomol Struct Dyn 2023; 41:8402-8416. [PMID: 36264092 DOI: 10.1080/07391102.2022.2134210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/03/2022] [Indexed: 10/24/2022]
Abstract
This research aims to screen out the effective bioactive compounds from Coriander (Coriandrum sativum L.), which may be novel potential inhibitors of Eubacterium rectale for the prevention of colorectal cancer (CRC). A series of 8 coriander-derived chemical compounds previously assessed for their anti-inflammatory, antioxidant, and antidiabetic activities were tested against Carbohydrate ABC transporter substrate-binding protein and compared to the standard inhibitor Acarbose, to support their use as novel Eubacterium rectale inhibitors. Herein, these derivatives were submitted to a thorough analysis of docking studies, in which detailed interactions of the selected phytocompounds with carbohydrate ABC transporter substrate-binding protein were revealed. Molecular docking analysis recommends Rutin, Gallocatechin, and Epigallocatechin as the most potential Eubacterium rectale inhibitors among the eight selected phytochemical compounds. Subsequently, the stability of the three selected phytochemical complexes was checked using molecular dynamics (MD) simulation at 100 ns and Molecular Mechanics combined with Poisson-Boltzmann Surface Area (MM-PBSA). The results show quite good stability for Rutin and Gallocatechin. In silico ADMET prediction was performed on the selected compounds, and the findings revealed a reasonably good ADMET profile for both Rutin and Gallocatechin. The current findings predict that Gallocatechin could be a better CRC preventive natural compound, and, further in vitro, in vivo and clinical studies may confirm its therapeutic potential.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Khalil El Khatabi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Meknes, Morocco
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Reda El-Mernissi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Meknes, Morocco
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Mohammed Aziz Ajana
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Meknes, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Meknes, Morocco
- EST Khenifra, Sultan Moulay Sliman University, Beni-Mellal, Morocco
| |
Collapse
|
14
|
Roy R, Sk MF, Tanwar O, Kar P. Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease. Mol Divers 2023; 27:1587-1602. [PMID: 35978064 PMCID: PMC9385416 DOI: 10.1007/s11030-022-10513-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/08/2022] [Indexed: 11/04/2022]
Abstract
To fight against the devastating coronavirus disease 2019 (COVID-19), identifying robust anti-SARS-CoV-2 therapeutics from all possible directions is necessary. To contribute to this effort, we selected a human metabolites database containing waters and lipid-soluble metabolites to screen against the 3-chymotrypsin-like proteases (3CLpro) protein of SARS-CoV-2. The top 8 hits from virtual screening displayed a docking score varying between ~ - 11 and ~ - 14 kcal/mol. Molecular dynamics simulations complement the virtual screening study in conjunction with the molecular mechanics generalized Born surface area (MM/GBSA) scheme. Our analyses revealed that (HMDB0132640) has the best glide docking score, - 14.06 kcal/mol, and MM-GBSA binding free energy, - 18.08 kcal/mol. The other three lead molecules are also selected along with the top molecule through a critical inspection of their pharmacokinetic properties. HMDB0132640 displayed a better binding affinity than the other three compounds (HMDB0127868, HMDB0134119, and HMDB0125821) due to increased favorable contributions from the intermolecular electrostatic and van der Waals interactions. Further, we have investigated the ligand-induced structural dynamics of the main protease. Overall, we have identified new compounds that can serve as potential leads for developing novel antiviral drugs against SARS-CoV-2 and elucidated molecular mechanisms of their binding to the main protease. Identification of probable hits from human metabolites against SARS-CoV-2 using integrated computational approaches-Missed against MS.
Collapse
Affiliation(s)
- Rajarshi Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India
| | - Omprakash Tanwar
- Department of Pharmacy, Shri G. S. Institute of Technology and Science, Indore, Madhya Pradesh, 452003, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India.
| |
Collapse
|
15
|
Damphathik C, Songsiriritthigul C, Lerdsri J, Jakmunee J, Wongnongwa Y, Jungsuttiwong S, Ortner A, Kalcher K, Samphao A. A novel immunosensor based on cobalt oxide nanocomposite modified single walled carbon nanohorns for the selective detection of aflatoxin B1. Talanta 2023; 258:124472. [PMID: 37013336 DOI: 10.1016/j.talanta.2023.124472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/13/2023] [Accepted: 03/18/2023] [Indexed: 03/29/2023]
Abstract
We developed a novel, sensitive, and selective platform for the specific determination of aflatoxin B1 (AFB1). Single-walled carbon nanohorns decorated by a cobalt oxide composite and gold nanoparticles were created to provide facile electron transfer and improve the sensor's sensitivity. In addition, we attributed the selectivity of the proposed sensor to the specific binding property of the anti-aflatoxin B1 antibody. We clarified the specific interaction of the proposed immunosensor to AFB1 using homology modeling combined with molecular docking. In the presence of AFB1, the current signal of the modified electrode reduced; this involved specific antibody-antigen binding, including hydrophobic hydrogen bonding and pi-pi stack interactions. The new AFB1 sensor platform showed two linearity ranges of 0.01-1 ng mL-1 and 1-100 ng mL-1, with the limit of detection at 0.0019 ng mL-1. We investigated the proposed immunosensor in real samples, including peanuts, certified reference material of a peanut sample (labeled 206 μg kg-1 AFB1), corn, and chicken feed. The sensor's accuracy was 86.1-104.4% recovery, which agrees with the reference HPLC technique using paired t-test analysis. The present work shows excellent performance for AFB1 detection and could be applied for food quality control or modified to detect other mycotoxins.
Collapse
|
16
|
Choudhary P, Singh T, Amod A, Singh S. Evaluation of phytoconstituents of Tinospora cordifolia against K417N and N501Y mutant spike glycoprotein and main protease of SARS-CoV-2- an in silico study. J Biomol Struct Dyn 2023; 41:4106-4123. [PMID: 35467486 DOI: 10.1080/07391102.2022.2062787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/02/2022] [Indexed: 10/18/2022]
Abstract
Coronavirus disease 2019 (COVID-19) caused appalling conditions over the globe, which is currently faced by the entire human population. One of the primary reasons behind the uncontrollable situation is the lack of specific therapeutics. In such conditions, drug repurposing of available drugs (viz. Chloroquine, Lopinavir, etc.) has been proposed, but various clinical and preclinical investigations indicated the toxicity and adverse side effects of these drugs. This study explores the inhibition potency of phytochemicals from Tinospora cordifolia (Giloy) against SARS CoV-2 drugable targets (spike glycoprotein and Mpro proteins) using molecular docking and MD simulation studies. ADMET, virtual screening, MD simulation, postsimulation analysis (RMSD, RMSF, Rg, SASA, PCA, FES) and MM-PBSA calculations were carried out to predict the inhibition efficacy of the phytochemicals against SARS CoV-2 targets. Tinospora compounds showed better binding affinity than the corresponding reference. Their binding affinity ranges from -9.63 to -5.68 kcal/mole with spike protein and -10.27 to -7.25 kcal/mole with main protease. Further 100 ns exhaustive simulation studies and MM-PBSA calculations supported favorable and stable binding of them. This work identifies Nine Tinospora compounds as potential inhibitors. Among those, 7-desacetoxy-6,7-dehydrogedunin was found to inhibit both spike (7NEG) and Mpro (7MGS and 6LU7) proteins, and Columbin was found to inhibit selected spike targets (7NEG and 7NX7). In all the analyses, these compounds performed well and confirms the stable binding. Hence the identified compounds, advocated as potential inhibitors can be taken for further in vitro and in vivo experimental validation to determine their anti-SARS-CoV-2 potential.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Princy Choudhary
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Tanu Singh
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Ayush Amod
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Sangeeta Singh
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| |
Collapse
|
17
|
Dehury B, Mishra S, Pati S. Structural insights into SARS-CoV-2 main protease conformational plasticity. J Cell Biochem 2023. [PMID: 37099673 DOI: 10.1002/jcb.30409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/30/2023] [Accepted: 04/11/2023] [Indexed: 04/28/2023]
Abstract
The spread of different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants underscores the need for insights into the structural properties of its structural and non-structural proteins. The highly conserved homo-dimeric chymotrypsin-like protease (3CL MPRO ), belonging to the class of cysteine hydrolases, plays an indispensable role in processing viral polyproteins that are involved in viral replication and transcription. Studies have successfully demonstrated the role of MPRO as an attractive drug target for designing antiviral treatments because of its importance in the viral life cycle. Herein, we report the structural dynamics of six experimentally solved structures of MPRO (i.e., 6LU7, 6M03, 6WQF, 6Y2E, 6Y84, and 7BUY including both ligand-free and ligand-bound states) at different resolutions. We have employed a structure-based balanced forcefield, CHARMM36m through state-of-the-art all-atoms molecular dynamics simulations at µ-seconds scale at room temperature (303K) and pH 7.0 to explore their structure-function relationship. The helical domain-III responsible for dimerization mostly contributes to the altered conformational states and destabilization of MPRO . A keen observation of the high degree of flexibility in the P5 binding pocket adjoining domain II-III highlights the reason for observation of conformational heterogeneity among the structural ensembles of MPRO . We also observe a differential dynamics of the catalytic pocket residues His41, Cys145, and Asp187, which may lead to catalytic impairment of the monomeric proteases. Among the highly populated conformational states of the six systems, 6LU7 and 7M03 forms the most stable and compact MPRO conformation with intact catalytic site and structural integrity. Altogether, our findings from this extensive study provides a benchmark to identify physiologically relevant structures of such promising drug targets for structure-based drug design and discovery of potent drug-like compounds having clinical potential.
Collapse
Affiliation(s)
- Budheswar Dehury
- Division of Bioinformatics, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Sarbani Mishra
- Division of Bioinformatics, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Division of Bioinformatics, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| |
Collapse
|
18
|
Wu J, Gao T, Guo H, Zhao L, Lv S, Lv J, Yao R, Yu Y, Ma F. Application of molecular dynamics simulation for exploring the roles of plant biomolecules in promoting environmental health. Sci Total Environ 2023; 869:161871. [PMID: 36708839 DOI: 10.1016/j.scitotenv.2023.161871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Understanding the dynamic changes of plant biomolecules is vital for exploring their mechanisms in the environment. Molecular dynamics (MD) simulation has been widely used to study structural evolution and corresponding properties of plant biomolecules at the microscopic scale. Here, this review (i) outlines structural properties of plant biomolecules, and the crucial role of MD simulation in advancing studies of the biomolecules; (ii) describes the development of MD simulation in plant biomolecules, determinants of simulation, and analysis parameters; (iii) introduces the applications of MD simulation in plant biomolecules, including the response of the biomolecules to multiple stresses, their roles in corrosive environments, and their contributions in improving environmental health; (iv) reviews techniques integrated with MD simulation, such as molecular biology, quantum mechanics, molecular docking, and machine learning modeling, which bridge gaps in MD simulation. Finally, we make suggestions on determination of force field types, investigation of plant biomolecule mechanisms, and use of MD simulation in combination with other techniques. This review provides comprehensive summaries of the mechanisms of plant biomolecules in the environment revealed by MD simulation and validates it as an applicable tool for bridging gaps between macroscopic and microscopic behavior, providing insights into the wide application of MD simulation in plant biomolecules.
Collapse
Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China.
| | - Tian Gao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Haijuan Guo
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Sidi Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Ruyi Yao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Yanyi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| |
Collapse
|
19
|
Kalhor H, Abolhasani H, Kalhor R, Komeili Movahhed T, Rahimi H. Interactions of heparin derivatives with recombinant human keratinocyte growth factor: Structural stability and bioactivity effect study. Proteins 2023; 91:542-554. [PMID: 36424813 DOI: 10.1002/prot.26448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 11/05/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
Heparin and heparan sulfate are important glycosaminoglycans that can regulate the activities of many vital proteins, especially the fibroblast growth factor (FGF) family. Because FGF7 (KGF) has an important role in tissue repair and maintaining the integrity of the mucosal barrier, recombinant human keratinocyte growth factor (rhKGF, palifermin) has been approved for the treatment of wound healing and oral cavity. Due to heparin plays an important role in the KGF signaling pathway, a more detailed study of the drug-drug interactions (DDIs) between rhKGF and heparin at the atomic level and investigating their synergistic effect on each other in terms of biology, especially in silico, is necessary for a better understanding of DDIs. In this study, DDIs between rhKGF and low-molecular weight heparin types (LMWH) were investigated. In this regard, scrutiny of the influence of the synergistic heparin types on the structure and biostability of rhKGF is accomplished using computational methods such as molecular docking and molecular dynamic simulations (MDs). Subsequently, the motion behavior of rhKGF in interaction with LMWHs was evaluated based on eigenvectors by using principal component analysis (PCA). Also, the binding free energies of rhKGF-LMWH complexes were calculated by the molecular mechanics/Poisson-Boltzmann surface area (MM-BPSA) method. The result showed that rhKGF-idraparinux (-6.9 kcal/mol) and rhKGF-heparin (-6.0 kcal/mol) complexes had significant binding affinity as well as they had a more stable binding to rhKGF than to other LMWH during 100 ns simulation. However, in order to confirm the curative effect of these drugs, clinical trials must be done.
Collapse
Affiliation(s)
- Hourieh Kalhor
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Hoda Abolhasani
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.,Department of Pharmacology, School of Medicine, Qom University of Medical Sciences, Qom, Iran
| | - Reyhaneh Kalhor
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.,Department of Genetics, Colleague of Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| | | | - Hamzeh Rahimi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Host-pathogen Interaction Department, Texas Biomedical Research Institute, San Antonio, Texas, USA
| |
Collapse
|
20
|
Mushebenge AG, Ugbaja SC, Mtambo SE, Ntombela T, Metu JI, Babayemi O, Chima JI, Appiah-Kubi P, Odugbemi AI, Ntuli ML, Khan R, Kumalo HM. Unveiling the Inhibitory Potentials of Peptidomimetic Azanitriles and Pyridyl Esters towards SARS-CoV-2 Main Protease: A Molecular Modelling Investigation. Molecules 2023; 28:molecules28062641. [PMID: 36985614 PMCID: PMC10051727 DOI: 10.3390/molecules28062641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 02/14/2023] [Accepted: 03/02/2023] [Indexed: 03/17/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for COVID-19, which was declared a global pandemic in March 2020 by the World Health Organization (WHO). Since SARS-CoV-2 main protease plays an essential role in the virus’s life cycle, the design of small drug molecules with lower molecular weight has been a promising development targeting its inhibition. Herein, we evaluated the novel peptidomimetic azatripeptide and azatetrapeptide nitriles against SARS-CoV-2 main protease. We employed molecular dynamics (MD) simulations to elucidate the selected compounds’ binding free energy profiles against SARS-CoV-2 and further unveil the residues responsible for the drug-binding properties. Compound 8 exhibited the highest binding free energy of −49.37 ± 0.15 kcal/mol, followed by compound 7 (−39.83 ± 0.19 kcal/mol), while compound 17 showed the lowest binding free energy (−23.54 ± 0.19 kcal/mol). In addition, the absorption, distribution, metabolism, and excretion (ADME) assessment was performed and revealed that only compound 17 met the drug-likeness parameters and exhibited high pharmacokinetics to inhibit CYP1A2, CYP2C19, and CYP2C9 with better absorption potential and blood-brain barrier permeability (BBB) index. The additional intermolecular evaluations suggested compound 8 as a promising drug candidate for inhibiting SARS-CoV-2 Mpro. The substitution of isopropane in compound 7 with an aromatic benzene ring in compound 8 significantly enhanced the drug’s ability to bind better at the active site of the SARS-CoV-2 Mpro.
Collapse
Affiliation(s)
- Aganze G. Mushebenge
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
| | - Samuel C. Ugbaja
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
- Correspondence: (S.C.U.); (H.M.K.)
| | - Sphamandla E. Mtambo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Pharmaceutical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Joy I. Metu
- National Institute for Nigerian Languages, Aba 453106, Nigeria;
| | - Oludotun Babayemi
- Cloneshouse Nigeria, 6th Floor, Left Wing, NICON Plaza, Plot 242, Muhammadu Buhari Way, Central Business District, Abuja 900103, Nigeria;
| | - Joy I. Chima
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
| | - Patrick Appiah-Kubi
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
| | - Adeshina I. Odugbemi
- South African National Bioinformatics Institute, Faculty of Natural Sciences, University of the Western Cape, Cape Town 7535, South Africa;
| | - Mthobisi L. Ntuli
- Department of Mathematics, Faculty of Applied Science, Durban University of Technology, Durban 4000, South Africa;
| | - Rene Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
- Correspondence: (S.C.U.); (H.M.K.)
| |
Collapse
|
21
|
Banjare L, Singh Y, Verma SK, Singh AK, Kumar P, Kumar S, Jain AK, Thareja S. Multifaceted 3D-QSAR analysis for the identification of pharmacophoric features of biphenyl analogues as aromatase inhibitors. J Biomol Struct Dyn 2023; 41:1322-1341. [PMID: 34963408 DOI: 10.1080/07391102.2021.2019122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Aromatase, a cytochrome P450 enzyme, is responsible for the conversion of androgens to estrogens, which fuel the multiplication of cancerous cells. Inhibition of estrogen biosynthesis by aromatase inhibitors (AIs) is one of the highly advanced therapeutic approach available for the treatment of estrogen-positive breast cancer. Biphenyl moiety aids lipophilicity to the conjugated scaffold and enhances the accessibility of the ligand to the target. The present study is focused on the investigation of, the mode of binding of biphenyl with aromatase, prediction of ligand-target binding affinities, and pharmacophoric features essential for favorable for aromatase inhibition. A multifaceted 3D-QSAR (SOMFA, Field and Gaussian) along with molecular docking, molecular dynamic simulations and pharmacophore mapping were performed on a series of biphenyl bearing molecules (1-33) with a wide range of aromatase inhibitory activity (0.15-920 nM). Among the generated 3D-QSAR models, the Force field-based 3D-QSAR model (R2 = 0.9151) was best as compared to SOMFA and Gaussian Field (R2=0.7706, 0.9074, respectively). However, all the generated 3D-QSAR models were statistically fit, robust enough, and reliable to explain the variation in biological activity in relation to pharmacophoric features of dataset molecules. A four-point pharmacophoric features with three acceptor sites (A), one aromatic ring (R) features, AAAR_1, were obtained with the site and survival score values 0.890 and 4.613, respectively. The generated 3D-QSAR plots in the study insight into the structure-activity relationship of dataset molecules, which may help in the designing of potent biphenyl derivatives as newer inhibitors of aromatase.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Laxmi Banjare
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur, Chhattisgarh, India
| | - Yogesh Singh
- Department of Pharmaceutical Sciences and Natural Products, School of Pharmaceutical Sciences Central, University of Punjab, Bathinda, Punjab, India
| | - Sant Kumar Verma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Atul Kumar Singh
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, School of Pharmaceutical Sciences Central, University of Punjab, Bathinda, Punjab, India
| | - Shashank Kumar
- Molecular Signaling and Drug Discovery Laboratory, Department of Biochemistry, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Akhlesh Kumar Jain
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur, Chhattisgarh, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, School of Pharmaceutical Sciences Central, University of Punjab, Bathinda, Punjab, India
| |
Collapse
|
22
|
Jantan I, Arshad L, Septama AW, Haque MA, Mohamed-Hussein ZA, Govender NT. Antiviral effects of phytochemicals against severe acute respiratory syndrome coronavirus 2 and their mechanisms of action: A review. Phytother Res 2023; 37:1036-1056. [PMID: 36343627 PMCID: PMC9878073 DOI: 10.1002/ptr.7671] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022]
Abstract
The worldwide spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to health, economic, environmental, and social aspects of human lives. Currently, there are no approved treatments that can effectively block the virus although several existing antimalarial and antiviral agents have been repurposed and allowed use during the pandemic under the emergency use authorization (EUA) status. This review gives an updated overview of the antiviral effects of phytochemicals including alkaloids, flavonoids, and terpenoids against the COVID-19 virus and their mechanisms of action. Search for natural lead molecules against SARS-CoV-2 has been focusing on virtual screening and in vitro studies on phytochemicals that have shown great promise against other coronaviruses such as SARS-CoV. Until now, there is limited data on in vivo investigations to examine the antiviral activity of plants in SARS-CoV-2-infected animal models and the studies were performed using crude extracts. Further experimental and preclinical investigations on the in vivo effects of phytochemicals have to be performed to provide sufficient efficacy and safety data before clinical studies can be performed to develop them into COVID-19 drugs. Phytochemicals are potential sources of new chemical leads for the development of safe and potent anti-SARS-CoV-2 agents.
Collapse
Affiliation(s)
- Ibrahim Jantan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Laiba Arshad
- Department of Pharmacy, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Abdi Wira Septama
- Research Center for Pharmaceutical Ingredient and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong Science Center, West Java, Indonesia
| | - Md Areeful Haque
- Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia.,Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Nisha T Govender
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| |
Collapse
|
23
|
Ahmed SI, Jamil S, Ismatullah H, Hussain R, Bibi S, Khandaker MU, Naveed A, Idris AM, Emran TB. A comprehensive perspective of traditional Arabic or Islamic medicinal plants as an adjuvant therapy against COVID-19. Saudi J Biol Sci 2023; 30:103561. [PMID: 36684115 PMCID: PMC9838045 DOI: 10.1016/j.sjbs.2023.103561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/09/2022] [Accepted: 01/08/2023] [Indexed: 01/15/2023] Open
Abstract
COVID-19 is a pulmonary disease caused by SARS-CoV-2. More than 200 million individuals are infected by this globally. Pyrexia, coughing, shortness of breath, headaches, diarrhoea, sore throats, and body aches are among the typical symptoms of COVID-19. The virus enters into the host body by interacting with the ACE2 receptor. Despite many SARS-CoV-2 vaccines manufactured by distinct strategies but any evidence-based particular medication to combat COVID-19 is not available yet. However, further research is required to determine the safety and effectiveness profile of the present therapeutic approaches. In this study, we provide a summary of Traditional Arabic or Islamic medicinal (TAIM) plants' historical use and their present role as adjuvant therapy for COVID-19. Herein, six medicinal plants Aloe barbadensis Miller, Olea europaea, Trigonella foenum-graecum, Nigella sativa, Cassia angustifolia, and Ficus carica have been studied based upon their pharmacological activities against viral infections. These plants include phytochemicals that have antiviral, immunomodulatory, antiasthmatic, antipyretic, and antitussive properties. These bioactive substances could be employed to control symptoms and enhance the development of a possible COVID-19 medicinal synthesis. To determine whether or if these TAIMs may be used as adjuvant therapy and are appropriate, a detailed evaluation is advised.
Collapse
Affiliation(s)
- Shabina Ishtiaq Ahmed
- Department of Plant Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000, Islamabad, Pakistan,The Standard College for Girls, 3/530 Paris Road, Sialkot Pakistan
| | - Sehrish Jamil
- The Standard College for Girls, 3/530 Paris Road, Sialkot Pakistan
| | - Humaira Ismatullah
- School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Rashid Hussain
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan,Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
| | - Mayeen Uddin Khandaker
- Center for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Selangor, Malaysia
| | - Aisha Naveed
- Caribbean Medical University, Willemastad, Curacao-Caribbean Island, Curaçao
| | - Abubakr M. Idris
- Department of Chemistry, College of Science, King Khalid University, Abha 62529, Saudi Arabia,Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 62529, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh,Corresponding author. Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| |
Collapse
|
24
|
Oloche JJ, Oluremi BB, Aruwa CE, Sabiu S. Molecular Modeling Identification of Key Secondary Metabolites from Xylopia aethiopica as Promising Therapeutics Targeting Essential Measles Viral Proteins. Evid Based Complement Alternat Med 2023; 2023:1575358. [PMID: 36818222 DOI: 10.1155/2023/1575358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/07/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023]
Abstract
This study computationally screened three key compounds (vanillin (VAN), oxophoebine (OPB), and dihydrochalcone (DHC)) derived from Xylopia aethiopica (Guinea pepper), a medicinal plant with known antiviral activity, against key druggable measles virus (MV) proteins (fusion protein (FUP), haemagglutinin protein (HMG), and phosphoprotein (PSP)). Each molecular species was subjected to a 100 ns molecular dynamics (MD) simulation following docking, and a range of postdynamic parameters including free binding energy and pharmacokinetic properties were determined. The docking scores of the resulting OPB-FUP (-5.4 kcal/mol), OPB-HMG (-8.1 kcal/mol), and OPB-PSP (-8.0 kcal/mol) complexes were consistent with their respective binding energy values (-25.37, -28.74, and -40.68 kcal/mol), and higher than that of the reference standard, ribavirin (RBV) in each case. Furthermore, all the investigated compounds were thermodynamically compact and stable, especially HMG of MV, and this observation could be attributed to the resulting intermolecular interactions in each system. Overall, OPB may possess inhibitory properties against MV glycoproteins (FUP and HMG) and PSP that play important roles in the replication of MV and measles pathogenesis. While OPB could serve as a scaffold for the development of novel MV fusion and entry inhibitors, further in vitro and in vivo evaluation is highly recommended.
Collapse
|
25
|
Han T, Luo Z, Ji L, Wu P, Li G, Liu X, Lai Y. Identification of natural compounds as SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation. Front Microbiol 2023; 13:1095068. [PMID: 36817101 PMCID: PMC9930647 DOI: 10.3389/fmicb.2022.1095068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/29/2022] [Indexed: 02/05/2023] Open
Abstract
Background Base mutations increase the contagiousness and transmissibility of the Delta and Lambda strains and lead to the severity of the COVID-19 pandemic. Molecular docking and molecular dynamics (MD) simulations are frequently used for drug discovery and relocation. Small molecular compounds from Chinese herbs have an inhibitory effect on the virus. Therefore, this study used computational simulations to investigate the effects of small molecular compounds on the spike (S) protein and the binding between them and angiotensin-converting enzyme 2 (ACE2) receptors. Methods In this study, molecular docking, MD simulation, and protein-protein analysis were used to explore the medicinal target inhibition of Chinese herbal medicinal plant chemicals on SARS-CoV-2. 12,978 phytochemicals were screened against S proteins of SARS-CoV-2 Lambda and Delta mutants. Results Molecular docking showed that 65.61% and 65.28% of the compounds had the relatively stable binding ability to the S protein of Lambda and Delta mutants (docking score ≤ -6). The top five compounds with binding energy with Lambda and Delta mutants were clematichinenoside AR2 (-9.7), atratoglaucoside,b (-9.5), physalin b (-9.5), atratoglaucoside, a (-9.4), Ochnaflavone (-9.3) and neo-przewaquinone a (-10), Wikstrosin (-9.7), xilingsaponin A (-9.6), ardisianoside G (-9.6), and 23-epi-26-deoxyactein (-9.6), respectively. Four compounds (Casuarictin, Heterophylliin D, Protohypericin, and Glansrin B) could interact with S protein mutation sites of Lambda and Delta mutants, respectively, and MD simulation results showed that four plant chemicals and spike protein have good energy stable complex formation ability. In addition, protein-protein docking was carried out to evaluate the changes in ACE2 binding ability caused by the formation of four plant chemicals and S protein complexes. The analysis showed that the binding of four plant chemicals to the S protein could reduce the stability of the binding to ACE2, thereby reducing the replication ability of the virus. Conclusion To sum up, the study concluded that four phytochemicals (Casuarictin, Heterophylliin D, Protohypericin, and Glansrin B) had significant effects on the binding sites of the SARS-CoV-2 S protein. This study needs further in vitro and in vivo experimental validation of these major phytochemicals to assess their potential anti-SARS-CoV-2. Graphical abstract.
Collapse
Affiliation(s)
- Tiantian Han
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ziqing Luo
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lichun Ji
- The Third Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peng Wu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Geng Li
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Geng Li, ✉
| | - Xiaohong Liu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China,Xiaohong Liu, ✉
| | - Yanni Lai
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China,Yanni Lai, ✉
| |
Collapse
|
26
|
Singh AK, Choudhary P, Singh S, Kumar S. In silico identification of potential γ-secretase inhibitor of marine-algal origin: an anticancer intervention. Molecular Simulation 2022. [DOI: 10.1080/08927022.2022.2159053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Princy Choudhary
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Sangeeta Singh
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| |
Collapse
|
27
|
Rudrapal M, Issahaku AR, Agoni C, Bendale AR, Nagar A, Soliman MES, Lokwani D. In silico screening of phytopolyphenolics for the identification of bioactive compounds as novel protease inhibitors effective against SARS-CoV-2. J Biomol Struct Dyn 2022; 40:10437-10453. [PMID: 34182889 DOI: 10.1080/07391102.2021.1944909] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Due to the unavailability specific drugs or vaccines (FDA approved) that can cure COVID-19, the development of potent antiviral drug candidates/therapeutic molecules against COVID-19 is urgently required. This study was aimed at in silico screening and study of polyphenolic phytochemical compounds in a rational way by virtual screening, molecular docking and molecular dynamics studies against SARS-CoV-2 main protease (Mpro) and papain-like protease (PLpro) enzymes. The objective of the study was to identify plant-derived polyphenolic compounds and/or flavonoid molecules as possible antiviral agents with protease inhibitory potential against SARS-CoV-2. In this study, we report plant-derived polyphenolic compounds (including flavonoids) as novel protease inhibitors against SARS-CoV-2. From virtual docking and molecular docking study, 31 polyphenolic compounds were identified as active antiviral molecules possessing well-defined binding affinity with acceptable ADMET, toxicity and lead-like or drug-like properties. Six polyphenolic compounds, namely, enterodiol, taxifolin, eriodictyol, leucopelargonidin, morin and myricetin were found to exhibit remarkable binding affinities against the proteases with taxifolin and morin exhibiting the highest binding affinity toward Mpro and PLpro respectively. Molecular dynamics simulation studies of these compounds in complex with the proteases showed that the binding of the compounds is characterized by structural perturbations of the proteases suggesting their antiviral activities. These compounds can therefore be investigated further by in vivo and in vitro techniques to assess their potential efficacy against SARS-CoV-2 and thus serve as the starting point for the development of potent antiviral agents against the deadly COVID-19.
Collapse
Affiliation(s)
- Mithun Rudrapal
- Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Pune, Maharashtra, India
| | - Abdul Rashid Issahaku
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Clement Agoni
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Atul R Bendale
- Sandip Institute of Pharmaceutical Sciences, Nashik, Maharashtra, India
| | - Akhil Nagar
- R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Deepak Lokwani
- R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| |
Collapse
|
28
|
Uddin MJ, Akhter H, Chowdhury U, Mawah J, Karim ST, Jomel M, Islam MS, Islam MR, Onin LAB, Ali MA, Efaz FM, Halim MA. Large scale peptide screening against main protease of SARS CoV-2. J Comput Chem 2022; 44:887-901. [PMID: 36478400 PMCID: PMC9877796 DOI: 10.1002/jcc.27050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/03/2022] [Accepted: 11/19/2022] [Indexed: 12/12/2022]
Abstract
The COVID-19 pandemic has been a public health emergency, with deadly forms constantly emerging around the world, highlighting the dire need for highly effective antiviral therapeutics. Peptide therapeutics show significant potential for this viral disease due to their efficiency, safety, and specificity. Here, two thousand seven hundred eight antibacterial peptides were screened computationally targeting the Main protease (Mpro) of SARS CoV-2. Six top-ranked peptides according to their binding scores, binding pose were investigated by molecular dynamics to explore the interaction and binding behavior of peptide-Mpro complexes. The structural and energetic characteristics of Mpro-DRAMP01760 and Mpro-DRAMP01808 complexes fluctuated less during a 250 ns MD simulation. In addition, three peptides (DRAMP01760, DRAMP01808, and DRAMP01342) bind strongly to Mpro protein, according to the free energy landscape and principal component analysis. Peptide helicity and secondary structure analysis are in agreement with our findings. Interaction analysis of protein-peptide complexes demonstrated that Mpro's residue CYS145, HIS41, PRO168, GLU166, GLN189, ASN142, MET49, and THR26 play significant contributions in peptide-protein attachment. Binding free energy analysis (MM-PBSA) demonstrated the energy profile of interacting residues of Mpro in peptide-Mpro complexes. To summarize, the peptides DRAMP01808 and DRAMP01760 may be highly Mpro specific, resulting disruption in a viral replication and transcription. The results of this research are expected to assist future research toward the development of antiviral peptide-based therapeutics for Covid-19 treatment.
Collapse
Affiliation(s)
- Md. Jaish Uddin
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh
| | - Hasina Akhter
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh
| | - Urmi Chowdhury
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh
| | - Jannatul Mawah
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh
| | - Sanzida Tul Karim
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh
| | - Mohammad Jomel
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh
| | - Md. Sirajul Islam
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh
| | - Mohammad Raqibul Islam
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh
| | - Latifa Afrin Bhuiyan Onin
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh
| | - Md. Ackas Ali
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh,Department of Chemistry and BiochemistryKennesaw State UniversityKennesawGeorgiaUSA
| | - Faiyaz Md. Efaz
- Division of Infectious Disease and Division of Computer‐Aided Drug DesignThe Red‐Green Research CentreDhakaBangladesh
| | - Mohammad A. Halim
- Department of Chemistry and BiochemistryKennesaw State UniversityKennesawGeorgiaUSA
| |
Collapse
|
29
|
Atoum MF, Padma KR, Don KR. Paving New Roads Using Allium sativum as a Repurposed Drug and Analyzing its Antiviral Action Using Artificial Intelligence Technology. Iran J Pharm Res 2022; 21:e131577. [PMID: 36915406 PMCID: PMC10007998 DOI: 10.5812/ijpr-131577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/23/2022] [Accepted: 12/17/2022] [Indexed: 01/22/2023]
Abstract
Context The whole universe is facing a coronavirus catastrophe, and prompt treatment for the health crisis is primarily significant. The primary way to improve health conditions in this battle is to boost our immunity and alter our diet patterns. A common bulb veggie used to flavor cuisine is garlic. Compounds in the plant that are physiologically active are present, contributing to its pharmacological characteristics. Among several food items with nutritional value and immunity improvement, garlic stood predominant and more resourceful natural antibiotic with a broad spectrum of antiviral potency against diverse viruses. However, earlier reports have depicted its efficacy in the treatment of a variety of viral illnesses. Nonetheless, there is no information on its antiviral activities and underlying molecular mechanisms. Objectives The bioactive compounds in garlic include organosulfur (allicin and alliin) and flavonoid (quercetin) compounds. These compounds have shown immunomodulatory effects and inhibited attachment of coronavirus to the angiotensin-converting enzyme 2 (ACE2) receptor and the Mpro of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Further, we have discussed the contradictory impacts of garlic used as a preventive measure against the novel coronavirus. Method The GC/MS analysis revealed 18 active chemicals, including 17 organosulfur compounds in garlic. Using the molecular docking technique, we report for the first time the inhibitory effect of the under-consideration compounds on the host receptor ACE2 protein in the human body, providing a crucial foundation for understanding individual compound coronavirus resistance on the main protease protein of SARS-CoV-2. Allyl disulfide and allyl trisulfide, which make up the majority of the compounds in garlic, exhibit the most potent activity. Results Conventional medicine has proven its efficiency from ancient times. Currently, our article's prime spotlight was on the activity of Allium sativum on the relegation of viral load and further highlighted artificial intelligence technology to study the attachment of the allicin compound to the SARS-CoV-2 receptor to reveal its efficacy. Conclusions The COVID-19 pandemic has triggered interest among researchers to conduct future research on molecular docking with clinical trials before releasing salutary remedies against the deadly malady.
Collapse
Affiliation(s)
- Manar Fayiz Atoum
- Faculty of Applied Health Sciences, Hashemite University, Zarqa, Jordan
- Corresponding Author: Department Medical Laboratory Sciences, Faculty Applied Health Sciences, The Hashemite University, 330127, Zarqa, Jordan.
| | - Kanchi Ravi Padma
- Department of Biotechnology, Sri Padmavati Mahila Visvavidyalayam (Women’s) University, Tirupati, India
| | - Kanchi Ravi Don
- Department of Oral Pathology and Microbiology, Bharath Institute of Higher Education and Research, Sree Balaji Dental College and Hospital, Chennai, India
| |
Collapse
|
30
|
Sharun K, Tiwari R, Yatoo MI, Natesan S, Megawati D, Singh KP, Michalak I, Dhama K. A comprehensive review on pharmacologic agents, immunotherapies and supportive therapeutics for COVID-19. Narra J 2022; 2:e92. [PMID: 38449903 PMCID: PMC10914132 DOI: 10.52225/narra.v2i3.92] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 03/08/2024]
Abstract
The emergence of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected many countries throughout the world. As urgency is a necessity, most efforts have focused on identifying small molecule drugs that can be repurposed for use as anti-SARS-CoV-2 agents. Although several drug candidates have been identified using in silico method and in vitro studies, most of these drugs require the support of in vivo data before they can be considered for clinical trials. Several drugs are considered promising therapeutic agents for COVID-19. In addition to the direct-acting antiviral drugs, supportive therapies including traditional Chinese medicine, immunotherapies, immunomodulators, and nutritional therapy could contribute a major role in treating COVID-19 patients. Some of these drugs have already been included in the treatment guidelines, recommendations, and standard operating procedures. In this article, we comprehensively review the approved and potential therapeutic drugs, immune cells-based therapies, immunomodulatory agents/drugs, herbs and plant metabolites, nutritional and dietary for COVID-19.
Collapse
Affiliation(s)
- Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Mohd I. Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Alusteng Srinagar, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Jammu and Kashmir, India
| | - Senthilkumar Natesan
- Department of Infectious Diseases, Indian Institute of Public Health Gandhinagar, Opp to Airforce station HQ, Gandhinagar, India
| | - Dewi Megawati
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar, Indonesia
- Department of Medical Microbiology and Immunology, University of California, Davis, California, USA
| | - Karam P. Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, Poland
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| |
Collapse
|
31
|
Mun CS, Hui LY, Sing LC, Karunakaran R, Ravichandran V. Multi-targeted molecular docking, pharmacokinetics, and drug-likeness evaluation of coumarin based compounds targeting proteins involved in development of COVID-19. Saudi J Biol Sci 2022; 29:103458. [PMID: 36187455 PMCID: PMC9512525 DOI: 10.1016/j.sjbs.2022.103458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
COVID-19 is a progressing pandemic of coronavirus disease-2019, which had drowned the whole world in a deep sorrow sea. Uncountable deaths were extending the list of deaths every single day. The present research was aimed to study the multi-target interaction of coumarins against COVID-19 using molecular docking analysis. The structure of coumarin compounds was checked for ADME and Lipinski rule of five by using SwissADME, an online tool. SARS-CoV-2 proteins such as RdRp, PLpro, Mpro and spike protein were collected from the Protein Data Bank. The molecular docking study was performed in the PyRx tool, and the molecular interactions were visualised by Discovery Studio Visualizer. All the coumarin compounds used in the study were obeyed Lipinski’s rule of 5 without any violations. All the three designed derivatives of phenprocoumon, hymecromone, and psoralen were showed high binding affinity and prominent interactions with the drug target. The presence of –OH groups in the compound, His41, a catalytic dyad in Mpro, number of and the distance of hydrogen bond interactions with SARS-CoV-2 targets was accountable for the high binding attractions. The modified drug structures possess better binding efficacy towards at least three targets compared to their parent compounds. Further, molecular dynamic studies can be suggested to find the ligand–protein complex stability. The present study outcome reveals that the designed coumarins can be synthesised and examined as a potent inhibitory drug of SARS-CoV-2.
Collapse
Affiliation(s)
- Chan Sook Mun
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Lok Yong Hui
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Lai Cong Sing
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Rohini Karunakaran
- Unit of Biochemistry, Faculty of Medicine, AIMST University, Semeling 08100, Kedah, Malaysia.,Centre of Excellence for Biomaterial Science, AIMST University, Semeling 08100, Kedah, Malaysia
| | - Veerasamy Ravichandran
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia.,Centre of Excellence for Biomaterial Science, AIMST University, Semeling 08100, Kedah, Malaysia.,Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| |
Collapse
|
32
|
Sedzro DM, Idris MO, Durojaye OA, Yekeen AA, Fadahunsi AA, Alakanse SO. Identifying Potential p53‐MDM2 Interaction Antagonists: An Integrated Approach of Pharmacophore‐Based Virtual Screening, Interaction Fingerprinting, MD Simulation and DFT Studies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Divine Mensah Sedzro
- MOE Key Laboratory of Membraneless Organelle and Cellular Dynamics Hefei National Laboratory for Physical Sciences at the Microscale University of Science and Technology of China Hefei Anhui 230027 China
- School of Life Sciences University of Science and Technology of China Hefei Anhui 230027 China
| | - Mukhtar Oluwaseun Idris
- School of Life Sciences University of Science and Technology of China Hefei Anhui 230027 China
| | - Olanrewaju Ayodeji Durojaye
- MOE Key Laboratory of Membraneless Organelle and Cellular Dynamics Hefei National Laboratory for Physical Sciences at the Microscale University of Science and Technology of China Hefei Anhui 230027 China
- School of Life Sciences University of Science and Technology of China Hefei Anhui 230027 China
- Department of Chemical Sciences Coal City University, Emene Enugu State Nigeria
- ACAII BIOHEALTH LTD, Ikotun Lagos State Nigeria
| | - Abeeb Abiodun Yekeen
- School of Life Sciences University of Science and Technology of China Hefei Anhui 230027 China
| | - Adeola Abraham Fadahunsi
- Graduate School of Biomedical Engineering (GSBSE) University of Maine Orono ME 04469 USA
- Department of Oncology the First Affiliated Hospital of USTC Division of Life Sciences and Medicine University of Science and Technology of China Hefei Anhui 230027 China
- School of Information Science and Technology University of Science and Technology of China Hefei Anhui 230027 China
| | - Suleiman Oluwaseun Alakanse
- School of Life Sciences University of Science and Technology of China Hefei Anhui 230027 China
- Department of Biochemistry Faculty of Life Sciences University of Ilorin Ilorin Kwara State Nigeria
| |
Collapse
|
33
|
Onyango H, Odhiambo P, Angwenyi D, Okoth P, Gong W. In Silico Identification of New Anti-SARS-CoV-2 Main Protease (Mpro) Molecules with Pharmacokinetic Properties from Natural Sources Using Molecular Dynamics (MD) Simulations and Hierarchical Virtual Screening. J Trop Med 2022; 2022:1-22. [PMID: 36263438 PMCID: PMC9576439 DOI: 10.1155/2022/3697498] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Infectious agents such as SARS-CoV, MERS-CoV, and SARS-CoV-2 have emerged in recent years causing epidemics with high mortality rates. The quick development of novel therapeutic compounds is required in the fight against such pathogenic agents. Unfortunately, the traditional drug development methods are time-consuming and expensive. In this study, computational algorithms were utilized for virtual screening of a library of natural compounds in the ZINC database for their affinity towards SARS-CoV-2 Mpro. Compounds such as cinanserin, nelfinavir, baicalin, baicalein, candesartan cilexetil, chloroquine, dipyridamole, and hydroxychloroquine have the ability to prevent SARS-CoV-2 Mpro from facilitating COVID 19 infection; thus, they treat COVID 19. However, these drugs majorly act to reduce the symptoms of the disease. No anti-viral drug against COVID 19 virus infection has been discovered and approved. Therefore, this study sought to explore natural inhibitors of SARS-CoV-2 Mpro to develop a pharmacophore model for virtual screening of natural compounds in the ZINC database as potential candidates for SARS-CoV-2 Mpro inhibitors and as therapeutic molecules against COVID 19. This study undertook in silico methods to identify the best anti-viral candidates targeting SAR-CoV-2 Mpro from natural sources in the ZINC database. Initially, reported anti-SARS-CoV-2 Mpro molecules were integrated into designing a pharmacophore model utilizing PharmaGist. Later, the pharmacophore model was loaded into ZINCPHARMER and screened against the ZINC database to identify new probable drug candidates. The root means square deviation (RMSD) values of the potential drug candidates informed the selection of some of them, which were docked with SARS-CoV-2 Mpro to comprehend their interactions. From the molecular docking results, the top four candidates (ZINC000254823011, ZINC000072307130, ZINC000013627512, and ZINC000009418994) against SARS-CoV-2 Mpro, with binding energies ranging from –8.2 kcal/mol to –8.6 kcal/mol, were examined for their oral bioavailability and other pharmacokinetic properties. Consequently, ZINC000072307130 emerged as the only orally bioavailable drug candidate with desirable pharmacokinetic properties. This candidate drug was used to perform MD simulations, and the outcomes revealed that ZINC000072307130 formed a stable complex with the viral main protease. Consequently, ZINC000072307130 emerges as a potential anti-SARS-CoV-2 Mpro inhibitor for the production of new COVID 19 drugs.
Collapse
|
34
|
Nada H, Elkamhawy A, Lee K. Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations. PeerJ 2022; 10:e14120. [PMID: 36225900 PMCID: PMC9549888 DOI: 10.7717/peerj.14120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/05/2022] [Indexed: 01/25/2023] Open
Abstract
The rapid spread of the coronavirus since its first appearance in 2019 has taken the world by surprise, challenging the global economy, and putting pressure on healthcare systems across the world. The introduction of preventive vaccines only managed to slow the rising death rates worldwide, illuminating the pressing need for developing effective antiviral therapeutics. The traditional route of drug discovery has been known to require years which the world does not currently have. In silico approaches in drug design have shown promising results over the last decade, helping to decrease the required time for drug development. One of the vital non-structural proteins that are essential to viral replication and transcription is the SARS-CoV-2 main protease (Mpro). Herein, using a test set of recently identified COVID-19 inhibitors, a pharmacophore was developed to screen 20 million drug-like compounds obtained from a freely accessible Zinc database. The generated hits were ranked using a structure based virtual screening technique (SBVS), and the top hits were subjected to in-depth molecular docking studies and MM-GBSA calculations over SARS-COV-2 Mpro. Finally, the most promising hit, compound (1), and the potent standard (III) were subjected to 100 ns molecular dynamics (MD) simulations and in silico ADME study. The result of the MD analysis as well as the in silico pharmacokinetic study reveal compound 1 to be a promising SARS-Cov-2 MPro inhibitor suitable for further development.
Collapse
Affiliation(s)
- Hossam Nada
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Badr University in Cairo, Cairo, Egypt
| | - Ahmed Elkamhawy
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea,Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Kyeong Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
| |
Collapse
|
35
|
Singh AK, Maurya S, Kumar S. Repurposing FDA-approved anti-diabetic drug to target H. pylori peptidyl deformylase using computer-based drug discovery approach. Molecular Simulation 2022. [DOI: 10.1080/08927022.2022.2130377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Affiliation(s)
- Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Santosh Maurya
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
| |
Collapse
|
36
|
Attiq N, Arshad U, Brogi S, Shafiq N, Imtiaz F, Parveen S, Rashid M, Noor N. Exploring the anti-SARS-CoV-2 main protease potential of FDA approved marine drugs using integrated machine learning templates as predictive tools. Int J Biol Macromol 2022; 220:1415-1428. [PMID: 36122771 PMCID: PMC9479384 DOI: 10.1016/j.ijbiomac.2022.09.086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/22/2022]
Abstract
Since the inception of COVID-19 pandemic in December 2019, socio-economic crisis begins to rise globally and SARS-CoV-2 was responsible for this outbreak. With this outbreak, currently, world is in need of effective and safe eradication of COVID-19. Hence, in this study anti-SAR-Co-2 potential of FDA approved marine drugs (Biological macromolecules) data set is explored computationally using machine learning algorithm of Flare by Cresset Group, Field template, 3D-QSAR and activity Atlas model was generated against FDA approved M-pro SARS-CoV-2 repurposed drugs including Nafamostat, Hydroxyprogesterone caporate, and Camostat mesylate. Data sets were categorized into active and inactive molecules on the basis of their structural and biological resemblance with repurposed COVID-19 drugs. Then these active compounds were docked against the five different M-pro proteins co-crystal structures. Highest LF VS score of Holichondrin B against all main protease co-crystal structures ranked it as lead drug. Finally, this new technique of drug repurposing remained efficient to explore the anti-SARS-CoV-2 potential of FDA approved marine drugs.
Collapse
Affiliation(s)
- Naila Attiq
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Uzma Arshad
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.
| | - Nusrat Shafiq
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan.
| | - Fazeelat Imtiaz
- Green Chemistry Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Nadia Noor
- Micro-biology Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| |
Collapse
|
37
|
Houchi S, Messasma Z. Exploring the inhibitory potential of Saussurea costus and Saussurea involucrata phytoconstituents against the Spike glycoprotein receptor binding domain of SARS-CoV-2 Delta (B.1.617.2) variant and the main protease (M pro) as therapeutic candidates, using Molecular docking, DFT, and ADME/Tox studies. J Mol Struct 2022; 1263:133032. [PMID: 35431327 PMCID: PMC8993769 DOI: 10.1016/j.molstruc.2022.133032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/20/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023]
Abstract
The B.1.617.2 Delta variant is considered to be the most infectious of all SARS-CoV2 variants. Here, an attempt has been made through in-silico screening of 55 bioactive compounds from two selected plants, Saussurea costus and Saussurea involucrata as potential inhibitors of two viral proteases, main protease Mpro (PDB ID:6LU7) and the RBD of SGP of Sars-CoV-2 B1.617.2 Delta variant (PDB ID:7ORB) where the binding energy, molecular interactions, ADMET/Tox, chemical descriptors and Quantum-Chemical Calculations were explored. Molecular docking results demonstrated that the three top docked compounds formed relatively stable complexes within the active site and displayed remarkable binding energy in the order of Tangshenoside III, Rutin and Hesperidin (-9.35, -9.14 and -8.57 kcal/mol, respectively) with Mpro and Rutin, Tangshenoside III and Hesperidin (-9.07, -7.71 and -7.57 kcal/mol) with RBD of SGP. These compounds are non-Mutagen and non-carcinogen. Therefore, according to the Lipinski's Rule of Five they exhibited three violations concerning hydrogen acceptor, donor and molecular weight. However, based on the Quantum-Chemical Calculations results the selected ligands have effective reactivity, as they showed lower band gaps. The difference of the ELUMO and EHOMO was low, ranging from 0.0639 to 0.0978 a.u, implying the strong affinity of these inhibitors towards the target proteins. Among the three inhibitors, Rutin exhibited higher reactivity against two viral proteases, main protease (Mpro) and the Sars-CoV-2 B1.617.2, as the band energy gap was lowest among all the three phytochemicals, 0.0639 a.u This could indicate that Rutincan be potential anti-viral drug candidates against the existing SARS-CoV-2, the B.1.617.2 Delta variant.
Collapse
Affiliation(s)
- Selma Houchi
- Department of Biochemistry, Laboratory of Applied Biochemistry, Faculty of Life and Nature Sciences, University of Ferhat Abbas Setif-1, Algeria
| | - Zakia Messasma
- Department of Process Engineering, Laboratory of Electrochemistry, Molecular Engineering and Redox Catalysis, Faculty of Technology, University of Ferhat Abbas Setif-1, 19000, Algeria
- Department of Chemistry, Faculty of Sciences, University of Ferhat Abbas Setif-1, 19000, Algeria
| |
Collapse
|
38
|
Krishna S, Krishna Murthy T, Divyashri G, Murahari M, Shukla R, Birendra Kumar S, Raj Singh T. Pharmacoinformatics based screening of combined synthetic and natural compounds to identify novel and in silico potential Bcl-2 inhibitors. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
39
|
Fuzo CA, Martins RB, Fraga-Silva TFC, Amstalden MK, Canassa De Leo T, Souza JP, Lima TM, Faccioli LH, Okamoto DN, Juliano MA, França SC, Juliano L, Bonato VLD, Arruda E, Dias-Baruffi M. Celastrol: A lead compound that inhibits SARS-CoV-2 replication, the activity of viral and human cysteine proteases, and virus-induced IL-6 secretion. Drug Dev Res 2022; 83:1623-1640. [PMID: 35989498 PMCID: PMC9539158 DOI: 10.1002/ddr.21982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 11/21/2022]
Abstract
The global emergence of coronavirus disease 2019 (COVID‐19) has caused substantial human casualties. Clinical manifestations of this disease vary from asymptomatic to lethal, and the symptomatic form can be associated with cytokine storm and hyperinflammation. In face of the urgent demand for effective drugs to treat COVID‐19, we have searched for candidate compounds using in silico approach followed by experimental validation. Here we identified celastrol, a pentacyclic triterpene isolated from Tripterygium wilfordii Hook F, as one of the best compounds out of 39 drug candidates. Celastrol reverted the gene expression signature from severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2)‐infected cells and irreversibly inhibited the recombinant forms of the viral and human cysteine proteases involved in virus invasion, such as Mpro (main protease), PLpro (papain‐like protease), and recombinant human cathepsin L. Celastrol suppressed SARS‐CoV‐2 replication in human and monkey cell lines and decreased interleukin‐6 (IL‐6) secretion in the SARS‐CoV‐2‐infected human cell line. Celastrol acted in a concentration‐dependent manner, with undetectable signs of cytotoxicity, and inhibited in vitro replication of the parental and SARS‐CoV‐2 variant. Therefore, celastrol is a promising lead compound to develop new drug candidates to face COVID‐19 due to its ability to suppress SARS‐CoV‐2 replication and IL‐6 production in infected cells.
Collapse
Affiliation(s)
- Carlos A Fuzo
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ronaldo B Martins
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thais F C Fraga-Silva
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Martin K Amstalden
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thais Canassa De Leo
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Juliano P Souza
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thais M Lima
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Lucia H Faccioli
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Débora Noma Okamoto
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Maria Aparecida Juliano
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Suzelei C França
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Luiz Juliano
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Vania L D Bonato
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Eurico Arruda
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marcelo Dias-Baruffi
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| |
Collapse
|
40
|
Li RY, Xie JL, Meng D, Deng P. Virtual screening of lead compounds for the treatment of Alzheimer’s disease based on multi-target strategy. Molecular Simulation 2022. [DOI: 10.1080/08927022.2022.2104453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Ruo-yu Li
- College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, People’s Republic of China
| | - Jia-li Xie
- College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, People’s Republic of China
| | - Dan Meng
- College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, People’s Republic of China
| | - Ping Deng
- College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, People’s Republic of China
- Chongqing Key Research Laboratory for Quality Evaluation and Safety Research of APIs, Chongqing, People’s Republic of China
| |
Collapse
|
41
|
Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
Collapse
Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
42
|
Yilmaz H, Gultekin Subasi B, Celebioglu HU, Ozdal T, Capanoglu E. Chemistry of Protein-Phenolic Interactions Toward the Microbiota and Microbial Infections. Front Nutr 2022; 9:914118. [PMID: 35845785 PMCID: PMC9284217 DOI: 10.3389/fnut.2022.914118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/25/2022] [Indexed: 12/12/2022] Open
Abstract
Along with health concerns, interest in plants as food and bioactive phytochemical sources has been increased in the last few decades. Phytochemicals as secondary plant metabolites have been the subject of many studies in different fields. Breakthrough for research interest on this topic is re-juvenilized with rising relevance in this global pandemics' era. The recent COVID-19 pandemic attracted the attention of people to viral infections and molecular mechanisms behind these infections. Thus, the core of the present review is the interaction of plant phytochemicals with proteins as these interactions can affect the functions of co-existing proteins, especially focusing on microbial proteins. To the best of our knowledge, there is no work covering the protein-phenolic interactions based on their effects on microbiota and microbial infections. The present review collects and defines the recent data, representing the interactions of phenolic compounds -primarily flavonoids and phenolic acids- with various proteins and explores how these molecular-level interactions account for the human health directly and/or indirectly, such as increased antioxidant properties and antimicrobial capabilities. Furthermore, it provides an insight about the further biological activities of interacted protein-phenolic structure from an antiviral activity perspective. The research on the protein-phenolic interaction mechanisms is of great value for guiding how to take advantage of synergistic effects of proteins and polyphenolics for future medical and nutritive approaches and related technologies.
Collapse
Affiliation(s)
- Hilal Yilmaz
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey
| | - Busra Gultekin Subasi
- Division of Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
- Hafik Kamer Ornek MYO, Sivas Cumhuriyet University, Sivas, Turkey
| | | | - Tugba Ozdal
- Department of Food Engineering, Faculty of Engineering and Natural Sciences, Istanbul Okan University, Istanbul, Turkey
| | - Esra Capanoglu
- Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Istanbul Technical University, Istanbul, Turkey
- *Correspondence: Esra Capanoglu
| |
Collapse
|
43
|
Abstract
The coronavirus disease (COVID-19) caused by SARS-CoV-2 is a big challenge and burning issue to the scientific community and doctors worldwide. Globally, COVID-19 has created a health disaster and adversely affects the economic growth. Although some vaccines have already emerged, no therapeutic medication has yet been approved by FDA for the treatment of COVID-19 patients. Traditionally, we have been using different medicinal plants like neem, tulsi, tea, and many spices like garlic, ginger, turmeric, black seed, onion, etc. for the treatment of flu-like diseases. In this paper, we are highlighting the recent research progress in the identification of natural products from the Indian medicinal plants and spices that have potential inhibition properties against SARS-CoV-2. This study will provide an initiative to stimulate further research by providing useful guidance to the medicinal chemists for designing new protease inhibitors effective against SARS-CoV-2 in future.
Collapse
Affiliation(s)
- Moumita Nath
- Department of Botany, Tripura University, Suryamaninagar, Tripura, India
| | - Pradip Debnath
- Department of Chemistry, Maharaja Bir Bikram College, Agartala, Tripura, India
| |
Collapse
|
44
|
Prajapati KS, Singh AK, Kushwaha PP, Shuaib M, Maurya SK, Gupta S, Senapati S, Singh SP, Waseem M, Kumar S. Withaniasomnifera phytochemicals possess SARS-CoV-2 RdRp and human TMPRSS2 protein binding potential. Vegetos 2022; 36:701-720. [PMID: 35729946 PMCID: PMC9199469 DOI: 10.1007/s42535-022-00404-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/22/2022] [Accepted: 05/01/2022] [Indexed: 02/06/2023]
Abstract
Abstract Coronavirus disease-19 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has infected approximately 26 million people and caused more than 6 million deaths globally. Spike (S)-protein on the outer surface of the virus uses human trans-membrane serine protease-2 (TMPRSS2) to gain entry into the cell. Recent reports indicate that human dipeptidyl peptidase-4 inhibitors (DPP4 or CD26) could also be utilized to check the S-protein mediated viral entry into COVID-19 patients. RNA dependent RNA polymerase (RdRp) is another key virulence protein of SARS-CoV-2 life cycle. The study aimed to identify the potential anti-SARS-CoV-2 inhibitors present in Withania somnifera (Solanaceae) using computer aided drug discovery approach. Molecular docking results showed that flavone glycoside, sugar alcohol, and flavonoid present in W. somnifera showed - 11.69, - 11.61, - 10.1, - 7.71 kcal/mole binding potential against S-protein, CD26, RdRp, and TMPRSS2 proteins. The major standard inhibitors of the targeted proteins (Sitagliptin, VE607, Camostat mesylate, and Remdesivir) showed the - 7.181, - 6.6, - 5.146, and - 7.56 kcal/mole binding potential. Furthermore, the lead phytochemicals and standard inhibitors bound and non-bound RdRp and TMPRSS2 proteins were subjected to molecular dynamics (MD) simulation to study the complex stability and change in protein conformation. The result showed energetically favorable and stable complex formation in terms of RMSD, RMSF, SASA, Rg, and hydrogen bond formation. Drug likeness and physiochemical properties of the test compounds exhibited satisfactory results. Taken together, the present study suggests the presence of potential anti-SARS-CoV-2 phytochemicals in W. somnifera that requires further validation in in vitro and in vivo studies. Graphical Abstract Supplementary information The online version contains supplementary material available at 10.1007/s42535-022-00404-4.
Collapse
Affiliation(s)
- Kumari Sunita Prajapati
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, 151401 India
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, 151401 India
| | - Prem Prakash Kushwaha
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, 151401 India
| | - Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, 151401 India
| | - Santosh Kumar Maurya
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, 151401 India
| | - Sanjay Gupta
- Department of Urology, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Sabyasachi Senapati
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, 151401 Bathinda, India
| | - Surya Pratap Singh
- Department of Bioscience and Biotechnology, Bansthali Vidyapith, Banasthali, Rajasthan India
| | - Mohammad Waseem
- Department of Zoology, Jagdam College, Jai Prakash University, Chapra, Bihar India
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, 151401 India
| |
Collapse
|
45
|
Muhammad S, Saba A, Khera RA, Al-Sehemi AG, Algarni H, Iqbal J, Alshahrani MY, Chaudhry AR. Virtual screening of potential inhibitor against breast cancer-causing estrogen receptor alpha (ERα): molecular docking and dynamic simulations. Molecular Simulation 2022. [DOI: 10.1080/08927022.2022.2072840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Shabbir Muhammad
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Afsheen Saba
- Department of Chemistry, College of Science, University of Agriculture, Faisalabad, Pakistan
| | - Rasheed Ahmad Khera
- Department of Chemistry, College of Science, University of Agriculture, Faisalabad, Pakistan
| | - Abdullah. G. Al-Sehemi
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - H. Algarni
- Department of Physics, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Javed Iqbal
- Department of Chemistry, College of Science, University of Agriculture, Faisalabad, Pakistan
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | | |
Collapse
|
46
|
Rana N, Singh AK, Shuaib M, Gupta S, Habiballah MM, Alkhanani MF, Haque S, Reshi MS, Kumar S. Drug Resistance Mechanism of M46I-Mutation-Induced Saquinavir Resistance in HIV-1 Protease Using Molecular Dynamics Simulation and Binding Energy Calculation. Viruses 2022; 14:v14040697. [PMID: 35458427 PMCID: PMC9031992 DOI: 10.3390/v14040697] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 02/06/2023] Open
Abstract
Drug-resistance-associated mutation in essential proteins of the viral life cycle is a major concern in anti-retroviral therapy. M46I, a non-active site mutation in HIV-1 protease has been clinically associated with saquinavir resistance in HIV patients. A 100 ns molecular dynamics (MD) simulation and MM-PBSA calculations were performed to study the molecular mechanism of M46I-mutation-based saquinavir resistance. In order to acquire deeper insight into the drug-resistance mechanism, the flap curling, closed/semi-open/open conformations, and active site compactness were studied. The M46I mutation significantly affects the energetics and conformational stability of HIV-1 protease in terms of RMSD, RMSF, Rg, SASA, and hydrogen formation potential. This mutation significantly decreased van der Waals interaction and binding free energy (∆G) in the M46I–saquinavir complex and induced inward flap curling and a wider opening of the flaps for most of the MD simulation period. The predominant open conformation was reduced, but inward flap curling/active site compactness was increased in the presence of saquinavir in M46I HIV-1 protease. In conclusion, the M46I mutation induced structural dynamics changes that weaken the protease grip on saquinavir without distorting the active site of the protein. The produced information may be utilized for the discovery of inhibitor(s) against drug-resistant HIV-1 protease.
Collapse
Affiliation(s)
- Nilottam Rana
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Sanjay Gupta
- Department of Urology, Pharmacology and Pathology, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Mahmoud M. Habiballah
- Medical Laboratory Technology Department, Jazan University, Jazan 45142, Saudi Arabia;
- SMIRES for Consultation in Specialized Medical Laboratories, Jazan University, Jazan 45142, Saudi Arabia
| | - Mustfa F. Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
| | - Mohd Salim Reshi
- Toxicology and Pharmacology Lab., Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu & Kashmir, India;
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
- Correspondence:
| |
Collapse
|
47
|
Kumar S, Shuaib M, Prajapati KS, Singh AK, Choudhary P, Singh S, Gupta S. A candidate triple-negative breast cancer vaccine design by targeting clinically relevant cell surface markers: an integrated immuno and bio-informatics approach. 3 Biotech 2022; 12:72. [PMID: 35223358 PMCID: PMC8859024 DOI: 10.1007/s13205-022-03140-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/07/2022] [Indexed: 02/05/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive, metastatic/invasive sub-class of breast cancer (BCa). Cell surface protein-derived multi-epitope vaccine-mediated targeting of TNBC cells could be a better strategy against the disease. Literature-based identified potential cell surface markers for TNBC cells were subjected to expression pattern and survival analysis in BCa patient sample using TCGA database. The cytotoxic and helper T-lymphocytes antigenic epitopes in the test proteins were identified, selected and fused together with the appropriate linkers and an adjuvant, to construct the multi-epitope vaccine (MEV). The immune profile, physiochemical property (PP) and world population coverage of the MEV was studied. Immune simulation, cloning in a suitable vector, molecular docking (against Toll-like receptors, MHC (I/II) molecules), and molecular dynamics simulations of the MEV was performed. Cell surface markers were differentially expressed in TNBC samples and showed poor survival in TNBC patients. Satisfactory PP and WPC (up to 89 and 99%) was observed. MEV significant stable binding with the immune molecules and induced the immune cells in silico. The designed vaccine has capability to elicit immune response which could be utilized to target TNBC alone/combination with other therapy. The experimental studies are required to check the efficacy of the vaccine. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03140-3.
Collapse
Affiliation(s)
- Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab 151401 India
| | - Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab 151401 India
| | - Kumari Sunita Prajapati
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab 151401 India
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab 151401 India
| | - Princy Choudhary
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh 211012 India
| | - Sangeeta Singh
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh 211012 India
| | - Sanjay Gupta
- Department of Urology, Case Western Reserve University, Cleveland, OH 44106 USA
| |
Collapse
|
48
|
Li J, Zhang Y, Pang H, Li SJ. Heparin interacts with the main protease of SARS-CoV-2 and inhibits its activity. Spectrochim Acta A Mol Biomol Spectrosc 2022; 267:120595. [PMID: 34815178 PMCID: PMC8591854 DOI: 10.1016/j.saa.2021.120595] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
The ability of SARS-CoV-2 to replicate in host cells is dependent on its main protease (Mpro, also called 3CLpro) that cut the viral precursor polyproteins and is a major target for antiviral drug design. Here, we showed that heparin interacts with the Mpro of SARS-CoV-2 and inhibits its activity. Protein fluorescence quenching showed that heparin strongly binds to the Mpro protein with dissociation constants KD of 16.66 and 31.60 μM at 25 and 35 °C, respectively. From thermodynamic parameters of the interaction, there are hydrophobic and hydrogen bond interactions between them. Fluorescence resonance energy transfer (FRET) assay demonstrated that heparin inhibits the proteolytic activity of Mpro with an inhibition constant Ki of 6.9 nM and a half maximal inhibitory concentrations (IC50) of 7.8 ± 2.6 nM. Furthermore, molecular docking analysis revealed that the recognition and binding groups of heparin within the active site of SARS-CoV-2 Mpro provide important new information for the characteristics of the interactions of heparin with the protease. Our finding suggested that heparin might have a potential role in inhibiting SARS-CoV-2 infection through inhibiting Mpro activity of SARS-CoV-2.
Collapse
Affiliation(s)
- Jinwen Li
- Department of Biophysics, School of Physics Science, The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin 300071, PR China
| | - Yantao Zhang
- College of Medicine, Zhengzhou University, Zhengzhou 450052, PR China
| | - Huimin Pang
- Department of Biophysics, School of Physics Science, The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin 300071, PR China.
| | - Shu Jie Li
- Department of Biophysics, School of Physics Science, The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin 300071, PR China; Qilu Institute of Technology, Shandong 250200, PR China.
| |
Collapse
|
49
|
Zackria AA, Pattabiraman R, Murthy TPK, Kumar SB, Mathew BB, Biju VG. Computational screening of natural compounds from Salvia plebeia R. Br. for inhibition of SARS-CoV-2 main protease. Vegetos 2022; 35:345-359. [PMID: 34690453 PMCID: PMC8523934 DOI: 10.1007/s42535-021-00304-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 09/17/2021] [Accepted: 09/21/2021] [Indexed: 02/02/2023]
Abstract
The novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has emerged to be the reason behind the COVID-19 pandemic. It was discovered in Wuhan, China and then began spreading around the world, impacting the health of millions. Efforts for treatment have been hampered as there are no antiviral drugs that are effective against this virus. In the present study, we have explored the phytochemical constituents of Salvia plebeia R. Br., in terms of its binding affinity by targeting COVID-19 main protease (Mpro) using computational analysis. Molecular docking analysis was performed using PyRx software. The ADMET and drug-likeness properties of the top 10 compounds showing binding affinity greater than or equal to - 8.0 kcal/mol were analysed using pkCSM and DruLiTo, respectively. Based on the docking studies, it was confirmed that Rutin and Plebeiosides B were the most potent inhibitors of the main protease of SARS-CoV-2 with the best binding affinities of - 9.1 kcal/mol and - 8.9 kcal/mol, respectively. Further, the two compounds were analysed by studying their biological activity using the PASS webserver. Molecular dynamics simulation analysis was performed for the selected protein-ligand complexes to confirm their stability at 300 ns. MM-PBSA provided the basis for analyzing the affinity of the phytochemicals towards Mpro by calculating the binding energy, and secondary structure analysis indicated the stability of protease structure when it is bound to Rutin and Plebeiosides B. Altogether, the study identifies Rutin and Plebeiosides B to be potent Mpro inhibitors of SARS-CoV-2. Graphic abstract Supplementary Information The online version contains supplementary material available at 10.1007/s42535-021-00304-z.
Collapse
Affiliation(s)
- Afraa Aqeel Zackria
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, Karnataka 560054 India
| | - Ramya Pattabiraman
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, Karnataka 560054 India
| | - T. P. Krishna Murthy
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, Karnataka 560054 India
| | - S. Birendra Kumar
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, Karnataka 560054 India
| | - Blessy Baby Mathew
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, Karnataka 560078 India
| | - Vinai George Biju
- Department of Computer Science and Engineering, Christ (Deemed-to-be University), Bengaluru, Karnataka 560060 India
| |
Collapse
|
50
|
Shahabadi N, Mahdavi M, Zendehcheshm S. Can polyoxometalates (POMs) prevent of coronavirus 2019-nCoV cell entry? Interaction of POMs with TMPRSS2 and spike receptor domain complexed with ACE2 (ACE2-RBD): Virtual screening approaches. Informatics in Medicine Unlocked 2022; 29:100902. [PMID: 35284620 PMCID: PMC8896857 DOI: 10.1016/j.imu.2022.100902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/14/2022] [Accepted: 03/03/2022] [Indexed: 12/22/2022] Open
Abstract
The unexpected appearance and global spread of COVID-19 create significant difficulties for healthcare systems and present an unusual challenge for the fast discovery of medicines to combat this fatal disease. Screening metallodrugs libraries from the medicinal inorganic chemistry society may expand the studied ‘chemical space’ and improve the probability of discovering effective anti-COVID drugs, including polyoxometalates. POMs are an oxygen-rich family of inorganic cluster systems that have previously been tested for antiviral action against different types of viruses. Human angiotensin-converting enzyme 2 (ACE2), human transmembrane protease serine 2 (TMPRSS2), and the SARS-CoV-2 spike glycoprotein are required for host cell-mediated viral entrance. Targeting these proteins demonstrates potential possibilities for preventing infections and transmissions in the initial stage. As a result, POMs with known antiviral effects were investigated for this purpose using molecular docking and dynamic simulations. This research shows that POMs can prevent SARS CoV-2 from entering cells by blocking TMPRSS2, which SARS-CoV-2 uses for spike glycoprotein priming. They may also engage with ACE2 and the spike glycoprotein and disrupt their binding by blocking the active sites. We think that a thorough investigation of POMs as possible anti-COVID-19 drugs will provide significant opportunities.
Collapse
|