1
|
Kashyap D, Jakhmola S, Tiwari D, Kumar R, Moorthy NSHN, Elangovan M, Brás NF, Jha HC. Plant derived active compounds as potential anti SARS-CoV-2 agents: an in-silico study. J Biomol Struct Dyn 2022; 40:10629-10650. [PMID: 34225565 DOI: 10.1080/07391102.2021.1947384] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Plants are a valued potential source of drugs for a variety of diseases and are often considered less toxic to humans. We investigated antiviral compounds that may potentially target SARS-CoV-2 antigenic spike (S) and host proteins; angiotensin-converting enzyme2 (ACE2), and transmembrane serine protease2 (TMPRSS2). We scrutinized 36 phytochemicals from 15 Indian medicinal plants known to be effective against RNA viruses via molecular docking. Besides, the TMPRSS2 structure was modeled and validated using the SWISS-MODEL. Docking was performed using Autodock Vina and 4.2 followed by visualization of the docking poses on Pymol version 2.4.0 and Discovery Studio Visualizer. Molecular docking showed that 12 out of 36 active compounds interacted efficiently with S, ACE2, and TMPRSS2 proteins. The ADMET profile generated using the swissADME and pkCSM server revealed that these compounds were possessed druggable properties. The Amber 12 simulation package was used to carry out energy minimizations and molecular dynamics (MD) simulations. The total simulation time for both S protein: WFA and S protein: WND complexes was 300 ns (100 ns per replica). A total of 120 structures were extracted from the last 60 ns of each MD simulation for further analysis. MM-PBSA and MM-GBSA were employed to assess the binding energy of each ligand and the receptor-binding domain of the viral S-protein. The methods suggested that WND and WFA showed thermodynamically favorable binding energies, and the S protein had a higher affinity with WND. Interestingly, Leu455 hotspot residue in the S protein, also predicted to participate in binding with ACE2, was engaged by WND and WFA. HighlightsPlants' natural active compounds may aid in the development of COVID-19 therapeutics.MD simulation study revealed stable binding of withanolide D and withaferin A with spike proteinWithanolide D and withaferin A could be effective against SARS-CoV-2 spike protein.Discovery of druggable agents that have less or lack of binding affinity with ACE2 to avoid the organs associated with comorbidities.According to ADMET selected phytochemicals may be used as druggable compounds.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Shweta Jakhmola
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Deeksha Tiwari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Rajesh Kumar
- Department of Physics, Indian Institute of Technology Indore, Indore, India
| | | | | | - Natércia F Brás
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| |
Collapse
|
2
|
Alshamrani M. Medicinal importance and chemosensing applications of Schiff base derivatives for the detection of metal ions: A review. MAIN GROUP CHEMISTRY 2022. [DOI: 10.3233/mgc-220091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Schiff bases, named after Hugo Schiff, are formed when primary amine reacts with carbonyl compounds (aldehyde or ketone) under specific conditions. Schiff bases are economical, simple synthetic routes, and easily accessible in laboratories. They have medicinal and biological applications such as antiviral, antioxidant, antifungal, anticancer, anthelmintic, antibacterial, antimalarial, anti-inflammatory, antiglycation, anti-ulcerogenic, and analgesic potentials. A number of Schiff bases are reported for the detection of various metal ions. They are also used as catalysts, polymer stabilizers, intermediates in organic synthesis, and corrosion inhibitors. In this review, we have highlighted the recent advancements in the development of bioactive Schiff base derivatives and their sensing applications for detecting metal cations. Additionally, various spectroscopic techniques for structural characterization, such as X-ray diffraction analysis (XRD), FT-IR, UV-vis, and NMR spectroscopy were also discussed.
Collapse
Affiliation(s)
- Meshal Alshamrani
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| |
Collapse
|
3
|
Shinde R, Suvarna V. Fatty Acid Biosynthesis: An Updated Review on KAS Inhibitors. Curr Drug Discov Technol 2022; 19:e110122200137. [PMID: 35021976 DOI: 10.2174/1570163819666220111113032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
Since the early twentieth century, with the isolation of penicillin and streptomycin in the 1940s, the modern era of anti-infective drug development has gained momentum. Due to the enormous success of early drug discovery, many infectious diseases were successfully prevented and eradicated. However, this initial hope was wrongheaded, and pathogens evolved as a significant threat to human health. Drug resistance develops as a result of natural selection's relentless pressure, necessitating the identification of new drug targets and the creation of chemotherapeutics that bypass existing drug resistance mechanisms. Fatty acid biosynthesis (FAS) is a crucial metabolic mechanism for bacteria during their growth and development. Several crucial enzymes involved in this biosynthetic pathway have been identified as potential targets for new antibacterial agents. In Escherichia coli (E. coli), this pathway has been extensively investigated. The present review focuses on progress in the development of Kas A, Kas B, and Fab H inhibitors as mono-therapeutic antibiotics.
Collapse
Affiliation(s)
- Rani Shinde
- Department of Quality Assurance, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai University, Mumbai, India
| | - Vasanti Suvarna
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai University, Mumbai, India
| |
Collapse
|
4
|
Puhl AC, Lane TR, Vignaux PA, Zorn KM, Capodagli GC, Neiditch MB, Freundlich JS, Ekins S. Computational Approaches to Identify Molecules Binding to Mycobacterium tuberculosis KasA. ACS OMEGA 2020; 5:29935-29942. [PMID: 33251429 PMCID: PMC7689923 DOI: 10.1021/acsomega.0c04271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/07/2020] [Indexed: 05/05/2023]
Abstract
Tuberculosis is caused by Mycobacterium tuberculosis (Mtb) and is a deadly disease resulting in the deaths of approximately 1.5 million people with 10 million infections reported in 2018. Recently, a key condensation step in the synthesis of mycolic acids was shown to require β-ketoacyl-ACP synthase (KasA). A crystal structure of KasA with the small molecule DG167 was recently described, which provided a starting point for using computational structure-based approaches to identify additional molecules binding to this protein. We now describe structure-based pharmacophores, docking and machine learning studies with Assay Central as a computational tool for the identification of small molecules targeting KasA. We then tested these compounds using nanoscale differential scanning fluorimetry and microscale thermophoresis. Of note, we identified several molecules including the Food and Drug Administration (FDA)-approved drugs sildenafil and flubendazole with K d values between 30-40 μM. This may provide additional starting points for further optimization.
Collapse
Affiliation(s)
- Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Thomas R. Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Patricia A. Vignaux
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Kimberley M. Zorn
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Glenn C. Capodagli
- Department
of Microbiology, Biochemistry, and Molecular Genetics, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Matthew B. Neiditch
- Department
of Microbiology, Biochemistry, and Molecular Genetics, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Joel S. Freundlich
- Department
of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
- Division
of Infectious Disease, Department of Medicine and the Ruy V. Lourenço
Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University - New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
- . Tel.: +1 215-687-1320
| |
Collapse
|
5
|
Anti-Tubercular Properties of 4-Amino-5-(4-Fluoro-3- Phenoxyphenyl)-4 H-1,2,4-Triazole-3-Thiol and Its Schiff Bases: Computational Input and Molecular Dynamics. Antibiotics (Basel) 2020; 9:antibiotics9090559. [PMID: 32878018 PMCID: PMC7560126 DOI: 10.3390/antibiotics9090559] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 12/26/2022] Open
Abstract
In the present investigation, the parent compound 4-amino-5-(4-fluoro-3-phenoxyphenyl)-4H-1,2,4-triazole-3-thiol (1) and its Schiff bases 2, 3, and 4 were subjected to whole-cell anti-TB against H37Rv and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) by resazurin microtiter assay (REMA) plate method. Test compound 1 exhibited promising anti-TB activity against H37Rv and MDR strains of MTB at 5.5 µg/mL and 11 µg/mL, respectively. An attempt to identify the suitable molecular target for compound 1 was performed using a set of triazole thiol cellular targets, including β-ketoacyl carrier protein synthase III (FABH), β-ketoacyl ACP synthase I (KasA), CYP121, dihydrofolate reductase, enoyl-acyl carrier protein reductase, and N-acetylglucosamine-1-phosphate uridyltransferase. MTB β-ketoacyl ACP synthase I (KasA) was identified as the cellular target for the promising anti-TB parent compound 1 via docking and molecular dynamics simulation. MM(GB/PB)SA binding free energy calculation revealed stronger binding of compound 1 compared with KasA standard inhibitor thiolactomycin (TLM). The inhibitory mechanism of test compound 1 involves the formation of hydrogen bonding with the catalytic histidine residues, and it also impedes access of fatty-acid substrates to the active site through interference with α5–α6 helix movement. Test compound 1-specific structural changes at the ALA274–ALA281 loop might be the contributing factor underlying the stronger anti-TB effect of compound 1 when compared with TLM, as it tends to adopt a closed conformation for the access of malonyl substrate to its binding site.
Collapse
|
6
|
Retraction: A facile sonochemical protocol for synthesis of 3-amino- and 4-amino-1,2,4-triazole derived Schiff bases as potential antibacterial agents. PLoS One 2020; 15:e0238168. [PMID: 32817635 PMCID: PMC7446843 DOI: 10.1371/journal.pone.0238168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
7
|
Sultan A, Ur Rehman MH, Sajjad N, Irfan A, Ullah I, Mustaqeem M, Saleem M, Rubab SL, Rafiq M, Khalid M, Kotwica-Mojzych K, Mojzych M. A facile sonochemical protocol for synthesis of 3-amino- and 4-amino-1,2,4-triazole derived Schiff bases as potential antibacterial agents. PLoS One 2020; 15:e0229891. [PMID: 32497076 PMCID: PMC7272133 DOI: 10.1371/journal.pone.0229891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/18/2020] [Indexed: 12/22/2022] Open
Abstract
A facile method has been developed for the synthesis of Schiff bases derived from substituted and unsubstituted 3-amino- and 4-amino-1,2,4-triazoles. Condensation of the aminotrizoles with a variety of aromatic aldehydes afforded desired Schiff bases in excellent yields in 3-5 minutes of exposure to ultra-sound. The synthesized compounds were characterized by means of IR, 1HNMR and Mass spectrometry. The synthesized compounds were also screened for their antibacterial potential against Gram-negative (Escherichia coli, Shigella sonnei, Pseudomonas aeruginosa and Salmonella typhi) and two Gram-positive (Staphylococcus aureus and Bacillus subtilis) strains.
Collapse
Affiliation(s)
- Aeysha Sultan
- Division of Science and Technology, Department of Chemistry, University of Education, Lahore, Pakistan
| | - Mian Habib Ur Rehman
- Division of Science and Technology, Department of Chemistry, University of Education, Lahore, Pakistan
| | - Noreen Sajjad
- Department of Chemistry, University of Lahore, Lahore, Pakistan
| | - Ali Irfan
- Department of Chemistry, University of Lahore Sargodha campus, Sargodha, Pakistan
| | - Irfan Ullah
- Department of Chemistry, University of Sargodha Sub-campus Bhakkar, Bhakkar, Pakistan
| | - Muhammad Mustaqeem
- Department of Chemistry, University of Sargodha Sub-campus Bhakkar, Bhakkar, Pakistan
| | - Muhammad Saleem
- Department of Chemistry, University of Sargodha Sub-campus Bhakkar, Bhakkar, Pakistan
| | - Syeda Laila Rubab
- Division of Science and Technology, Department of Chemistry, University of Education, Lahore, Pakistan
| | - Muhammad Rafiq
- Department of Physiology and Biochemistry, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Muhammad Khalid
- Department of Chemistry, Khwaja Ghulam Fareed University of Science and Technology, Rahimyar Khan, Pakistan
| | - Katarzyna Kotwica-Mojzych
- Chair and Department of Histology, Embryology and Cytophisiology, Medical University of Lublin, (Collegium Medicum), Lublin, Poland
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, Siedlce, Poland
| |
Collapse
|