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Nandikolla A, Khetmalis YM, Venkata Siva Kumar B, Chandu A, Karan Kumar B, Shetye G, Ma R, Murugesan S, Franzblau SG, Chandra Sekhar KVG. Design, synthesis and biological evaluation of phenanthridine amide and 1,2,3-triazole analogues against Mycobacterium tuberculosis. RSC Med Chem 2023; 14:1549-1561. [PMID: 37593576 PMCID: PMC10429663 DOI: 10.1039/d3md00115f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/29/2023] [Indexed: 08/19/2023] Open
Abstract
The phenanthridine core exhibits antitubercular activity, according to reports from the literature. Several 1,2,3-triazole-based heterocyclic compounds are well-known antitubercular agents. A series of twenty-five phenanthridine amide and 1,2,3-triazole derivatives are synthesized and analyzed using ESI-MS, 1HNMR, and 13CNMR on the basis of our earlier findings that phenanthridine and 1,2,3-triazoles shown good antitubercular activity. The synthesized phenanthridine amide and 1,2,3-triazole analogues were tested in vitro against Mycobacterium tuberculosis H37Rv and minimum inhibitory concentration (MIC) values were determined utilizing non-replicating and replicating low-oxygen recovery assay (LORA) and microplate Alamar Blue assay (MABA) methodologies. The phenanthridine amide derivative PA-01 had an MIC of 61.31 μM in MABA and 62.09 μM in the LORA technique, showing intense anti-TB activity. Amongst the phenanthridine triazole derivatives, PT-09, with MICs of 41.47 and 78.75 μM against the tested strain of Mtb in both MABA and LORA was the most active one. The final analogues' drug-likeness is predicted using absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies. The most active compounds PA-01 and PT-09 were further subjected to in silico docking studies. Using the Glide module of Schrodinger, molecular docking analysis was carried out to estimate the plausible binding pattern of PA-01 and PT-09 at the active site of Mycobacterial DNA topoisomerase II (PDB code: 5BS8). Further, molecular dynamics studies of PA-01 and PT-09 were also carried out.
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Affiliation(s)
- Adinarayana Nandikolla
- Department of Chemistry, Birla Institute of Technology and Science, Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal Hyderabad - 500078 Telangana India +91 40 66303527
| | - Yogesh Mahadu Khetmalis
- Department of Chemistry, Birla Institute of Technology and Science, Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal Hyderabad - 500078 Telangana India +91 40 66303527
| | - Boddupalli Venkata Siva Kumar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal Hyderabad - 500078 Telangana India +91 40 66303527
| | - Ala Chandu
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani Pilani Campus Pilani-333031 Rajasthan India
| | - Banoth Karan Kumar
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani Pilani Campus Pilani-333031 Rajasthan India
| | - Gauri Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago 833 South Wood Street Chicago IL 60612 USA
| | - Rui Ma
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago 833 South Wood Street Chicago IL 60612 USA
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani Pilani Campus Pilani-333031 Rajasthan India
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago 833 South Wood Street Chicago IL 60612 USA
| | - Kondapalli Venkata Gowri Chandra Sekhar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal Hyderabad - 500078 Telangana India +91 40 66303527
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Pishgouii F, Lotfi S, Sedaghati E. Anti-AChE and Anti-BuChE Screening of the Fermentation Broth Extracts from Twelve Aspergillus Isolates and GC-MS and Molecular Docking Studies of the Most Active Extracts. Appl Biochem Biotechnol 2023; 195:5199-5216. [PMID: 37129742 DOI: 10.1007/s12010-023-04548-0] [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] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Nowadays, the administration of cholinesterase enzyme (acetylcholinesterase: AChE and butyrylcholinesterase: BuChE) inhibitors is very common for the symptomatic treatment of Alzheimer's disease and the other forms of dementia and CNS disorders. In this paper, the anti-AChE and anti-BuChE activities of the fermentation broth ethyl acetate extracts from twelve Aspergillus isolates were evaluated by Ellman method. The results showed that A1 (Aspergillus flavus) and A5 (Aspergillus tubingensis, isolate 1) extracts with IC50 values of 46.77 μg/mL and 75.85 μg/mL possess the greatest ability to inhibit AChE and BuChE, respectively. GC-MS analysis of the extracts (A1 and A5) demonstrated that two alkaloids named 14-methyl-16-azabicyclo[10.3.1]hexadeca-1(15),12(16),13-triene (MAHT) and 6-chloro-2-methyl-7,8,9,10-tetrahydro-phenanthridine (CMTP) account for the highest percentage of A1 (26.95%) and A5 (25.5%) extracts, respectively. A 2-pyrazoline derivative, 5-hydroxy-3-(4-pyridinyl)-5-trifluoromethyl-1-(2,4,6-trimethylphenoxyacetyl)- (PHPTT), also constituted the high percentage (9.54%) of A5 extract. The anticholinesterase and neuroprotective effects of some 2-pyrazoline derivatives have been previously reported. The interaction study of MAHT with human AChE and CMTP and PHPTT with human BuChE using molecular docking indicated that these alkaloids bind to the active site gorge of the enzymes with high affinity. The best docking scores of MAHT, CMTP, and PHPTT were -7.1, -8.2, and -9.7 kcal/mol, respectively.
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Affiliation(s)
- Fatemeh Pishgouii
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Safa Lotfi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Ebrahim Sedaghati
- Department of Plant Protection, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
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Padariya M, Baginski M, Babak M, Kalathiya U. Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme. Biophys Chem 2022; 291:106909. [DOI: 10.1016/j.bpc.2022.106909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/27/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]
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Kaushik S, Chang CEA. Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association. Front Mol Biosci 2021; 8:659687. [PMID: 34041265 PMCID: PMC8142692 DOI: 10.3389/fmolb.2021.659687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Ligand–protein association is the first and critical step for many biological and chemical processes. This study investigated the molecular association processes under different environments. In biology, cells have different compartments where ligand–protein binding may occur on a membrane. In experiments involving ligand–protein binding, such as the surface plasmon resonance and continuous flow biosynthesis, a substrate flow and surface are required in experimental settings. As compared with a simple binding condition, which includes only the ligand, protein, and solvent, the association rate and processes may be affected by additional ligand transporting forces and other intermolecular interactions between the ligand and environmental objects. We evaluated these environmental factors by using a ligand xk263 binding to HIV protease (HIVp) with atomistic details. Using Brownian dynamics simulations, we modeled xk263 and HIVp association time and probability when a system has xk263 diffusion flux and a non-polar self-assembled monolayer surface. We also examined different protein orientations and accessible surfaces for xk263. To allow xk263 to access to the dimer interface of immobilized HIVp, we simulated the system by placing the protein 20Å above the surface because immobilizing HIVp on a surface prevented xk263 from contacting with the interface. The non-specific interactions increased the binding probability while the association time remained unchanged. When the xk263 diffusion flux increased, the effective xk263 concentration around HIVp, xk263–HIVp association time and binding probability decreased non-linearly regardless of interacting with the self-assembled monolayer surface or not. The work sheds light on the effects of the solvent flow and surface environment on ligand–protein associations and provides a perspective on experimental design.
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Affiliation(s)
- Shivansh Kaushik
- Department of Chemistry, University of Chemistry, Riverside, CA, United States
| | - Chia-En A Chang
- Department of Chemistry, University of Chemistry, Riverside, CA, United States
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