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Sekar V, Ramasamy G, Ravikumar C, Muthurajan R, Uthandi S, Kandasamy R, Ganapati PS. Targeting bone cancer with 4-Allylbenzene-1,2-diol purified from Piper betle L.: an in silico and cytotoxicity scrutiny. J Biomol Struct Dyn 2023; 41:15446-15459. [PMID: 36905677 DOI: 10.1080/07391102.2023.2188952] [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: 05/13/2022] [Accepted: 03/01/2023] [Indexed: 03/13/2023]
Abstract
Piper betle L., a well-known medicinal plant with rich source of bioactive compounds, is widely used in several therapeutics. The present study was performed to scrutinize the anti-cancer potential of compounds P. betle petiole by means of in silico studies, purification of 4-Allylbenzene-1,2-diol from petioles and assessing its cytotoxicity on bone cancer metastasis. Subsequent to SwissADME screening, 4-Allylbenzene-1,2-diol and Alpha terpineol were chosen for molecular docking together with eighteen approved drugs against fifteen important bone cancer targets accompanied with molecular dynamics simulation studies. 4-Allylbenzene-1,2-diol was found to be multi-targeting, interacted effectively with all targets, particularly exhibited good stability with MMP9 and MMP2 during molecular dynamics simulations and Molecular Mechanics- Generalized Born and Surface Area (MM-GBSA) analysis using Schrodinger. Later, the compound was isolated, purified and the cytotoxicity studies on MG63 bone cancer cell lines confirmed the cytotoxicity nature (75.98% at 100 µg/ml concentration). The results demonstrated the compound as a matrix metalloproteinase inhibitor, and therefore 4-Allylbenzene-1,2-diol may possibly be prescribed in targeted therapy for alleviating the bone cancer metastasis upon further wet lab experimental validations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vinusri Sekar
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, TN, India
| | - Gnanam Ramasamy
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, TN, India
| | - Caroline Ravikumar
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, TN, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, TN, India
| | - Sivakumar Uthandi
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, TN, India
| | - Rajamani Kandasamy
- Department of Medicinal and Aromatic crops, Tamil Nadu Agricultural University, Coimbatore, TN, India
| | - Patil Santosh Ganapati
- Department of Physical Sciences and Information Technology, Tamil Nadu Agricultural University, Coimbatore, TN, India
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Gurushankar K, Rimac H, Nadezhda P, Grishina M. Exploring the potential and identifying Withania somnifera alkaloids as novel dihydrofolate reductase (DHFR) inhibitors by the AlteQ method. J Biomol Struct Dyn 2023; 41:13963-13976. [PMID: 36762693 DOI: 10.1080/07391102.2023.2175727] [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: 10/07/2022] [Accepted: 01/29/2023] [Indexed: 02/11/2023]
Abstract
There is an urgent need to discover and develop novel drugs to combat Mycobacterium tuberculosis, the causative agent of tuberculosis (TB) in humans. Alkaloids have been shown to have wide-ranging therapeutic application and could be ideal candidates for drug development, and research is underway to develop new anti-tubercular drugs from natural sources. In this regard, the current research deals with finding novel lead compounds from the Withania somnifera (WS) plant. Broad health benefits of WS are due to the presence of diverse chemical constituents which include anaferine and anahygrine and which belong to the alkaloid family. In the present study, these two compounds have been theoretically studied to understand their electronic properties using the density functional theory (DFT) at the B3LYP/6-311 + G (d,p) level. HOMO and LUMO properties and molecular electrostatic potential (MEP) surface were calculated. Further, to understand the mechanism of action of these compounds and to identify their putative drug target, molecular docking and dynamics studies were employed against Mycobacterium tuberculosis dihydrofolate reductase (DHFR). It was determined that NADP+ affects stability of the complexes by reducing fluctuations of residues 14-23 and 117-126. It was also found that Ile5 and Gln28 play an important role in complexation. Electron density analysis (using the AlteQ method) of the intermolecular region, analyzing both the anaferin-NADP+ and anahygrin-NADP+ complexes showed that anaferin and anahygrin complexes are more stable in the presence of NADP+. It has been established that in most intermolecular contacts the contribution of the ligand to the electron density is greater than that of NADP+. The present study thus provides an excellent way to analyze the effect of anaferine and anahygrine in essential processes of M. tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Krishnamoorthy Gurushankar
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu, India
| | - Hrvoje Rimac
- Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Palko Nadezhda
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
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Potential Inhibitors of Monkeypox Virus Revealed by Molecular Modeling Approach to Viral DNA Topoisomerase I. Molecules 2023; 28:molecules28031444. [PMID: 36771105 PMCID: PMC9919579 DOI: 10.3390/molecules28031444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/05/2023] Open
Abstract
The monkeypox outbreak has become a global public health emergency. The lack of valid and safe medicine is a crucial obstacle hindering the extermination of orthopoxvirus infections. The identification of potential inhibitors from natural products, including Traditional Chinese Medicine (TCM), by molecular modeling could expand the arsenal of antiviral chemotherapeutic agents. Monkeypox DNA topoisomerase I (TOP1) is a highly conserved viral DNA repair enzyme with a small size and low homology to human proteins. The protein model of viral DNA TOP1 was obtained by homology modeling. The reliability of the TOP1 model was validated by analyzing its Ramachandran plot and by determining the compatibility of the 3D model with its sequence using the Verify 3D and PROCHECK services. In order to identify potential inhibitors of TOP1, an integrated library of 4103 natural products was screened via Glide docking. Surface Plasmon Resonance (SPR) was further implemented to assay the complex binding affinity. Molecular dynamics simulations (100 ns) were combined with molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) computations to reveal the binding mechanisms of the complex. As a result, three natural compounds were highlighted as potential inhibitors via docking-based virtual screening. Rosmarinic acid, myricitrin, quercitrin, and ofloxacin can bind TOP1 with KD values of 2.16 μM, 3.54 μM, 4.77 μM, and 5.46 μM, respectively, indicating a good inhibitory effect against MPXV. The MM/PBSA calculations revealed that rosmarinic acid had the lowest binding free energy at -16.18 kcal/mol. Myricitrin had a binding free energy of -13.87 kcal/mol, quercitrin had a binding free energy of -9.40 kcal/mol, and ofloxacin had a binding free energy of -9.64 kcal/mol. The outputs (RMSD/RMSF/Rg/SASA) also indicated that the systems were well-behaved towards the complex. The selected compounds formed several key hydrogen bonds with TOP1 residues (TYR274, LYS167, GLY132, LYS133, etc.) via the binding mode analysis. TYR274 was predicted to be a pivotal residue for compound interactions in the binding pocket of TOP1. The results of the enrichment analyses illustrated the potential pharmacological networks of rosmarinic acid. The molecular modeling approach may be acceptable for the identification and design of novel poxvirus inhibitors; however, further studies are warranted to evaluate their therapeutic potential.
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Okella H, Okello E, Mtewa AG, Ikiriza H, Kaggwa B, Aber J, Ndekezi C, Nkamwesiga J, Ajayi CO, Mugeni IM, Ssentamu G, Ochwo S, Odongo S, Tolo CU, Kato CD, Engeu PO. ADMET profiling and molecular docking of potential antimicrobial peptides previously isolated from African catfish, Clarias gariepinus. Front Mol Biosci 2022; 9:1039286. [PMID: 36567944 PMCID: PMC9772024 DOI: 10.3389/fmolb.2022.1039286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Amidst rising cases of antimicrobial resistance, antimicrobial peptides (AMPs) are regarded as a promising alternative to traditional antibiotics. Even so, poor pharmacokinetic profiles of certain AMPs impede their utility necessitating, a careful assessment of potential AMPs' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties during novel lead exploration. Accordingly, the present study utilized ADMET scores to profile seven previously isolated African catfish antimicrobial peptides (ACAPs). After profiling, the peptides were docked against approved bacterial protein targets to gain insight into their possible mode of action. Promising ACAPs were then chemically synthesized, and their antibacterial activity was validated in vitro utilizing the broth dilution method. All seven examined antimicrobial peptides passed the ADMET screening, with two (ACAP-IV and ACAP-V) exhibiting the best ADMET profile scores. The ACAP-V had a higher average binding energy (-8.47 kcal/mol) and average global energy (-70.78 kcal/mol) compared to ACAP-IV (-7.60 kcal/mol and -57.53 kcal/mol), with the potential to penetrate and disrupt bacterial cell membrane (PDB Id: 2w6d). Conversely, ACAP-IV peptide had higher antibacterial activity against E. coli and S. aureus (Minimum Inhibitory Concentration, 520.7 ± 104.3 μg/ml and 1666.7 ± 416.7 μg/ml, respectively) compared to ACAP-V. Collectively, the two antimicrobial peptides (ACAP-IV and ACAP-V) are potential novel leads for the food, cosmetic and pharmaceutical industries. Future research is recommended to optimize the expression of such peptides in biological systems for extended evaluation.
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Affiliation(s)
- Hedmon Okella
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States,Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda,*Correspondence: Hedmon Okella,
| | - Emmanuel Okello
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Andrew Glory Mtewa
- Chemistry Section, Malawi Institute of Technology, Malawi University of Science and Technology, Limbe, Malawi
| | - Hilda Ikiriza
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Bruhan Kaggwa
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda,Department of Pharmacy, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Jacqueline Aber
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda,Department of Pharmacy, Faculty of Medicine, Gulu University, Gulu, Uganda
| | | | - Joseph Nkamwesiga
- International Livestock Research Institute, Nairobi, Kenya,Institut für Virologie, Freie Universität, Berlin, Germany
| | - Clement Olusoji Ajayi
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Ivan Mulongo Mugeni
- Medical Entomology Laboratory, Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Geofrey Ssentamu
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Sylvester Ochwo
- Center for Animal Health and Food Safety, University of Minnesota, St. Paul, MN, United States
| | - Steven Odongo
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Casim Umba Tolo
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Charles Drago Kato
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Patrick Ogwang Engeu
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda
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Browne RB, Goswami N, Borah P, Roy JD. Computational approaches for evaluation of isobavachin as potential inhibitor against t877a and w741l mutations in prostate cancer. J Biomol Struct Dyn 2022; 41:2398-2418. [PMID: 35118933 DOI: 10.1080/07391102.2022.2032353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Prostate cancer is the World's second most common cancer, with the fifth-highest male mortality rate. Point mutations such as T877A and W741L are frequently seen in advanced prostate cancer patients, conferring drug-resistance and hence driving cancer growth. Such occurrence of drug resistance in prostate cancer necessitates designing of suitable ligands to ensure better interactions with the receptors which can block the progression of the disease. The present study focus on the modification of plant-derived flavonoids that might act as inhibitors against such point mutations namely, T877A and W741L. In T877A mutation threonine is substituted by alanine at the 877 codon and W741L mutation, tryptophan is substituted by lysine at the 741 codon in prostate cancer. The study revolved on the aspect of the evaluation of Isobavachin and its derivatives as a potential agent to tackle such point mutations by using the in silico approach. A total of 98 molecular dockings were performed to find the ligand-receptor complexes with the lowest binding energy employing Autodock Software to conduct the blind and site-specific docking. Additionally, ligands were screened for Drug-likeness and toxicity using several tools yielding eight possible drug candidates. Based on the results of Molecular Docking, Drug-likeness, and ADMET testing, ten structures, including six complexes and three receptors were subjected to molecular dynamics simulation of 100 ns covering RMSD, RMSF, Rg, and MM/PBSA. Based on the simulation results, Isobavachin, IsoMod4, and IsoMod7 were concluded to be stable and exhibited potential properties for developing a novel drug to combat prostate cancer and its associated drug-resistance.
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Affiliation(s)
- Rene Barbie Browne
- Department of Biochemistry, Assam Don Bosco University, Guwahati, Assam, India
| | - Nabajyoti Goswami
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Guwahati, Assam, India
| | - Probodh Borah
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Guwahati, Assam, India
| | - Jayanti Datta Roy
- Department of Bio-Sciences, Assam Don Bosco University, Guwahati, Assam, India
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Singh R, Bhardwaj VK, Sharma J, Purohit R, Kumar S. In-silico evaluation of bioactive compounds from tea as potential SARS-CoV-2 nonstructural protein 16 inhibitors. J Tradit Complement Med 2022; 12:35-43. [PMID: 34099976 PMCID: PMC8172245 DOI: 10.1016/j.jtcme.2021.05.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/29/2021] [Accepted: 05/29/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND AND AIM A novel coronavirus, called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been found to cause COVID-19 in humans and some other mammals. The nonstructural protein 16 (NSP16) of SARS-CoV-2 plays a significant part in the replication of viruses and suppresses the ability of innate immune system to detect the virus. Therefore, inhibiting NSP16 can be a secure path towards identifying a potent medication against SARS-CoV-2. Tea (Camellia sinensis) polyphenols have been reported to exhibit potential treatment options against various viral diseases. METHODS We conducted molecular docking and structural dynamics studies with a set of 65 Tea bioactive compounds to illustrate their ability to inhibit NSP16 of SARS-CoV-2. Moreover, post-simulations end state thermodynamic free energy calculations were estimated to strengthen our results. RESULTS AND CONCLUSION Six bioactive tea molecules showed better docking scores than the standard molecule sinefungin. These results were further validated by MD simulations, where Theaflavin compound demonstrated lower binding free energy in comparison to the standard molecule sinefungin. The compound theaflavin could be considered as a novel lead compound for further evaluation by in-vitro and in-vivo studies.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jatin Sharma
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
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Azam F, Eid EEM, Almutairi A. Targeting SARS-CoV-2 main protease by teicoplanin: A mechanistic insight by docking, MM/GBSA and molecular dynamics simulation. J Mol Struct 2021; 1246:131124. [PMID: 34305175 PMCID: PMC8286173 DOI: 10.1016/j.molstruc.2021.131124] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 07/05/2021] [Accepted: 07/14/2021] [Indexed: 12/16/2022]
Abstract
First emerged in late December 2019, the outbreak of novel severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) pandemic has instigated public-health emergency around the globe. Till date there is no specific therapeutic agent for this disease and hence, the world is craving to identify potential antiviral agents against SARS-CoV-2. The main protease (MPro) is considered as an attractive drug target for rational drug design against SARS-CoV-2 as it is known to play a crucial role in the viral replication and transcription. Teicoplanin is a glycopeptide class of antibiotic which is regularly used for treating Gram-positive bacterial infections, has shown potential therapeutic efficacy against SARS-CoV-2 in vitro. Therefore, in this study, a mechanistic insight of intermolecular interactions between teicoplanin and SARS-CoV-2 MPro has been scrutinized by molecular docking. Both monomeric and dimeric forms of MPro was used in docking involving blind as well as defined binding site based on the known inhibitor. Binding energies of teicoplanin-MPro complexes were estimated by Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) computations from docking and simulated trajectories. The dynamic and thermodynamics constraints of docked drug in complex with target proteins under specific physiological conditions was ascertained by all-atom molecular dynamics simulation of 100 ns trajectory. Root mean square deviation and fluctuation of carbon α chain justified the stability of the bound complex in biological environments. The outcomes of current study are supposed to be fruitful in rational design of antiviral drugs against SARS-CoV-2.
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