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Dhanalakshmi B, Anil Kumar BM, Srinivasa Murthy V, Srinivasa SM, Vivek HK, Sennappan M, Rangappa S. Design, synthesis and docking studies of novel 4-aminophenol-1,2,4-oxadiazole hybrids as apoptosis inducers against triple negative breast cancer cells targeting MAP kinase. J Biomol Struct Dyn 2024; 42:5841-5857. [PMID: 37529915 DOI: 10.1080/07391102.2023.2239912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/17/2023] [Indexed: 08/03/2023]
Abstract
In our study, a series of novel 4-aminophenol benzamide-1,2,4-oxadiazole hybrid analogues have been designed and synthesized by condensing 4-hydroxyphenyl arylamides (3a-c) and 5-chloromethyl-3-aryl-1,2,4-oxadiazoles (6a-d). The structure of the synthesised compounds was verified by various spectroscopic techniques (1H NMR, 13C NMR, IR and LC-MS). All the prepared compounds were subjected to in silico and in vitro antiproliferative study against TNBC cell lines MDA-MB-468 and MDA-MB-231. The investigations revealed that compound 7k significantly promoted apoptosis against MDA-MB-468 and MDA-MB-231 cells with IC50 values of 22.31 µM and 26.27 µM, respectively. Compound 7k interacted with crucial active sites of MAPK and exhibited the highest docking score of -7.06 kcal/mol. Docking was validated with molecular dynamic studies with simulation for 100 ns, depicting various stable interactions with MAPK. Consequently, 7k forms stable H-Bonds and π-π stacking with amino acid residues along with π-cation. Our investigations reveal that the in vitro antiproliferative study of 7k was in good correlation with the in silico studies. Hence, 7k serves as a potential novel lead for the inhibition of TNBCs by downregulating MAPK P38.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Boregowda Dhanalakshmi
- Department of Chemistry, School of Engineering, Dayananda Sagar University, Bengaluru, Karnataka, India
- Department of Chemistry, Rajeev Institute of Technology, Visvesvaraya Technological University, Hassan, Karnataka, India
| | - Belagal Motatis Anil Kumar
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, B.G Nagara, Karnataka, India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, B.G Nagara, Karnataka, India
| | | | - Sudhanva Muddenahalli Srinivasa
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, B.G Nagara, Karnataka, India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, B.G Nagara, Karnataka, India
| | - Hamse Kameshwar Vivek
- Department of Biochemistry, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, B.G Nagara, Karnataka, India
- Department of Biochemistry, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, B.G Nagara, Karnataka, India
| | - Madhappan Sennappan
- Department of Chemistry, Dayananda Sagar College of Engineering, Bangalore, Karnataka, India
| | - Shobith Rangappa
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, B.G Nagara, Karnataka, India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, B.G Nagara, Karnataka, India
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Baothman O, M Ali EM, Hosawi S, E Konozy EH, Abu Zeid IM, Ahmad A, Altayb HN. Multi-targeted therapeutic potential of stigmasterol from the Euphorbia ammak plant in treating lung and breast cancer. Comput Biol Chem 2024; 110:108037. [PMID: 38460436 DOI: 10.1016/j.compbiolchem.2024.108037] [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: 01/17/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
Cancer is the most prevalent disease globally, which presents a significant challenge to the healthcare industry, with breast and lung cancer being predominant malignancies. This study used RNA-seq data from the TCGA database to identify potential biomarkers for lung and breast cancer. Tumor Necrosis Factor (TNFAIP8) and Sulfite Oxidase (SUOX) showed significant expression variation and were selected for further study using structure-based drug discovery (SBDD). Compounds derived from the Euphorbia ammak plant were selected for in-silico study with both TNFAIP8 and SUOX. Stigmasterol had the greatest binding scores (normalized scores of -8.53 kcal/mol and -9.69 kcal/mol) with both proteins, indicating strong stability in their binding pockets throughout the molecular dynamics' simulation. Although Stigmasterol first changed its initial conformation (RMSD = 0.5 nm with the starting conformation) in SUOX, it eventually reached a stable conformation (RMSD of 1.5 nm). The compound on TNFAIP8 showed a persistent shape (RMSD of 0.35 nm), indicating strong protein stability. The binding free energy of the complex was calculated using the MM/GBSA technique; TNFAIP8 had a ΔGTOTAL of -24.98 kcal/mol, with TYR160 being the most significant residue, contributing -2.52 kcal/mol. On the other hand, the SUOX complex had a binding free energy of -16.87 kcal/mol, with LEU151 being the primary contributor (-1.17 kcal/mol). Analysis of the complexes' free energy landscape unveiled several states with minimum free energy, indicating robust interactions between the protein and ligand. In its conclusion, this work emphasises the favourable ability of Stigmasterol to bind with prospective targets for lung and breast cancer, indicating the need for more experimental study.
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Affiliation(s)
- Othman Baothman
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Ehab M M Ali
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Division of Biochemistry, Chemistry Department, Faculty of Science Tanta University, Tanta 31527, Egypt
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Emadeldin Hassan E Konozy
- Laboratory of Proteomics and Glycoproteins, Biotechnology Park, Africa City of Technology, Khartoum, the Sudan
| | - Isam M Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hisham N Altayb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia.
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Shivankar BR, Bhandare VV, Joshi K, Patil VS, Dhotare PS, Sonawane KD, Krishnamurty S. Investigation of cathinone analogs targeting human dopamine transporter using molecular modeling. J Biomol Struct Dyn 2024:1-16. [PMID: 38698732 DOI: 10.1080/07391102.2024.2335303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 03/20/2024] [Indexed: 05/05/2024]
Abstract
In a step towards understanding the structure-property relationship among Synthetic Cathinones (SCs), a combined methodology based on Density Functional Theory (DFT), Administration, Distribution, Metabolism, Excretion, and Toxicity (ADMET) predictions, docking and molecular dynamics simulations have been applied to correlate physicochemical descriptors of various SCs to their biological activity. The results from DFT and molecular docking studies correlate well with each other explaining the biological activity trends of the studied SCs. Quantum mechanical descriptors viz. polarizability, electron affinity, ionization potential, chemical hardness, electronegativity, molecular electrostatic potential, and ion interaction studies unravel the distinguishingly reactive nature of Group D (pyrrolidine substituted) and Group E (methylenedioxy and pyrrolidine substituted) compounds. According to ADMET analysis, Group D and Group E molecules have a higher probability of permeating through the blood-brain barrier. Molecular docking results indicate that Phe76, Ala77, Asp79, Val152, Tyr156, Phe320, and Phe326 constitute the binding pocket residues of hDAT in which the most active ligands MDPV, MDPBP, and MDPPP are bound. Finally, to validate the derived quantum chemical descriptors and docking results, Molecular Dynamics (MD) simulations are performed with homology-modelled hDAT (human dopamine transporter). The MD simulation results revealed that the majority of SCs remain stable within the hDAT protein's active sites via non-bonded interactions after 100 ns long simulations. The findings from DFT, ADMET analysis, molecular docking, and molecular dynamics simulation studies complement each other suggesting that pyrrolidine-substituted SCs (Group D and E), specifically, MPBP and PVN are proven potent SCs along with MDPV, validating various experimental observations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bhavana R Shivankar
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - Krati Joshi
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, India
| | - Vishal S Patil
- Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, India
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
| | | | | | - Sailaja Krishnamurty
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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da Fonseca CAR, Prado VC, Paltian JJ, Kazmierczak JC, Schumacher RF, Sari MHM, Cordeiro LM, da Silva AF, Soares FAA, Oliboni RDS, Luchese C, Cruz L, Wilhelm EA. 4-(Phenylselanyl)-2H-chromen-2-one-Loaded Nanocapsule Suspension-A Promising Breakthrough in Pain Management: Comprehensive Molecular Docking, Formulation Design, and Toxicological and Pharmacological Assessments in Mice. Pharmaceutics 2024; 16:269. [PMID: 38399323 PMCID: PMC10892109 DOI: 10.3390/pharmaceutics16020269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
Therapies for the treatment of pain and inflammation continue to pose a global challenge, emphasizing the significant impact of pain on patients' quality of life. Therefore, this study aimed to investigate the effects of 4-(Phenylselanyl)-2H-chromen-2-one (4-PSCO) on pain-associated proteins through computational molecular docking tests. A new pharmaceutical formulation based on polymeric nanocapsules was developed and characterized. The potential toxicity of 4-PSCO was assessed using Caenorhabditis elegans and Swiss mice, and its pharmacological actions through acute nociception and inflammation tests were also assessed. Our results demonstrated that 4-PSCO, in its free form, exhibited high affinity for the selected receptors, including p38 MAP kinase, peptidyl arginine deiminase type 4, phosphoinositide 3-kinase, Janus kinase 2, toll-like receptor 4, and nuclear factor-kappa β. Both free and nanoencapsulated 4-PSCO showed no toxicity in nematodes and mice. Parameters related to oxidative stress and plasma markers showed no significant change. Both treatments demonstrated antinociceptive and anti-edematogenic effects in the glutamate and hot plate tests. The nanoencapsulated form exhibited a more prolonged effect, reducing mechanical hypersensitivity in an inflammatory pain model. These findings underscore the promising potential of 4-PSCO as an alternative for the development of more effective and safer drugs for the treatment of pain and inflammation.
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Affiliation(s)
- Caren Aline Ramson da Fonseca
- Graduate Program in Biochemistry and Bioprospecting, Biochemical Pharmacology Research Laboratory, Federal University of Pelotas, Pelotas CEP 96010-900, RS, Brazil; (C.A.R.d.F.); (J.J.P.); (C.L.)
| | - Vinicius Costa Prado
- Graduate Program in Pharmaceutical Sciences, Pharmaceutical Technology Laboratory, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil;
| | - Jaini Janke Paltian
- Graduate Program in Biochemistry and Bioprospecting, Biochemical Pharmacology Research Laboratory, Federal University of Pelotas, Pelotas CEP 96010-900, RS, Brazil; (C.A.R.d.F.); (J.J.P.); (C.L.)
| | - Jean Carlo Kazmierczak
- Graduate Program in Chemistry, Chemistry Department, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil; (J.C.K.); (R.F.S.)
| | - Ricardo Frederico Schumacher
- Graduate Program in Chemistry, Chemistry Department, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil; (J.C.K.); (R.F.S.)
| | | | - Larissa Marafiga Cordeiro
- Graduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil; (L.M.C.); (A.F.d.S.); (F.A.A.S.)
| | - Aline Franzen da Silva
- Graduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil; (L.M.C.); (A.F.d.S.); (F.A.A.S.)
| | - Felix Alexandre Antunes Soares
- Graduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil; (L.M.C.); (A.F.d.S.); (F.A.A.S.)
| | - Robson da Silva Oliboni
- Center for Chemical, Pharmaceutical, and Food Sciences, CCQFA, Federal University of Pelotas, Pelotas CEP 96010-900, RS, Brazil;
| | - Cristiane Luchese
- Graduate Program in Biochemistry and Bioprospecting, Biochemical Pharmacology Research Laboratory, Federal University of Pelotas, Pelotas CEP 96010-900, RS, Brazil; (C.A.R.d.F.); (J.J.P.); (C.L.)
| | - Letícia Cruz
- Graduate Program in Pharmaceutical Sciences, Pharmaceutical Technology Laboratory, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil;
| | - Ethel Antunes Wilhelm
- Graduate Program in Biochemistry and Bioprospecting, Biochemical Pharmacology Research Laboratory, Federal University of Pelotas, Pelotas CEP 96010-900, RS, Brazil; (C.A.R.d.F.); (J.J.P.); (C.L.)
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Uttarkar A, Rao V, Bhat D, Niranjan V. Disaggregation of amyloid-beta fibrils via natural metabolites using long timescale replica exchange molecular dynamics simulation studies. J Mol Model 2024; 30:61. [PMID: 38321243 DOI: 10.1007/s00894-024-05860-0] [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] [Received: 09/05/2023] [Accepted: 01/30/2024] [Indexed: 02/08/2024]
Abstract
CONTEXT Amyloid fibrils are self-assembled fibrous protein aggregates that are associated with several presently incurable diseases such as Alzheimer's. disease that is characterized by the accumulation of amyloid fibrils in the brain, which leads to the formation of plaques and the death of brain cells. Disaggregation of amyloid fibrils is considered a promising approach to cure Alzheimer's disease. The mechanism of amyloid fibril formation is complex and not fully understood, making it difficult to develop drugs that can target the process. Diacetonamine and cystathionine are potential lead compounds to induce disaggregation of amyloid fibrils. METHODS In the current research, we have used long timescale molecular simulation studies and replica exchange molecular dynamics (REMD) for 1000 ns (1 μs) to examine the mechanisms by which natural metabolites can disaggregate amyloid-beta fibrils. Molecular docking was carried out using Glide and with prior protein minimization and ligand preparation. We focused on a screening a database of natural metabolites, as potential candidates for disaggregating amyloid fibrils. We used Desmond with OPLS 3e as a force field. MM-GBSA calculations were performed. Blood-brain barrier permeability, SASA, and radius of gyration parameters were calculated.
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Affiliation(s)
- Akshay Uttarkar
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore, 560059, affiliated to Visvesvaraya Technological University, Belagavi, 590018, India
| | - Vibha Rao
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore, 560059, affiliated to Visvesvaraya Technological University, Belagavi, 590018, India
| | - Dhrithi Bhat
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore, 560059, affiliated to Visvesvaraya Technological University, Belagavi, 590018, India
| | - Vidya Niranjan
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore, 560059, affiliated to Visvesvaraya Technological University, Belagavi, 590018, India.
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Dhanalakshmi B, Anil Kumar BM, Muddenahalli Srinivasa S, Vivek HK, Sennappan M, Rangappa S, Srinivasa Murthy V. Design and synthesis of 4-aminophenol-1,3,4-oxadiazole derivative potentiates apoptosis by targeting MAP kinase in triple negative breast cancer cells. J Biomol Struct Dyn 2023:1-16. [PMID: 37948299 DOI: 10.1080/07391102.2023.2274973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/18/2023] [Indexed: 11/12/2023]
Abstract
Women below 40 years greatly suffer from triple negative breast cancers (TNBCs). Compared to other breast cancer cases, the poor prognosis and lower survival rate of TNBC patients make it an alarming task to save the human era from this dreadful disease. Therefore, identifying potential novel leads is urgently required to combat the TNBC. To discover a novel anticancer agent, we synthesized a series of novel 4-aminophenolbenzamide-1,3,4 oxadiazole hybrid analogues (7a-l). The structure of the compounds was confirmed by spectral methods (1H & 13C NMR, IR and MS). All the compounds were subjected to their in-silico and in-vitro antiproliferative studies against the TNBC cell lines MDA-MB-468 and MDA-MB-231. The investigations revealed that 7i has significantly promoted apoptosis against MDA-MB-468 and MDA-MB-231 cells with IC50 values of 16.89 and 19.43 µM, respectively. Molecular docking of 7i, with MAPK has exhibited the highest binding score of -7.10 kcal/mol by interacting with crucial amino acids present at the active sites. Molecular docking is further validated with molecular dynamic studies with simulation for 100 ns, depicting various stable interactions with MAPK. Compound 7i, forms stable H-bonds and π-π stacking with amino acid residues. Molecular dynamic simulation (MDS) reveals that hydrophobic and water bridges were very prominent for 7i to bind, with the amino acid residues in close proximity to the active site of p38 MAPK. The investigations show that the In-vitro antiproliferative study of 7i agreed with the in-silico studies. Collectively, our investigations depict 7i as a potent novel lead for the inhibition of TNBCs by targeting p38 MAPK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Boregowda Dhanalakshmi
- Department of Chemistry, School of Engineering, Dayananda Sagar University, Bengaluru, India
- Department of Chemistry, Rajeev Institute of Technology, Visvesvaraya Technological University, Hassan, India
| | - Belagal Motatis Anil Kumar
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, Nagamangala,India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, Nagamangala, India
| | - Sudhanva Muddenahalli Srinivasa
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, Nagamangala,India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, Nagamangala, India
| | - Hamse Kameshwar Vivek
- Department of Biotechnology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, Nagamangala, India
- Department of Biochemistry, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, Nagamangala, India
| | - Madhappan Sennappan
- Department of Chemistry, Dayananda Sagar College of Engineering, Bengaluru, India
| | - Shobith Rangappa
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, Nagamangala,India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, Nagamangala, India
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Ahmed S, Bhat AR, Rahiman AK, Dongre RS, Hasan AH, Niranjan V, C L, Sheikh SA, Jamalis J, Berredjem M, Kawsar SMA. Green synthesis, antibacterial and antifungal evaluation of new thiazolidine-2,4-dione derivatives: molecular dynamic simulation, POM study and identification of antitumor pharmacophore sites. J Biomol Struct Dyn 2023:1-17. [PMID: 37768136 DOI: 10.1080/07391102.2023.2258404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
In this study, a series of thiazolidine-2,4-dione derivatives 3a-i were synthesized and evaluated for antibacterial activity against Gram-positive and Gram-negative strains of Bacillus licheniformis, Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus. Newly prepared thiazolidine (TZD) derivatives were further screened separately for in vitro antifungal activity against cultures of fungal species, namely, Aspergillus niger, Alternaria brassicicola, Chaetomium murorum, Fusarium oxysporum, Lycopodium sp. and Penicillium notatum. The electron-donating substituents (-OH and -OCH3) and electron-withdrawing substituents (-Cl and -NO2) on the attached arylidene moieties of five-membered heterocyclic ring enhanced the broad spectrum of antimicrobial and antifungal activities. The molecular docking study has revealed that compound 3h strongly interacts with the catalytic residues of the active site of the β-carbonic anhydrase (P. aeruginosa) and has the best docking score. In silico pharmacokinetics studies showed the drug-likeness and non-toxic nature of the synthesized compounds, which indicates the combined antibacterial, antiviral and antitumor pharmacophore sites of the targeted drug. This work demonstrates that potential TZD derivatives bind to different types of bacterial and fungal pathogens for circumventing their activities and opens avenues for the development of newer drug candidates that can target bacterial and fungal pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sumeer Ahmed
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | - Ajmal R Bhat
- Department of Chemistry, RTM Nagpur University, Nagpur, India
| | - Aziz Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | | | - Aso Hameed Hasan
- Department of Chemistry, College of Science, University of Garmian, Kalar, Iraq
| | - Vidya Niranjan
- Department of Biotechnology, R V College of Engineering, Bengaluru, India
| | - Lavanya C
- Department of Biotechnology, R V College of Engineering, Bengaluru, India
| | - S A Sheikh
- Department of Physics, National Institute of Technology, Srinagar, Kashmir, India
| | - Joazaizulfazli Jamalis
- Faculty of Science, Department of Chemistry, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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Niranjan V, Uttarkar A, Ramakrishnan A, Muralidharan A, Shashidhara A, Acharya A, Tarani A, Kumar J. De Novo Design of Anti-COVID Drugs Using Machine Learning-Based Equivariant Diffusion Model Targeting the Spike Protein. Curr Issues Mol Biol 2023; 45:4261-4284. [PMID: 37232740 DOI: 10.3390/cimb45050271] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/07/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
The drug discovery and research for an anti-COVID-19 drug has been ongoing despite repurposed drugs in the market. Over time, these drugs were discontinued due to side effects. The search for effective drugs is still under process. The role of Machine Learning (ML) is critical in the search for novel drug compounds. In the current work, using the equivariant diffusion model, we built novel compounds targeting the spike protein of SARS-CoV-2. Using the ML models, 196 de novo compounds were generated which had no hits on any major chemical databases. These novel compounds fulfilled all the criteria of ADMET properties to be lead-like and drug-like compounds. Of the 196 compounds, 15 were docked with high confidence in the target. These compounds were further subjected to molecular docking, the best compound having an IUPAC name of (4aS,4bR,8aS,8bS)-4a,8a-dimethylbiphenylene-1,4,5,8(4aH,4bH,8aH,8bH)-tetraone and a binding score of -6.930 kcal/mol. The principal compound is labeled as CoECG-M1. Density Function Theory (DFT) and Quantum optimization was carried out along with the study of ADMET properties. This suggests that the compound has potential drug-like properties. The docked complex was further subjected to MD simulations, GBSA, and metadynamics simulations to gain insights into the stability of binding. The model can be in the future modified to improve the positive docking rate.
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Affiliation(s)
- Vidya Niranjan
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Akshay Uttarkar
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Ananya Ramakrishnan
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Anagha Muralidharan
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Abhay Shashidhara
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Anushri Acharya
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Avila Tarani
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Jitendra Kumar
- Bangalore Bioinnovation Centre (BBC), Helix Biotech Park, Electronics City Phase 1, Bengaluru 560100, Karnataka, India
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Setlur AS, K C, Bhattacharjee R, Kumar J, Niranjan V. Deciphering the interaction mechanism of natural actives against larval proteins of Aedes aegypti to identify potential larvicides: a computational biology analysis. J Biomol Struct Dyn 2023; 41:12480-12502. [PMID: 36688316 DOI: 10.1080/07391102.2023.2166993] [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: 07/25/2022] [Accepted: 01/04/2023] [Indexed: 01/24/2023]
Abstract
Aedes aegypti is the target for repellents to curb incidences of vector-borne diseases. Stopping breeding of this mosquito species at its larval stages helps in controlling spread of insect-borne diseases. Therefore, the present study focused on deciphering the mechanism of interaction of selected natural actives against larval proteins of A. aegypti to identify potential natural alternative larvicides. 65 larval proteins were identified from literature, whose structures were modelled and validated using RaptorX and ProCheck. 11 natural actives were selected for predicting their ligand properties and toxicities via Toxicity Estimation Software Tool and ProTox-II. Molecular docking studies were carried out using POAP followed by 100 ns molecular dynamic simulation studies for top three best docked complexes to better understand the robustness of docking, complex stabilities and molecular mechanisms of interactions. Toxicity predictions revealed that 6 molecules belonged to toxicity class 4, and five to toxicity class 5, implying that they were all safe to use. Complexes goniothalamin-translation elongation factor (-10 kcal/mol), andrographolide-acetyl-CoA C-myristoyltransferase (-9.2 kcal/mol) and capillin-translation elongation factor (-8.4 kcal/mol) showed best binding energies. When simulated, capillin-translation elongation factor showed most stability, while the remaining two also evidenced robust docking. Evolutionary studies for top two larval proteins disclosed 100 other insect species in which these proteins can be targeted using various larvicides. Protein-protein interaction network analysis revealed several protein pathways that might be affected due to aforesaid naturals. Therefore, this study provides computational insights into the molecular interaction of naturals against larval proteins, acting as potential natural larvicides.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anagha S Setlur
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
| | - Chandrashekar K
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
| | | | - Jitendra Kumar
- Bangalore Bio-innovation Centre (BBC), Helix Biotech Park, Electronic City Phase-I, Bangalore, Karnataka, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
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S. Setlur A, Karunakaran C, Pandey S, Sarkar M, Niranjan V. Molecular interaction studies of thymol via molecular dynamic simulations and free energy calculations using multi-target approach against Aedes aegypti proteome to decipher its role as mosquito repellent. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2159054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Anagha S. Setlur
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
| | | | - Shruti Pandey
- Research and Development, Reckitt Benckiser India Pvt. Ltd., Gurgaon, Haryana, India
| | - Manas Sarkar
- Research and Development, Reckitt Benckiser India Pvt. Ltd., Gurgaon, Haryana, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
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Design of Novel Coumarin Derivatives as NUDT5 Antagonists That Act by Restricting ATP Synthesis in Breast Cancer Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010089. [PMID: 36615284 PMCID: PMC9822328 DOI: 10.3390/molecules28010089] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Breast cancer, a heterogeneous disease, is among the most frequently diagnosed diseases and is the second leading cause of death due to cancer among women after lung cancer. Phytoactives (plant-based derivatives) and their derivatives are safer than synthetic compounds in combating chemoresistance. In the current work, a template-based design of the coumarin derivative was designed to target the ADP-sugar pyrophosphatase protein. The novel coumarin derivative (2R)-2-((S)-sec-butyl)-5-oxo-4-(2-oxochroman-4-yl)-2,5-dihydro-1H-pyrrol-3-olate was designed. Molecular docking studies provided a docking score of -6.574 kcal/mol and an MM-GBSA value of -29.15 kcal/mol. Molecular dynamics simulation studies were carried out for 500 ns, providing better insights into the interaction. An RMSD change of 2.4 Å proved that there was a stable interaction and that there was no conformational change induced to the receptor. Metadynamics studies were performed to calculate the unbinding energy of the principal compound with NUDT5, which was found to be -75.171 kcal/mol. In vitro validation via a cytotoxicity assay (MTT assay) of the principal compound was carried out with quercetin as a positive control in the MCF7 cell line and with an IC50 value of 55.57 (+/-) 0.7 μg/mL. This work promoted the research of novel natural derivatives to discover their anticancer activity.
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Erdogan Orhan I, Deniz FSS, Salmas RE, Irmak S, Acar OO, Turgut GC, Sen A, Zbancioc AM, Luca SV, Skiba A, Skalicka-Woźniak K, Tataringa G. Evaluation of Anti-Alzheimer Activity of Synthetic Coumarins by Combination of in Vitro and in Silico Approaches. Chem Biodivers 2022; 19:e202200315. [PMID: 36282001 DOI: 10.1002/cbdv.202200315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/19/2022] [Indexed: 12/27/2022]
Abstract
Series of synthetic coumarin derivatives (1-16) were tested against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), two enzymes linked to the pathology of Alzheimer's disease (AD). Compound 16 was the most active AChE inhibitor with IC50 32.23±2.91 μM, while the reference (galantamine) had IC50 =1.85±0.12 μM. Compounds 9 (IC50 75.14±1.82 μM), 13 (IC50 =16.14±0.43 μM), were determined to be stronger BChE inhibitors than the reference galantamine (IC50 =93.53±2.23 μM). The IC50 value of compound 16 for BChE inhibition (IC50 =126.56±11.96 μM) was slightly higher than galantamine. The atomic interactions between the ligands and the key amino acids inside the binding cavities were simulated to determine their ligand-binding positions and free energies. The three inhibitory coumarins (9, 13, 16) were next tested for their effects on the genes associated with AD using human neuroblastoma (SH-SY5Y) cell lines. Our data indicate that they could be considered for further evaluation as new anti-Alzheimer drug candidates.
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Affiliation(s)
- Ilkay Erdogan Orhan
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| | - F Sezer Senol Deniz
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| | | | - Sule Irmak
- Pamukkale University, Faculty of Arts & Sciences, Department of Biology, 20070, Denizli, Turkey
| | - Ozden Ozgun Acar
- Pamukkale University, Seed Breeding & Genetics Application Research Center, 20070, Denizli, Turkey
| | - Gurbet Celik Turgut
- Pamukkale University, Faculty of Applied Sciences, Organic Agriculture Management, Civril, 20680, Denizli, Turkey
| | - Alaattin Sen
- Pamukkale University, Faculty of Arts & Sciences, Department of Biology, 20070, Denizli, Turkey.,Abdullah Gul University, Faculty of Life and Natural Sciences, Department of Molecular Biology and Genetics, 38080, Kayseri, Turkey
| | - Ana-Maria Zbancioc
- University of Medicine and Pharmacy Grigore T. Popa Iasi, Faculty of Pharmacy, Romania
| | - Simon Vlad Luca
- Biothermodynamics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Adrianna Skiba
- Department of Natural Products Chemistry, Medical University of Lublin, 20-093, Lublin, Poland
| | | | - Gabriela Tataringa
- University of Medicine and Pharmacy Grigore T. Popa Iasi, Faculty of Pharmacy, Romania
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Setlur AS, K C, Pandey S, Sarkar M, Niranjan V. Comprehensive Molecular Interaction Studies to Construe the Repellent/Kill Activity of Geraniol During Binding Event Against Aedes aegypti Proteins. Mol Biotechnol 2022; 65:726-740. [PMID: 36169809 DOI: 10.1007/s12033-022-00560-7] [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: 05/18/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022]
Abstract
Aedes aegypti is an etiological agent for dengue, chikungunya, zika, and yellow fever viruses. With the advent of the use of natural alternatives as repellents, their precise mode of action during the event of binding is still unclear. Geraniol is one such bioactive natural that has been previously shown to have some insecticide properties. Thus, the present study aimed to understand the mechanism of the binding event of geraniol with the whole proteome of A. aegypti. Twenty protein target categories were shortlisted for the mosquito, wherein the proteins were downloaded with respect to the reference proteome. Conserved domain analysis was performed for the same using the CDD search tool to find the proteins that have common domains. 309 proteins were modeled using RaptorX standalone tool, and validated using Ramachandran plots from SAVES v6.0 from ProCheck. These modeled and validated proteins were then docked against geraniol, using POAP software, for understanding the binding energies. The top 3 best-docked complexes were then analyzed for their stabilities and event of binding via 100 ns simulation studies using DESMOND's Maestro environment. The docking results showed that the geraniol-voltage-gated sodium channel had the best energy of - 7.1 kcal/mol, followed by geraniol-glutathione-S-transferase (- 6.8 kcal/mol) and geraniol-alpha esterase (- 6.8 kcal/mol). The simulations for these 3 complexes revealed that several residues of the proteins interacted well with geraniol at a molecular level, and all three docked complexes were found to be stable when simulated (RMSD: 16-18 Å, 3.6-4.8 Å, 4.8-5.6 Å, respectively). Thus, the present study provides insights into the mechanism of the binding event of geraniol with the major A. aegypti targets, thereby, assisting the use of geraniol as a natural repellent.
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Affiliation(s)
- Anagha S Setlur
- Department of Biotechnology, RV College of Engineering, Bangalore, 560059, India
| | - Chandrashekar K
- Department of Biotechnology, RV College of Engineering, Bangalore, 560059, India
| | - Shruti Pandey
- Research and Development, Reckitt Benckiser India Pvt. Ltd., Gurgaon, Haryana, 122001, India
| | - Manas Sarkar
- Research and Development, Reckitt Benckiser India Pvt. Ltd., Gurgaon, Haryana, 122001, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bangalore, 560059, India.
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Mycobacterium Time-Series Genome Analysis Identifies AAC2′ as a Potential Drug Target with Naloxone Showing Potential Bait Drug Synergism. Molecules 2022; 27:molecules27196150. [PMID: 36234683 PMCID: PMC9571707 DOI: 10.3390/molecules27196150] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
The World Health Organization has put drug resistance in tuberculosis on its list of significant threats, with a critical emphasis on resolving the genetic differences in Mycobacterium tuberculosis. This provides an opportunity for a better understanding of the evolutionary progression leading to anti-microbial resistance. Anti-microbial resistance has a great impact on the economic stability of the global healthcare sector. We performed a timeline genomic analysis from 2003 to 2021 of 578 mycobacterium genomes to understand the pattern underlying genomic variations. Potential drug targets based on functional annotation was subjected to pharmacophore-based screening of FDA-approved phyto-actives. Reaction search, MD simulations, and metadynamics studies were performed. A total of 4,76,063 mutations with a transition/transversion ratio of 0.448 was observed. The top 10 proteins with the least number of mutations were high-confidence drug targets. Aminoglycoside 2′-N-acetyltransferase protein (AAC2′), conferring resistance to aminoglycosides, was shortlisted as a potential drug target based on its function and role in bait drug synergism. Gentamicin-AAC2′ binding pose was used as a pharmacophore template to screen 10,570 phyto-actives. A total of 66 potential hits were docked to obtain naloxone as a lead—active with a docking score of −6.317. Naloxone is an FDA-approved drug that rapidly reverses opioid overdose. This is a classic case of a repurposed phyto-active. Naloxone consists of an amine group, but the addition of the acetyl group is unfavorable, with a reaction energy of 612.248 kcal/mol. With gentamicin as a positive control, molecular dynamic simulation studies were performed for 200 ns to check the stability of binding. Metadynamics-based studies were carried out to compare unbinding energy with gentamicin. The unbinding energies were found to be −68 and −74 kcal/mol for naloxone and gentamycin, respectively. This study identifies naloxone as a potential drug candidate for a bait drug synergistic approach against Mycobacterium tuberculosis.
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Uttarkar A, Niranjan V. Brefeldin A variant via combinatorial screening acts as an effective antagonist inducing structural modification in EPAC2. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2110271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Akshay Uttarkar
- Department of Biotechnology, R V College of Engineering, Rashtreeya Sikshana Samithi Trust, Bengaluru, India
| | - Vidya Niranjan
- Department of Biotechnology, R V College of Engineering, Rashtreeya Sikshana Samithi Trust, Bengaluru, India
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