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Gowtham H, Revanasiddappa PD, Murali M, Singh SB, Abhilash M, Pradeep S, Shivamallu C, Achar RR, Silina E, Stupin V, Manturova N, Shati AA, Alfaifi MY, Elbehairi SEI, Kollur SP. Secondary metabolites of Trichoderma spp. as EGFR tyrosine kinase inhibitors: Evaluation of anticancer efficacy through computational approach. PLoS One 2024; 19:e0296010. [PMID: 38266021 PMCID: PMC10824427 DOI: 10.1371/journal.pone.0296010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/01/2023] [Indexed: 01/26/2024] Open
Abstract
The present study explores the epidermal growth factor receptor (EGFR) tyrosine kinase inhibition efficacy of secondary metabolites in Trichoderma spp. through molecular docking, molecular dynamics (MD) simulation and MM-PBSA approach. The result of molecular docking confirmed that out of 200 metabolites screened, three metabolites such as Harzianelactone A, Pretrichodermamide G and Aspochalasin M, potentially bound with the active binding site of EGFR tyrosine kinase domain(PDB ID: 1M17) with a threshold docking score of ≤- 9.0 kcal/mol when compared with the standard EGFR inhibitor (Erlotinib). The MD simulation was run to investigate the potential for stable complex formation in EGFR tyrosine kinase domain-unbound/lead metabolite (Aspochalasin M)-bound/standard inhibitor (Erlotinib)-bound complex. The MD simulation analysis at 100 ns revealed that Aspochalasin M formed the stable complex with EGFR. Besides, the in silico predication of pharmacokinetic properties further confirmed that Aspochalasin M qualified the drug-likeness rules with no harmful side effects (viz., hERG toxicity, hepatotoxicity and skin sensitization), non-mutagenicity and favourable logBB value. Moreover, the BOILED-Egg model predicted that Aspochalasin M showed a higher gastrointestinal absorption with improved bioavailability when administered orally and removed from the central nervous system (CNS). The results of the computational studies concluded that Aspochalasin M possessed significant efficacy in binding EGFR's active sites compared to the known standard inhibitor (Erlotinib). Therefore, Aspochalasin M can be used as a possible anticancer drug candidate and further in vitro and in vivo experimental validation of Aspochalasin M of Trichoderma spp. are required to determine its anticancer potential.
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Affiliation(s)
- H.G. Gowtham
- Department of PG Studies in Biotechnology, Nrupathunga University, Bangalore, Karnataka, India
| | | | | | | | - M.R. Abhilash
- Department of Studies in Environmental Science, University of Mysore, Mysore, India
| | - Sushma Pradeep
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ekaterina Silina
- Department of Human Pathology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Victor Stupin
- Department of Hospital Surgery, NI. Pirogov Russian National Research Medical University, Moscow, Russia
| | - Natalia Manturova
- Department of Hospital Surgery, NI. Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | | | - Shiva Prasad Kollur
- School of Physical Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysuru, Karnataka, India
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2
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Kumari N, Singh D, Singh P, Mishra A, Gond C, Ojha H, Tiwari AK. Biological Evaluation and Binding Mechanism of 5-HT 7 Specific Arylpiperazinyl-Alkyl Benzothiazolone: Radiobiology and Photo-physical Studies. J Fluoresc 2024; 34:341-352. [PMID: 37249676 DOI: 10.1007/s10895-023-03266-4] [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: 01/26/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023]
Abstract
Diversely substituted methoxy derivatives of arylpiperazinyl-alkyl benzothiazolone has been evaluated as specific probe for 5HT7. To determine the best methoxy derivative for 5HT7 receptor affinity, we synthesised a number of 2-benzothiazolone arylalkyl piperazine derivatives. In-vitro/vivo studies with C-2 substituted [11C]ABT showed 5HT7 specific binding. The radiochemical purity of [11C]ABT was found to be more than 99% with radiochemical stability persistence for more than 1.5 hr at 25 °C. The interaction of BSA and ABT has been analysed by photophysical studies for better understanding of properties such as adsortion, distribution, metabolism and elemination (ADME). The interaction between ABT and BSA was analyzed by using the UV-vis and fluorescence spectra. UV-vis spectra analyzed the changes in primary structure of BSA on its interaction with ABT. ABT showed quenched fluorescence emission intensity of tryptophan residues in BSA via static quenching mechanism. This study might help to understand how ABT binds to serum protein or subsequently to know the ADME of this drug candidate.
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Affiliation(s)
- Neelam Kumari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
- CBRN Protection and decontamination research group, Division of Cyclotron and Radiological, Nuclear and Imaging Sciences, Institute of Nuclear Medicine and Allied Sciences, Timarpur, 110054, Delhi, India
- Department of Chemistry, Sri Venkateswara College, University of Delhi, Benito JuarezMarg, New Delhi, 110021, India
| | - Deepika Singh
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
| | - Priya Singh
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
| | - Akanksha Mishra
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
| | - Chandraprakash Gond
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
| | - Himanshu Ojha
- CBRN Protection and decontamination research group, Division of Cyclotron and Radiological, Nuclear and Imaging Sciences, Institute of Nuclear Medicine and Allied Sciences, Timarpur, 110054, Delhi, India
| | - Anjani Kumar Tiwari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India.
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3
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Ghadirian F, Abbasi H, Bavi O, Naeimabadi A. How living cells are affected during the cold atmospheric pressure plasma treatment. Free Radic Biol Med 2023; 205:141-150. [PMID: 37295538 DOI: 10.1016/j.freeradbiomed.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
When the electric discharge process is limited by high voltage electrodes shielding, the ionization measure would be controlled to less than one percent and the temperature to less than 37 °C even at atmospheric pressure, so-called cold atmospheric pressure plasma (CAP). CAP has been found to have profound medical applications in association with its reactive oxygen and nitrogen species (ROS/RNS). In this way that during plasma exposure, the subjected medium (e.g. cell cytoplasmic membrane in plasma therapy) interacts with ROS/RNS. Accordingly, a precise study of the mentioned interactions and their consequences on the cells' behavior changes, is necessary. The results lead to the reduction of possible risks and provide the opportunity of optimizing the efficacy of CAP before the development of CAP applications in the field of plasma medicine. In this report molecular dynamic (MD) simulation is used to investigate the mentioned interactions and a proper and compatible comparison with the experimental results is presented. Based on this, the effects of H2O2, NO and O2 on the living cell's membrane are investigated in biological conditions. Our results show that: i) The hydration of phospholipid polar heads would be enhanced associated with the H2O2 presence. ii) A new definition of the surface area assigned to each phospholipid (APL), more reliable and compatible with the physical expectations, is introduced. iii) The long-term behavior of NO and O2 is their penetration into the lipid bilayer and sometimes passing through the membrane into the cell. The latter would be an indication of internal cells' pathways activation leading to modification of cells' function.
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Affiliation(s)
- Fatemeh Ghadirian
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran
| | - Hossein Abbasi
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran.
| | - Omid Bavi
- Department of Mechanical Engineering, Shiraz University of Technology, Shiraz, Iran
| | - Aboutorab Naeimabadi
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran
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Gowtham HG, Ahmed F, Anandan S, Shivakumara CS, Bilagi A, Pradeep S, Shivamallu C, Shati AA, Alfaifi MY, Elbehairi SEI, Achar RR, Silina E, Stupin V, Murali M, Kollur SP. In Silico Computational Studies of Bioactive Secondary Metabolites from Wedelia trilobata against Anti-Apoptotic B-Cell Lymphoma-2 (Bcl-2) Protein Associated with Cancer Cell Survival and Resistance. Molecules 2023; 28:molecules28041588. [PMID: 36838574 PMCID: PMC9959492 DOI: 10.3390/molecules28041588] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
In the present study, the binding affinity of 52 bioactive secondary metabolites from Wedelia trilobata towards the anti-apoptotic B-cell lymphoma-2 (Bcl-2) protein (PDB: 2W3L) structure was identified by using in silico molecular docking and molecular dynamics simulation. The molecular docking results demonstrated that the binding energies of docked compounds with Bcl-2 protein ranged from -5.3 kcal/mol to -10.1 kcal/mol. However, the lowest binding energy (-10.1 kcal/mol) was offered by Friedelin against Bcl-2 protein when compared to other metabolites and the standard drug Obatoclax (-8.4 kcal/mol). The molecular dynamics simulations revealed that the Friedelin-Bcl-2 protein complex was found to be stable throughout the simulation period of 100 ns. Overall, the predicted Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties of Friedelin are relatively better than Obatoclax, with the most noticeable differences in many parameters where Friedelin has no AMES toxicity, hepatotoxicity, and skin sensitization. The ADMET profiling of selected compounds supported their in silico drug-likeness properties. Based on the computational analyses, the present study concluded that Friedelin of W. trilobata was found to be the potential inhibitor of the Bcl-2 protein, which merits attention for further in vitro and in vivo studies before clinical trials.
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Affiliation(s)
| | - Faiyaz Ahmed
- Department of Clinical Nutrition, College of Applied Health Sciences in Ar Rass, Qassim University, Al Qassim Region, Ar Rass 51921, Saudi Arabia
| | - Satish Anandan
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar 563103, Karnataka, India
| | - C. S. Shivakumara
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar 563103, Karnataka, India
| | - Ashween Bilagi
- Department of Integrative Medicine, Sri Devaraj Urs Academy of Higher Education and Research, Kolar 563103, Karnataka, India
| | - Sushma Pradeep
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru 570015, India
- Correspondence: (C.S.); (M.M.); (S.P.K.)
| | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha 9004, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha 9004, Saudi Arabia
| | - Serag Eldin I. Elbehairi
- Biology Department, Faculty of Science, King Khalid University, Abha 9004, Saudi Arabia
- Cell Culture Lab, Egyptian Organization for Biological Products and Vaccines (VACSERA Holding Company), 51 Wezaret El-Zeraa St., Giza 12511, Egypt
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Ekaterina Silina
- Institute of Biodesign and Modeling of Complex Systems, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Victor Stupin
- Department of Hospital Surgery, N.I. Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Mahadevamurthy Murali
- Department of Studies in Botany, University of Mysore, Manasagangotri, Mysuru 570006, Karnataka, India
- Correspondence: (C.S.); (M.M.); (S.P.K.)
| | - Shiva Prasad Kollur
- School of Physical Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysuru 570026, Karnataka, India
- Correspondence: (C.S.); (M.M.); (S.P.K.)
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5
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Singh D, Kaur L, Singh P, Datta A, Pathak M, Tiwari AK, Ojha H, Singhal R. Luminescence and in-silico studies of binding interactions of arylpiperazinyl-butylbenzoxazolone based synthetic compounds with bovine serum albumin. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Gowtham HG, Murali M, Singh SB, Shivamallu C, Pradeep S, Shivakumar CS, Anandan S, Thampy A, Achar RR, Silina E, Stupin V, Ortega-Castro J, Frau J, Flores-Holguín N, Amruthesh KN, Kollur SP, Glossman-Mitnik D. Phytoconstituents of Withania somnifera unveiled Ashwagandhanolide as a potential drug targeting breast cancer: Investigations through computational, molecular docking and conceptual DFT studies. PLoS One 2022; 17:e0275432. [PMID: 36201520 PMCID: PMC9536605 DOI: 10.1371/journal.pone.0275432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Breast cancer is the second most common malignancy in females worldwide and poses a great challenge that necessitates the identification of novel therapeutic agents from several sources. This research aimed to study the molecular docking and molecular dynamics simulations of four proteins (such as PDB: 6CBZ, 1FDW, 5GWK and 2WTT) with the selected phytochemicals from Withania somnifera to identify the potential inhibitors for breast cancer. The molecular docking result showed that among 44 compounds, two of them, Ashwagandhanolide and Withanolide sulfoxide have the potential to inhibit estrogen receptor alpha (ERα), 17-beta-hydroxysteroid -dehydrogenase type 1 (17β-HSD1), topoisomerase II alpha (TOP2A) and p73 tetramerization domain that are expressed during breast cancer. The molecular dynamics (MD) simulations results suggested that Ashwagandhanolide remained inside the binding cavity of four targeted proteins and contributed favorably towards forming a stable protein-ligand complex throughout the simulation. Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties confirmed that Ashwagandhanolide is hydrophobic and has moderate intestinal permeability, good intestinal absorption, and poor skin permeability. The compound has a relatively low VDss value (-1.652) and can be transported across ABC transporter and good central nervous system (CNS) permeability but did not easily cross the blood-brain barrier (BBB). This compound does not possess any mutagenicity, hepatotoxicity and skin sensitization. Based on the results obtained, the present study highlights the anticancer potential of Ashwagandhanolide, a compound from W. somnifera. Furthermore, in vitro and in vivo studies are necessary to perform before clinical trials to prove the potentiality of Ashwagandhanolide.
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Affiliation(s)
| | - Mahadevamurthy Murali
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | | | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Sushma Pradeep
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - C. S. Shivakumar
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
| | - Satish Anandan
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
- * E-mail: (SA); (KNA); (SPK); (DGM)
| | - Anjana Thampy
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ekaterina Silina
- Department of Human Pathology, I. M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Victor Stupin
- Department of Hospital Surgery, N.I. Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | | | - Juan Frau
- Departament de Química, Universitat de les Illes Balears, Palma de Malllorca, Spain
| | - Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chih, México
| | - Kestur Nagaraj Amruthesh
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysore, Karnataka, India
- * E-mail: (SA); (KNA); (SPK); (DGM)
| | - Shiva Prasad Kollur
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), University of the South Pacific, Laucala Campus, Suva, Fiji
- Department of Sciences, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysore, Karnataka, India
- * E-mail: (SA); (KNA); (SPK); (DGM)
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chih, México
- * E-mail: (SA); (KNA); (SPK); (DGM)
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Adhikari A, Pandey A, Kumar D, Tiwari AK. Determination of Hybrid TSPO Ligands with Minimal Impact of SNP
(rs6971) through Molecular Docking and MD Simulation Study. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210413130326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
In an endeavor to ascertain high-affinity TSPO ligands with minimal single
nucleotide polymorphism (SNP), six hybrid molecules have been identified as new leads for future
inflammation PET imaging.
Objective:
Genesis for chemical design was encouraged from structural families of well-known ligands
FEBMP and PBR28/ DAA1106 that have demonstrated remarkable TSPO binding characteristics.
Methods:
All proposed hybrid ligands 1-6 are subjected to molecular docking and simulation studies
with wild and mutant protein to study their interactions, binding, consistency of active conformations
and are correlated with well-established TSPO ligands.
Results:
Each hybrid ligand demonstrate better docking score > -11.00 kcal/mol with TSPO with
respect to gold standard PK11195, i.e., -11.00 kcal/mol for 4UC3 and -12.94 kcal/mol for 4UC1. On
comparison with FEBMP and GE-180 (-12.57, -7.24 kcal/mol for 4UC3 and -14.10, -11.32
kcal/mol for 4UC1), ligand 3 demonstrates maximum docking energy (> -15.50 kcal/mol) with
minimum SNP (0.26 kcal/mol).
Discussion:
Presence of strong hydrogen bond Arg148-3.27Å (4UC1) and Trp50-2.43Å, Asp28-
2.57Å (4UC3) apart from short-range interactions, including π–π interactions with the aromatic residues,
such as (Trp39, Phe46, Trp135) and (Trp39, Trp108), attributes towards its strong binding.
Conclusion:
Utilizing the results of binding energy, we concluded stable complex formation of these
hybrid ligands that could bind to TSPO with the least effect of SNP with similar interactions to
known ligands. Overall, ligand 3 stands out as the best ligand having insignificant deviations per
residue of protein that can be further explored and assessed in detail for future inflammation PET
application after subsequent detailed biological evaluation.
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Affiliation(s)
- Anupriya Adhikari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Anwesh Pandey
- Department of
Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Devesh Kumar
- Department of
Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Anjani K. Tiwari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
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Çapan İ, Shehu A, Sert Y, Çelik İ, Erol M, Koca İ, Servi S. Synthesis, molecular docking, molecular dynamics and evaluation of Drug-Likeness properties of the fused N-Formyl pyrazoline substituted new dehydroepiandrosterone derivatives. J Biomol Struct Dyn 2022; 41:2492-2503. [PMID: 35132941 DOI: 10.1080/07391102.2022.2034667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The hybrid molecules bearing heterocyclic structures in the A or D rings of steroids have significant biological activity. 16 (E)-Hetereoarylidene steroids were synthesized from the reaction of different heteroaromatic carbaldehydes and trans-Dehydroepiandrosterone (DHEA) in a basic medium. Then, synthesis of the N-formyl pyrazoline substituted new DHEA derivatives were carried out from the reaction of hydrazine hydrate and 16 (E)-hetereoarylidene steroids. The structures of the synthesized compounds were elucidated by elemental analysis, FT-IR, 1H NMR, and 13C NMR spectroscopy. To investigate the activation pathway of synthesized N-formyl pyrazoline substituted steroid derivatives, a molecular docking study was performed on human cytochrome P450-(CYP17A1: PDB ID 5IRQ) with the help of the free AutoDock Vina. 100 ns molecular dynamic simulation process was performed to monitor the behavior of the complex structure formed by CYP17A1 and to calculate the stability over time of 2a and 2d (-9.8 kcal/mol), which gave the lowest value according to the results obtained in the molecular docking study with AutoDock Vina. Accordingly, RMSD, RMSF, Rg, and SASA analyzes of 2a and 2d were performed, and MMPBSA was calculated. Lastly, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) analyses of the novel steroid derivatives were investigated.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- İrfan Çapan
- Department of Material and Material Processing Technologies, Technical Sciences Vocational College, Gazi University, Ankara, Turkey
| | - Abdulmalik Shehu
- Department of Chemistry, Faculty of Science, Federal University Dutse, Dutse, Jigawa, Nigeria
| | - Yusuf Sert
- Sorgun Vocational School, Yozgat Bozok University, Yozgat, Turkey
| | - İsmail Çelik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Meryem Erol
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - İrfan Koca
- Department of Chemistry, Faculty of Art & Sciences, Yozgat Bozok University, Yozgat, Turkey
| | - Süleyman Servi
- Department of Chemistry, Faculty of Science, Fırat University, Elazığ, Turkey
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9
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Kumari N, Kaul A, Deepika, Srivastava K, Mishra G, Bhagat S, Singh VK, KumarTiwari A. [99mTc-BBPA]: A possible SPECT agent to understand role of 18-kDa translocator protein (PBR/TSPO) during neuro-glial interaction. Bioorg Chem 2022; 121:105678. [DOI: 10.1016/j.bioorg.2022.105678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/11/2021] [Accepted: 02/08/2022] [Indexed: 11/02/2022]
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10
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Singh D, Aggarwal S, Singh VK, Pratap R, Mishra AK, Tiwari AK. Lanthanide (Ln 3+) complexes of bifunctional chelate: Synthesis, physicochemical study and interaction with human serum albumin (HSA). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 244:118808. [PMID: 32846304 DOI: 10.1016/j.saa.2020.118808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/21/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Bifunctional chelate EDTA-bis amide (N,N'-bis (tyramide)ethylenediamine-N,N'-diacetic acid) that has ability to mimic natural amino acids was synthesized and analyzed by various spectroscopic techniques. The physicochemical studies were performed to calculate the various thermodynamic and kinetic parameters for the synthesized poly-amino carboxylate ligand. The two protonation constant (pka's = 3.460 and 6.722) of the prepared ligand and stability constants (log KML's = 15.8, 18.1, 16.2, 18.4, 17.5, 18.9, 13.6 and 12.8) of the complexes formed with Ce3+, Sm3+, Eu3+, Gd3+, Tb3+, Lu3+, Zn2+ and Cu2+ were determined by potentiometric titration using 0.1 M Me4NOH as non-aqueous base. The formation kinetics of [EuEDTA-TA2]+ and [CeEDTA-TA2]+ was studied and the rate constants were found to be 2.95 × 10-5 s-1 and 4.414 × 10-5 s-1respectively including the exchange reaction of [EuEDTA-TA2]+ with Zn2+ and Cu2+ spectrophotometrically. The Eu(III) complex of EDTA(TA)2 gives three emission bands at 480 nm, 540 nm and 610 nm (λmax = 270 nm, excitation) which shows efficacy of the ligand as an optical imaging agent. Molecular docking studies with Human Serum Albumin (HSA: PDB 1E78) showed binding pattern with the residues Arg218, Arg222, Lys195 and Lys444 in sub domain II A of site I via hydrogen bond and identifies the ligand-HSA interaction and specific insight for transportation to the target sites. Subsequently, fluorescence spectroscopy was performed at λex = 350 nm binding constant for HSA was 5.847 × 104 M-1 which showed effective quenching effect.
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Affiliation(s)
- Deepika Singh
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Lucknow, India
| | - Swati Aggarwal
- Institute of Nuclear Medicine and Allied Sciences, DRDO, Timarpur, New Delhi, India; Department of Chemistry, University of Delhi, New Delhi, India; Kalindi College, Department of Chemistry, University of Delhi, New Delhi, India
| | | | - Ramendra Pratap
- Department of Chemistry, University of Delhi, New Delhi, India
| | - Anil Kumar Mishra
- Institute of Nuclear Medicine and Allied Sciences, DRDO, Timarpur, New Delhi, India
| | - Anjani Kumar Tiwari
- Institute of Nuclear Medicine and Allied Sciences, DRDO, Timarpur, New Delhi, India; Department of Chemistry, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Lucknow, India.
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11
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Bharadwaj S, Rao AK, Dwivedi VD, Mishra SK, Yadava U. Structure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM/MM affinity estimation. J Biomol Struct Dyn 2020; 39:2338-2351. [PMID: 32216596 DOI: 10.1080/07391102.2020.1747545] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent Zika virus (ZIKV) outbreak and association with human diseases such as neurological disorders have raised global health concerns. However, in the absence of an approved anti-ZIKV drug has generated urgency for the drug development against ZIKV infection. Here, structure-based virtual screening of 8589 bioactive compounds, screened at the substrate-binding site of ZIKV nonstructural 5 (NS5)-based structure N-terminal methyltransferase (MTase) domain followed by ADMET (absorption, distribution, metabolism, excretion and toxicity) profiling concluded the four potential lead inhibitors, i.e. (4-acetylamino-benzenesulfonylamino)-acetic acid (F3342-0450), 3-(5-methylfuran-2-yl)-N-(4-sulfamoylphenyl)propanamide (F1736-0142), 8-(2-hydroxy-ethylamino)-1,3-dimethyl-7-(3-methyl-benzyl)-3,7-dihydro-purine-2,6-dione (F0886-0080) and N-[4-(aminosulfonyl)phenyl]-2,3-dihydro-1,4-benzodioxine-2-carboxamide (F0451-2187). Collectively, extra precision docking and Density Functional Theory(DFT) calculations studies identified the F3342-0450 molecule, having strong interactions on the active site of MTase, further supported by molecular dynamics simulation, binding affinity and hybrid QM/MM calculations, suggest a new drug molecule for the antiviral drug development against ZIKV infection. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shiv Bharadwaj
- Sabanci University Nanotechnology Research and Application Center, Istanbul, Turkey
| | - Akhilesh Kumar Rao
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| | - Vivek Dhar Dwivedi
- Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Sarad Kumar Mishra
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
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12
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Chadha N, Singh D, Milton MD, Mishra G, Daniel J, Mishra AK, Tiwari AK. Computational prediction of interaction and pharmacokinetics profile study for polyamino-polycarboxylic ligands on binding with human serum albumin. NEW J CHEM 2020. [DOI: 10.1039/c9nj05594k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human serum albumin (HSA) is one of the most abundant plasma proteins available in blood and responsible for transport of fatty acids, drugs and metabolites at its binding sites which are very important for the assessment of pharmacokinetics profile of the polyamino-polycarboxylic ligands.
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Affiliation(s)
- Nidhi Chadha
- Division of Cyclotron and Radiopharmaceutical Sciences
- Institute of Nuclear Medicine and Allied Sciences
- Delhi 110054
- India
- Department of Chemistry
| | - Dushyant Singh
- Department of Chemistry
- Christ Church P. G. College
- C S J M University
- Kanpur
- India
| | | | - Gauri Mishra
- Department of Zoology
- Swami Shraddhanand College
- University of Delhi
- Delhi 110036
- India
| | - Joseph Daniel
- Department of Chemistry
- Christ Church P. G. College
- C S J M University
- Kanpur
- India
| | - Anil K. Mishra
- Division of Cyclotron and Radiopharmaceutical Sciences
- Institute of Nuclear Medicine and Allied Sciences
- Delhi 110054
- India
| | - Anjani K. Tiwari
- Division of Cyclotron and Radiopharmaceutical Sciences
- Institute of Nuclear Medicine and Allied Sciences
- Delhi 110054
- India
- Department of Chemistry
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13
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Pottel J, Moitessier N. Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering. J Chem Inf Model 2015; 55:2657-71. [PMID: 26623941 DOI: 10.1021/acs.jcim.5b00525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein engineers have long been hard at work to harness biocatalysts as a natural source of regio-, stereo-, and chemoselectivity in order to carry out chemistry (reactions and/or substrates) not previously achieved with these enzymes. The extreme labor demands and exponential number of mutation combinations have induced computational advances in this domain. The first step in our virtual approach is to predict the correct conformations upon mutation of residues (i.e., rebuilding side chains). For this purpose, we opted for a combination of molecular mechanics and statistical data. In this work, we have developed automated computational tools to extract protein structural information and created conformational libraries for each amino acid dependent on a variable number of parameters (e.g., resolution, flexibility, secondary structure). We have also developed the necessary tool to apply the mutation and optimize the conformation accordingly. For side-chain conformation prediction, we obtained overall average root-mean-square deviations (RMSDs) of 0.91 and 1.01 Å for the 18 flexible natural amino acids within two distinct sets of over 3000 and 1500 side-chain residues, respectively. The commonly used dihedral angle differences were also evaluated and performed worse than the state of the art. These two metrics are also compared. Furthermore, we generated a family-specific library for kinases that produced an average 2% lower RMSD upon side-chain reconstruction and a residue-specific library that yielded a 17% improvement. Ultimately, since our protein engineering outlook involves using our docking software, Fitted/Impacts, we applied our mutation protocol to a benchmarked data set for self- and cross-docking. Our side-chain reconstruction does not hinder our docking software, demonstrating differences in pose prediction accuracy of approximately 2% (RMSD cutoff metric) for a set of over 200 protein/ligand structures. Similarly, when docking to a set of over 100 kinases, side-chain reconstruction (using both general and biased conformation libraries) had minimal detriment to the docking accuracy.
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Affiliation(s)
- Joshua Pottel
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC, Canada H3A 0B8
| | - Nicolas Moitessier
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC, Canada H3A 0B8
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14
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Yadav A, Kumar R, Sunkaria A, Singhal N, Kumar M, Sandhir R. Evaluation of potential flavonoid inhibitors of glyoxalase-I based on virtual screening and in vitro studies. J Biomol Struct Dyn 2015; 34:993-1007. [PMID: 26108947 DOI: 10.1080/07391102.2015.1064830] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Glyoxalase-I (GLO-I) is a component of the ubiquitous detoxification system involved in the conversion of methylglyoxal (MG) to d-lactate in the glycolytic pathway. MG toxicity arises from its ability to form advanced glycation end products. GLO-I has been reported to be frequently overexpressed in various types of cancer cells. In this study, we performed structure-based virtual screening of focused flavonoids commercial library to identify potential and specific inhibitors of GLO-I. The compounds were ranked based on Glide extra precision docking score and five hits (curcumin, quercetin, morin, naringin and silibinin) were selected on the basis of their interaction with active site amino acid residues of GLO-I. Mixed mode QM/MM calculation was performed on the top-scoring hit to ascertain the role of zinc ion in ligand binding. In addition, the identified hits were subjected to MM/GBSA binding energy prediction, ADME prediction and similarity studies. The hits were tested in vitro for cell viability, and GLO-I inhibition. Naringin (ST072162) was found to be most potent inhibitor of GLO-I among the identified hits with highest glide XP dock score of -14.906. These findings suggest that naringin could be a new scaffold for designing inhibitors against GLO-I with potential application as anticancer agents.
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Affiliation(s)
- Aarti Yadav
- a Department of Biochemistry , Panjab University , Chandigarh , India
| | - Rajnish Kumar
- b University Institute of Pharmaceutical Sciences , Panjab University , Chandigarh , India
| | - Aditya Sunkaria
- a Department of Biochemistry , Panjab University , Chandigarh , India
| | - Nitin Singhal
- c Department of Food Science and Technology , National Agri-Food Biotechnology Institute , Mohali , India
| | - Manoj Kumar
- b University Institute of Pharmaceutical Sciences , Panjab University , Chandigarh , India
| | - Rajat Sandhir
- a Department of Biochemistry , Panjab University , Chandigarh , India
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