1
|
Geetha R, Meera MR, Vijayakumar C, Premkumar R, Milton Franklin Benial A. Synthesis, spectroscopic characterization, molecular docking and in vitro cytotoxicity investigations on 8-Amino-6-Methoxy Quinolinium Picrate: a novel breast cancer drug. J Biomol Struct Dyn 2023; 41:1753-1766. [PMID: 34984960 DOI: 10.1080/07391102.2021.2024259] [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] [Indexed: 02/02/2023]
Abstract
Density Functional Theory (DFT) studies of the 8-Amino-6-Methoxy Quinolinium Picrate (8A6MQP) molecule have been carried out with extensive and accurate investigations of detailed vibrational and spectroscopic investigations as well as validated experimentally. The 8A6MQP sample was synthesized and characterized using FT-IR, FT-Raman, FT-NMR and UV-Vis spectroscopic techniques. Subsequently, the optimized molecular structure and harmonic resonance frequencies of the molecule were computed based on DFT/B3LYP method with a 6-311G++(d,p) basis set using the Gaussian 09 program. The experimental and calculated vibrational wavenumbers were assigned. The absorption spectrum of the molecule was computed in the liquid phase (ethanol), which exhibits n to л* electronic transition and compared with the observed UV-Vis spectrum. Frontier molecular orbital analysis shows the molecular reactivity and kinetic stability of the molecule. The Mulliken atomic charge distribution and molecular electrostatic potential surface analysis of the molecule validate the reactive site of the molecule. The natural bond orbital analysis proves the bioactivity of the molecule. Molecular docking analysis indicates that the 8A6MQP molecule inhibits the action of DNA topoisomerase 2-alpha protein, which is associated with breast cancer. In addition, the in vitro cytotoxicity analysis of the 8A6MQP molecule against human cervical cancer cell lines (ME180) and human breast cancer cell lines (MDA MB 231) were determined by MTT assay, which evidences that the title molecule exhibits higher inhibition against the breast cancer cell lines compared to that of cervical cancer cell lines. Hence, the present study paves the way for the development of novel drugs in the treatment of breast cancer.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- R Geetha
- Research scholar, Department of Physics, St. Jude's College, Thoothoor, Affiliated to Manonmanium Sundaranar University, Abishekapatti, Tirunelveli, Tamil Nadu, India
| | - M R Meera
- Department of Physics, Sree Ayyappa College for Women, Chunkankadai, Nagercoil, Tamil Nadu, India
| | - C Vijayakumar
- Department of Physics, St. Jude's College, Thoothoor, Kanyakumari District, Tamil Nadu, India
| | - R Premkumar
- PG and Research Department of Physics, N.M.S.S.V.N. College, Madurai, Tamil Nadu, India
| | | |
Collapse
|
2
|
Liu T, Chen J, Fan C, Wu C, Sun T. Crystal structure, DFT calculation, molecular docking, in vitro biological activity evaluation and in silico drug-likeness prediction of (E)-N-(4-bromophenyl)-4-(2-(2-hydroxybenzylidene) hydrazine-1-carbonyl) benzenesulfonamide. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
|
3
|
Amin MM, Abuo-Rahma GEDA, Shaykoon MSA, Marzouk AA, Abourehab MAS, Saraya RE, Badr M, Sayed AM, Beshr EAM. Design, synthesis, cytotoxic activities, and molecular docking of chalcone hybrids bearing 8-hydroxyquinoline moiety with dual tubulin/EGFR kinase inhibition. Bioorg Chem 2023; 134:106444. [PMID: 36893547 DOI: 10.1016/j.bioorg.2023.106444] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
The present study established thirteen novel 8-hydroxyquinoline/chalcone hybrids3a-mof hopeful anticancer activity. According to NCI screening and MTT assay results, compounds3d-3f, 3i,3k,and3ldisplayed potent growth inhibition on HCT116 and MCF7 cells compared to Staurosporine. Among these compounds,3eand3fshowed outstanding superior activity against HCT116 and MCF7 cells and better safety toward normal WI-38 cells than Staurosporine. The enzymatic assay revealed that3e,3d, and3ihad goodtubulin polymerization inhibition (IC50 = 5.3, 8.6, and 8.05 µM, respectively) compared to the reference Combretastatin A4 (IC50 = 2.15 µM). Moreover,3e,3l, and3fexhibited EGFR inhibition (IC50 = 0.097, 0.154, and 0.334 µM, respectively) compared to Erlotinib (IC50 = 0.056 µM). Compounds3eand3fwere investigated for their effects on the cell cycle, apoptosis induction, andwnt1/β-cateningene suppression. The apoptosis markers Bax, Bcl2, Casp3, Casp9, PARP1, and β-actin were detected by Western blot. In-silico molecular docking, physicochemical, and pharmacokinetic studies were implemented for the validation of dual mechanisms and other bioavailability standards. Hence, Compounds3eand3fare promising antiproliferative leads with tubulin polymerization and EGFR kinase inhibition.
Collapse
Affiliation(s)
- Mohammed M Amin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Gamal El-Din A Abuo-Rahma
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia 61519, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, Minia 61519, Egypt.
| | - Montaser Sh A Shaykoon
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Adel A Marzouk
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt; National Center for Natural Products Research, School of Pharmacy, University of Mississippi, MS 38677, USA
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Roshdy E Saraya
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Port Said University, Port Said 42515, Egypt
| | - Mohamed Badr
- Department of Biochemistry, Faculty of Pharmacy, Menoufia University, Menoufia, Egypt
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, 62513 Beni-Suef, Egypt
| | - Eman A M Beshr
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia 61519, Egypt.
| |
Collapse
|
4
|
Quantum control of optoelectronic and thermodynamic properties of dopamine molecule in external electric field : A DFT and TD-DFT study. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2023.114051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
5
|
Sheena Mary Y, Shyma Mary Y, Armaković S, Armaković SJ, Yadav R, Celik I, Razavi R. Investigation of reactive properties, adsorption on fullerene, DFT, molecular dynamics simulation of an anthracene derivative targeting dihydrofolate reductase and human dUTPase. J Biomol Struct Dyn 2022; 40:10952-10961. [PMID: 34278966 DOI: 10.1080/07391102.2021.1953602] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Anthracenes are aromatic compounds with flexible structure and reactivity which are of great interest to theoretical and experimental chemists. Theoretical investigations of 1,4-dihydroxy-5,8-bis[2-(2-hydroxyethylamino)ethylamino]anthracene-9,10-dione (Mitoxantrone) (DDEA) based on density functional theory, molecular dynamics and adsorption on fullerene are reported in the present research. The suitable situation for adsorption with fullerene (C60) is the cyclohex-2-ene-1,4-dione ring of DDEA. Selected quantum-molecular descriptors have been calculated to predict the most reactive sites of the DDEA molecule. Interactions of DDEA with water have been studied using MD simulations. MD simulations were also used to study solubility parameter, a significant quantity for the development of pharmaceutical formulations. The affinity of DDEA on human dihydrofolate reductase and deoxyuridine triphosphatase enzymes was investigated by MD simulation of the protein-ligand complex obtained by molecular docking study.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | | | - Stevan Armaković
- Faculty of Sciences, Department of Physics, University of Novi Sad, Novi Sad, Serbia
| | - Sanja J Armaković
- Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad, Novi Sad, Serbia
| | - Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Razieh Razavi
- Department of Chemistry, Faculty of Science, University of Jiroft, Jiroft, Iran
| |
Collapse
|
6
|
Kaur P, Anuradha, Chandra A, Tanwar T, Sahu SK, Mittal A. Emerging quinoline- and quinolone-based antibiotics in the light of epidemics. Chem Biol Drug Des 2022; 100:765-785. [PMID: 35128812 DOI: 10.1111/cbdd.14025] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/03/2021] [Accepted: 01/23/2022] [Indexed: 01/25/2023]
Abstract
Pandemics are large-scale outbreaks of infectious disease that can greatly increase morbidity and mortality all the globe. Since past 1990 till twentieth century, these infectious diseases have been major threat all over the globe associated with poor hygiene and sanitation. In light of these epidemics, researches have gained enormous rise in the developing the potential therapeutic treatment. Thus, revolutionized antibiotics have led to the near eradication of such ailments. Around 50 million prescription of antibiotics written in US per year according to center for disease control and prevention (CDC) report. There is a wide range of antibiotics available which differ in their usage and their mechanism of action. Among these quinoline and quinolone class of antibiotics get attention as they show tremendous potential in fighting the epidemics. Quinoline and quinolone comprise of two rings along with substitutions at different positions which is synthetically obtained by structural modifications of quinine. Quinoline and quinolone antibiotics exhibit extensive activities approved by FDA in the treatment of the several ailments such as gastrointestinal infections, urinary tract infections, prostate inflammation, malaria, gonorrhea, skin infection, colorectal cancer, respiratory tract infections. These are active against both gram-negative and gram-positive bacteria. This basic core of quinoline and quinolone is vital due to its capability of targeting the pathogen causing disease and beneficial in treating the infectious disease. They inhibit the synthesis of nucleic acid of bacteria which results in the rupture of bacterial chromosome due to the interruption of enzymes such as DNA gyrase and topoisomerase IV. There are various quinoline and quinolone compounds that are synthetically derived by applying different synthesis approaches which show a wide range of pharmacological activities in several diseases. The most commonly used are fluoro, chloro, and hydroxychloro derivatives of quinoline and quinolone. These compounds are helpful in the treatment of numerous epidemics as a chief and combination therapy. These quinoline and quinolone pharmacophore fascinate the interest of researchers as they inhibit the entry of virus in host cell and cease its replication by blocking the host receptor glycosylation and proteolytic processing. They act as immune modulator by inhibiting autophagy and reduction of both lysosomal activity and production of cytokine. Therefore, quinoline and quinolone derivatives attain significance in area of research and treatment of various life-threatening epidemics such as SARS, Zika virus, Ebola virus, dengue, and COVID-19 (currently). In this chapter, the research and advancements of quinoline- and quinolone-based antibiotics in epidemic management are briefly discussed.
Collapse
Affiliation(s)
- Paranjeet Kaur
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Anuradha
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Avik Chandra
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Tamanna Tanwar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Sanjeev Kumar Sahu
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Amit Mittal
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| |
Collapse
|
7
|
Investigation on interaction of quinoline with primary alcohols: An understanding on dielectric dispersion and relaxation dynamics over a wide frequency regime. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
8
|
Valencia J, Sánchez-Velasco OA, Saavedra-Olavarría J, Hermosilla-Ibáñez P, Pérez EG, Insuasty D. N-Arylation of 3-Formylquinolin-2(1 H)-ones Using Copper(II)-Catalyzed Chan-Lam Coupling. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238345. [PMID: 36500438 PMCID: PMC9735505 DOI: 10.3390/molecules27238345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 12/02/2022]
Abstract
3-formyl-2-quinolones have attracted the scientific community's attention because they are used as versatile building blocks in the synthesis of more complex compounds showing different and attractive biological activities. Using copper-catalyzed Chan-Lam coupling, we synthesized 32 new N-aryl-3-formyl-2-quinolone derivatives at 80 °C, in air and using inexpensive phenylboronic acids as arylating agents. 3-formyl-2-quinolones and substituted 3-formyl-2-quinolones can act as substrates, and among the products, the p-methyl derivative 9a was used as a substrate to obtain different derivatives such as alcohol, amine, nitrile, and chalcone.
Collapse
Affiliation(s)
- Jhesua Valencia
- Departamento de Química y Biología, División de Ciencias Básicas, Universidad del Norte, Km 5 Vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Oriel A. Sánchez-Velasco
- Department of Organic Chemistry, Faculty of Chemistry and Pharmacy, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Jorge Saavedra-Olavarría
- Department of Organic Chemistry, Faculty of Chemistry and Pharmacy, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Patricio Hermosilla-Ibáñez
- Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Materials Chemistry Department, Faculty of Chemistry and Biology, University of Santiago, Chile, Santiago 9170022, Chile
| | - Edwin G. Pérez
- Department of Organic Chemistry, Faculty of Chemistry and Pharmacy, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Correspondence: (E.G.P.); (D.I.)
| | - Daniel Insuasty
- Departamento de Química y Biología, División de Ciencias Básicas, Universidad del Norte, Km 5 Vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.G.P.); (D.I.)
| |
Collapse
|
9
|
Hou X, Gong X, Mao L, Zhao J, Yang J. Discovery of Novel 1,2,3-triazole Derivatives as IDO1 Inhibitors. Pharmaceuticals (Basel) 2022; 15:1316. [PMID: 36355488 PMCID: PMC9695734 DOI: 10.3390/ph15111316] [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] [Received: 10/10/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 10/29/2023] Open
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) has received much attention as an immunomodulatory enzyme in the field of cancer immunotherapy. While several IDO1 inhibitors have entered clinical trials, there are currently no IDO1 inhibitor drugs on the market. To explore potential IDO1 inhibitors, we designed a series of compounds with urea and 1,2,3-triazole structures. Organic synthesis and IDO1 enzymatic activity experiments verified the molecular-level activities of the designed compounds, and the IC50 value of compound 3a was 0.75 μM. Molecular docking and quantum mechanical studies further explained the binding mode and reaction potential of compound 3a with IDO1. Our research has resulted in a series of novel IDO1 inhibitors, which is beneficial to the development of drugs targeting IDO1 in numerous cancer diseases.
Collapse
Affiliation(s)
- Xixi Hou
- The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Xiaoqing Gong
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Longfei Mao
- The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Jie Zhao
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Jianxue Yang
- The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
- School of Nursing, Henan University of Science and Technology, 263 Kaiyuan Road, Luoyang 471003, China
| |
Collapse
|
10
|
Siekierka A, Yalcinkaya F. Selective cobalt-exchange membranes for electrodialysis dedicated for cobalt recovery from lithium, cobalt and nickel solutions. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
11
|
Zochedh A, Priya M, Chakaravarthy C, Sultan AB, Kathiresan T. Experimental and Computational Evaluation of Syringic Acid – Structural, Spectroscopic, Biological Activity and Docking Simulation. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2118332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Azar Zochedh
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, India
| | - Mohana Priya
- Department of Bioinformatics, School of Distance Education, Bharathiar University, Coimbatore, India
| | - Cibe Chakaravarthy
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, India
| | - Asath Bahadur Sultan
- Condensed Matter Physics Laboratory, Department of Physics, International Research Centre, Kalasalingam Academy of Research and Education, Krishnankoil, India
| | - Thandavarayan Kathiresan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, India
| |
Collapse
|
12
|
Ranjith P, Ignatious A, Panicker CY, Sureshkumar B, Armakovic S, Armakovic SJ, Van Alsenoy C, Anto P. Spectroscopic investigations, DFT calculations, molecular docking and MD simulations of 3-[(4-Carboxyphenyl) carbamoyl]-4-hydroxy-2-oxo-1, 2-dihydroxy quinoline-6-carboxylic acid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
13
|
Unequal Behaviour between Hydrolysable Functions of Nirmatrelvir under Stress Conditions: Structural and Theoretical Approaches in Support of Preformulation Studies. Pharmaceutics 2022; 14:pharmaceutics14081720. [PMID: 36015346 PMCID: PMC9412384 DOI: 10.3390/pharmaceutics14081720] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/02/2022] [Accepted: 08/16/2022] [Indexed: 12/02/2022] Open
Abstract
Nirmatrelvir is an antiviral drug approved for the treatment of COVID-19. The available dosage form consists of tablets marketed under the brand name PAXLOVID®. Although knowledge of nirmatrelvir’s intrinsic stability may be useful for any potential development of other pharmaceutical forms, no data regarding this matter is available to date. Preliminary forced degradation studies have shown that the molecule is stable under oxidative and photolytic conditions, while hydrolytic conditions, both acidic and basic, have proven deleterious. Indeed, the molecule presents a priori several functions that can undergo hydrolysis, i.e., three amide moieties and a nitrile function. However, considering the degradation products formed under forced conditions and which were detected and identified by LC-UV-HRMSn, the hydrolysis process leading to their formation is selective since it involved only 2 of the 4 hydrolysable functions of the molecule. Ab initio studies based on density functional theory (DFT) have helped better understand these reactivity differences in aqueous media. Some hydrolyzable functions of nirmatrelvir differ from others in terms of electrostatic potential and Fukui functions, and this seems to correlate with the forced degradation outcomes.
Collapse
|
14
|
Zochedh A, Priya M, Shunmuganarayanan A, Thandavarayan K, Sultan AB. Investigation on structural, spectroscopic, DFT, biological activity and molecular docking simulation of essential oil Gamma-Terpinene. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
15
|
Al-Otaibi JS, Mary YS, Mary S, Trivedi R, Chakraborty B, Yadav R, Celik I, Soman S. DFT and MD investigations of the biomolecules of phenothiazine derivatives: interactions with gold and water molecules and investigations in search of effective drug for SARS-CoV-2. J Biomol Struct Dyn 2022:1-12. [PMID: 35470781 DOI: 10.1080/07391102.2022.2068649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Theoretical analyses of two phenothiazine derivatives, 10-[3-(dimethylamino)-2-methylpropyl]phenothiazine-2-carbonitrile (CYM) and 2-[4-[3-(2-chlorophenothiazin-10-yl)propyl]piperazin-1-yl]ethanol (PAZ) are reported using density functional theory (DFT) and molecular dynamics (MD) simulations. Spectroscopic studies, different electronic and chemical parameters are predicted. Red and yellow in electrostatic potential plot is in rings and oxygen atom in PAZ and C≡N and rings in CYM are sensitive to nucleophilic attacks. The blue in hydrogen atoms refer to electrophilic attack in both PAZ and CYM. Stability of the protein-ligand complex formed with these derivatives and angiotensin-converting enzyme 2 (ACE2) was investigated using MD simulation. Radius of gyration of C-alpha atom of 6VW1 displayed the conformational convergence toward a compact structure leading to stable 6VW1-ligand complex which are also in agreement with root mean square fluctuation (RMSF) values. Localized area predicts reactive sites for Au and H2O molecules interaction with these compounds for further practical applications. Charge density is localized on both molecules and also tries to move toward Au-Au dimer and water molecule and such they are expected to contribute to the sensing performance. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Ravi Trivedi
- Department of Physics, Indian Institute of Technology, Mumbai, India
| | - Brahmananda Chakraborty
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Sreejit Soman
- Stemskills Research and Education Lab Private Limited, Faridabad, Hariyana, India
| |
Collapse
|
16
|
Ullah Z, Sonawane PM, Mary YS, Mary YS, Yohannan Panicker C, Churchill DG. A foundational theoreticalAl 12E 12(E = N, P) adsorption and quinolone docking study: cage–quinolone pairs, optics and possible therapeutic and diagnostic applications. J Biomol Struct Dyn 2022; 41:3630-3646. [PMID: 35380095 DOI: 10.1080/07391102.2022.2053742] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This combined Al12E12 (E = N, P) surface adsorption and docking study describes the new possibility of prospective potential probing(photophysical/optical) and therapy(medicinal/biochemical) with these adsorbent conjugates. DFT investigations were undertaken herein to help generate geometrical models and better understand the possible favorable adsorption energetics. We attempt to explain their adsorption behaviors and docking involving SARS-CoV-2 viruses (PDB)to assess their possible pharmaceutical potential against the pandemic virus (COVID-19). The adsorption behavior of 8-hydroxy-2-methylquinoline (MQ) and its halogenated derivatives, 5,7-diiodo-8-hydroxy-2-methylquinoline (MQI), 5,7-dichloro-8-hydroxy-2-methylquinoline (MQCl), and 5,7-dibromo-8-hydroxy-2-methylquinoline (MQBr), with aluminum-nitrogen (AlN), and aluminum-phosphorous (AlP) fullerene-like nanocages is reported. A decrease in the hardness of the nanoclusters when adsorbed with drug molecules resulted in an incrementally improved chemical softness (see e.g., Hard-Soft Acid Base theory) indicating that reactivity of the drug molecule in the resulting complex increases upon cluster chemical adsorption. The energy gap is found to be maximized for AlN-MQ and minimized for AlP-MQI; the reduced density gradient (RDG) iso-surfaces and AIM studies also corroborated this. Therefore, these two were found, respectively, to be the least and most electrically conductive of the species under study. We selected a simple medicinal building block (chelator)in addition to selecting the cluster based on previous literature reports. Important parameters such as gap energies and global indices were determined. We assessed NLO properties. The SARS-CoV-2 virus PDB docking data for 6VW1, 6VYO, 6WKQ, 7AD1, 7AOL, 7B3C, were enlisted as ligand targets for studies of docking (PatchDock Server) using the requisite PDB geometries (For the structure of 6VW1, kindly see reference, 2020; For the structure of 6VYO kindly see reference, 2020; For the structure of 6WKQ kindly see reference, 2020; For the structure of 7AD1 kindly see reference, 2021; For the structure of 7AOL kindly see reference, 2021; For the structure of 7B3C kindly see reference, 2021). Such findings indicate that the AlN-drug conjugation have inhibitory effect against these selected receptors.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Zakir Ullah
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Graduate School of Energy, Environment, Water and Sustainability (EEWS) Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
- Convergence Research Center for Insect Vectors, Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, South Korea
| | - Prasad M. Sonawane
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Department of Chemistry & Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | | | | | | | - David G. Churchill
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Therapeutic Bioengineering Section, KAIST Institute for Health Science and Technology (KIHST), Daejeon, Republic of Korea
| |
Collapse
|
17
|
Sunder Raj D, Kesavan DK, Kottaisamy CPD, Kumar VP, Hopper W, Sankaran U. Atomic level and structural understanding of natural ligands inhibiting Helicobacter pylori peptide deformylase through ligand and receptor based screening, SIFT, molecular dynamics and DFT - a structural computational approach. J Biomol Struct Dyn 2022; 41:3440-3461. [PMID: 35293845 DOI: 10.1080/07391102.2022.2050946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Helicobacter pylori is a Gram-negative microaerophilic gastric pathogen, responsible for the cause of peptic ulcer around half of the global population. Although several antibiotics and combination therapies have been employed for H. pylori-related gastric ulcer and cancer regiments, identifying potent inhibitors for specific targets of this bacterium will help assessing better treatment periodicity and methods to eradicate H. pylori. Herein, 1,000,000 natural compounds were virtually screened against Helicobacter pylori Peptide deformylase (HpPDF). Pharmacophore hypotheses were created using ligand and receptor-based pharmacophore modeling of GLIDE. Stringent HTVS and IFD docking protocol of GLIDE predicted leads with stable intermolecular bonds and scores. Molecular dynamics simulation of HpPDF was carried out for 100 ns using GROMACS. Hits ZINC00225109 and ZINC44896875 came up with a glide score of -9.967 kcal/mol and -12.114 kcal/mol whereas; reference compound actinonin produced a glide score of -9.730 kcal/mol. Binding energy values of these hits revealed the involvement of significant Van der Waals and Coulomb forces and the deduction of lipophilic forces that portray the deep hydrophobic residues in the S1pocket of H. pylori. The DFT analysis established the electron density-based features of the molecules and observed that the results correlate with intermolecular docking interactions. Analysis of the MD trajectories revealed the crucial residues involved in HpPDF - ligand binding and the conformational changes in the receptor. We have identified and deciphered the crucial features necessary for the potent ligand binding at catalytic site of HpPDF. The resulting ZINC natural compound hits from the study could be further employed for potent drug development.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Divya Sunder Raj
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, India
| | | | | | - V Prasanth Kumar
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, India
| | - Waheetha Hopper
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur Campus, Chennai, India
| | | |
Collapse
|
18
|
Al-Otaibi JS, Sheena Mary Y, Shyma Mary Y, Acharjee N. Quantum Mechanical Investigation into the Adsorption Pattern of Clomipramine and Methotrimeprazine HCl with Graphene and Fullerene. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2041678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Nivedita Acharjee
- Department of Chemistry, Durgapur Government College, District-Paschim Bardhaman, West Bengal, India
| |
Collapse
|
19
|
S Al-Otaibi J, Mary YS, Mary YS, Thomas R. Evidence of cluster formation of croconic acid with Ag, Au and Cu cages, enhancement of electronic properties and Raman activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120233. [PMID: 34358780 DOI: 10.1016/j.saa.2021.120233] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/21/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Investigation of the adsorption properties croconic acid (CCA) with metal clusters (mC: Ag, Au and Cu) are reported using DFT method. CCA is found to form stable cluster with transition metal clusters of copper, silver and gold. The drug-cluster complexaton energy is slightly more for the copper nanocluster-drug complex. Non-covalent interaction analysis indicated that strong interactions and weak van der Waal interaction is present between drug and metal clusters. Dipole moment of the drug-gold cluster is found to be higher than that of the other systems. SERS studies demonstrates improved Raman signals for multiple wavenumbers of all CCA-metal cluster complexes. Mulliken charge analysis show that all CCA oxygen atom's charge changes due to the interactions with the mCs. Clustering of CCA with metal cages enhances the medicinal properties and the metal nanoclusters will act as a drug carrier of CCA.
Collapse
Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | | | | | - Renjith Thomas
- Deparment of Chemsitry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| |
Collapse
|
20
|
Wang D, Zhang L, Xiao F, Mao GJ, Deng GJ. Electrochemical Selective C3-Thiolation of Quinolines. Org Chem Front 2022. [DOI: 10.1039/d2qo00148a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An electrochemical method has been developed to achieve C3-thiolation of quinoline compounds. This new strategy highlights the maximum atom economy, direct conversion and also the use of simple and readily...
Collapse
|
21
|
Al-Otaibi JS, Mary YS, Mary YS, Ullah Z, Kwon HW. Adsorption behavior and solvent effects of an adamantane-triazole derivative on metal clusters – DFT simulation studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118242] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
22
|
Raslan RR, Hessein SA, Fouad SA, Shmiess NAM. Synthesis and antitumor evaluation of some new thiazolopyridine, nicotinonitrile, pyrazolopyridine, and polyhydroquinoline derivatives using ceric ammonium nitrate as a green catalyst. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Reham R. Raslan
- Department of Chemistry Faculty of Science (Girl's) Al‐Azhar University Cairo Egypt
| | - Sadia A. Hessein
- Department of Chemistry Faculty of Science (Girl's) Al‐Azhar University Cairo Egypt
| | - Sawsan A. Fouad
- Department of Chemistry Faculty of Science (Girl's) Al‐Azhar University Cairo Egypt
| | - Nadia A. M. Shmiess
- Department of Chemistry Faculty of Science (Girl's) Al‐Azhar University Cairo Egypt
| |
Collapse
|
23
|
Synthesis, spectroscopic characterization, DFT, molecular docking and in vitro antibacterial potential of novel quinoline derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
24
|
Mary YS, Sheena Mary Y, Thomas R, Narayana B. Detailed Study of Three Halogenated Benzylpyrazole Acetamide Compounds with Potential Anticancer Properties. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1988997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | - Renjith Thomas
- Deparment of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| | - B. Narayana
- Department of Chemistry, Mangalore University, Mangaluru, Karnataka, India
| |
Collapse
|
25
|
Reactivity properties and adsorption behavior of a triazole derivative – DFT and MD simulation studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
26
|
Walunj Y, Shinde A, Borde K, Abhale Y, Bobade V, Mhaske PC. Synthesis, Anticancer and Antimicrobial Screening of New Naphthalenyl-Thiazole and Quinolinyl-Thiazole. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1991963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Yogesh Walunj
- Post-Graduate Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
- Department of Chemistry, Hutatma Rajguru College (Affiliated to Savitribai Phule Pune University), Khed, Pune, India
| | - Abhijit Shinde
- Post-Graduate Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
| | - Krishna Borde
- Post-Graduate Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
| | - Yogita Abhale
- Department of Chemistry, Government College, Daman, UT–DNH & DD (Affiliated to Veer Narmad South Gujarat University), India
| | - Vivek Bobade
- Post-Graduate Department of Chemistry, H. P. T. Arts and R. Y. K. Science College (Affiliated to Savitribai Phule Pune University), Nashik, India
| | - Pravin C. Mhaske
- Post-Graduate Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
| |
Collapse
|
27
|
Thakare P, Shinde A, Dakhane S, Chavan A, Bobade VD, Mhaske PC. Synthesis and biological evaluation of novel 4‐(6‐substituted quinolin‐4‐yl)‐
N
‐aryl thiazol‐2‐amine derivatives as potential antimicrobial agents. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Prashant Thakare
- Department of Chemistry S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University) Pune India
| | - Abhijit Shinde
- Department of Chemistry S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University) Pune India
| | - Sagar Dakhane
- Department of Chemistry Abasaheb Garware College (Affiliated to Savitribai Phule Pune University) Pune India
| | - Abhijit Chavan
- Department of Chemistry S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University) Pune India
| | - Vivek D. Bobade
- Department of Chemistry H. P. T. Arts and R. Y. K. Science College (Affiliated to Savitribai Phule Pune University) Nashik India
| | - Pravin C. Mhaske
- Department of Chemistry S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University) Pune India
| |
Collapse
|
28
|
Mary YS, Mary YS, Armaković S, Armaković SJ, Yadav R, Celik I, Mane P, Chakraborty B. Stability and reactivity study of bio-molecules brucine and colchicine towards electrophile and nucleophile attacks: Insight from DFT and MD simulations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116192] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
29
|
Sheena Mary Y, Shyma Mary Y. Adsorption of Phenothiazine Derivatives on Graphene – DFT, Docking and MD Simulation. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1946570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
30
|
Fandos R, Rodríguez-Delgado A, Rodríguez A, Romero I, Organero JÁ, Álvarez E. Pathways to Metal–Ligand Cooperation in Quinoline-Based Titanium(IV) Pincers: Nonelectrophilic N-methylation, Deprotonation, and Dihydropyridine Formation. Organometallics 2021. [DOI: 10.1021/acs.organomet.1c00105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rosa Fandos
- Instituto de Nanociencia, Nanotecnología y Materiales Moleculares (INAMOL), Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Antonio Rodríguez-Delgado
- Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, C/Américo Vespucio, 49, Isla de la Cartuja, 41092 Sevilla, Spain
| | - Ana Rodríguez
- ETS Ingenieros Industriales, Campus de Ciudad Real, Universidad de Castilla-La Mancha, Avda. Camilo José Cela, 3, 13071 Ciudad Real, Spain
| | - Iván Romero
- Instituto de Nanociencia, Nanotecnología y Materiales Moleculares (INAMOL), Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Juan Ángel Organero
- Instituto de Nanociencia, Nanotecnología y Materiales Moleculares (INAMOL), Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, Avda. Carlos III, s/n, 45071 Toledo, Spain
| | - Eleuterio Álvarez
- Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, C/Américo Vespucio, 49, Isla de la Cartuja, 41092 Sevilla, Spain
| |
Collapse
|
31
|
Computational Study of Sorbic Acid Drug Adsorption onto Coronene/Fullerene/Fullerene-Like X12Y12 (X = Al, B and Y = N, P) Nanocages: DFT and Molecular Docking Investigations. J CLUST SCI 2021. [DOI: 10.1007/s10876-021-02106-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
32
|
Hayani S, Thiruvalluvar AA, Baba YF, Rodi YK, Muthunatesan S, Chahdi FO, Mague JT, Ibrahimi BE, Anouar EH, Sebbar NK, Essassi EM. Synthesis, structure elucidation, Hirshfeld surface analysis, DFT, molecular docking and Monte Carlo simulation of new quinoline-4-carboxylate derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
33
|
Anju A, Chaturvedi S, Chaudhary V, Pant P, Hussain F, Mishra AK. Virtual screening of quinoline derived library for SARS-COV-2 targeting viral entry and replication. J Biomol Struct Dyn 2021; 40:8464-8493. [PMID: 34032180 PMCID: PMC8171009 DOI: 10.1080/07391102.2021.1913228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic infection has claimed many lives and added to the social, economic, and psychological distress. The contagious disease has quickly spread to almost 218 countries and territories following the regional outbreak in China. As the number of infected populations increases exponentially, there is a pressing demand for anti-COVID drugs and vaccines. Virtual screening provides possible leads while extensively cutting down the time and resources required for ab-initio drug design. We report structure-based virtual screening of a hundred plus library of quinoline drugs with established antiviral, antimalarial, antibiotic or kinase inhibitor activity. In this study, targets having a role in viral entry, viral assembly, and viral replication have been selected. The targets include: 1) RBD of receptor-binding domain spike protein S 2) Mpro Chymotrypsin main protease 3) Ppro Papain protease 4) RNA binding domain of Nucleocapsid Protein, and 5) RNA Dependent RNA polymerase from SARS-COV-2. An in-depth analysis of the interactions and G-score compared to the controls like hydroxyquinoline and remdesivir has been presented. The salient results are (1) higher scoring of antivirals as potential drugs (2) potential of afatinib by scoring as better inhibitor, and (3) biological explanation of the potency of afatinib. Further MD simulations and MM-PBSA calculations showed that afatinib works best to interfere with the the activity of RNA dependent RNA polymerase of SARS-COV-2, thereby inhibiting replication process of single stranded RNA virus. Communicated by Ramaswamy H. Sarma
Collapse
Affiliation(s)
- Anju Anju
- Department of Chemistry, University of Delhi, Delhi, India.,Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization Brig, Delhi, India
| | - Shubhra Chaturvedi
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization Brig, Delhi, India
| | - Vishakha Chaudhary
- Department of Chemistry, University of Delhi, Delhi, India.,Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization Brig, Delhi, India
| | - Pradeep Pant
- Department of Chemistry, Indian Institute of Technology, New Delhi, India
| | | | - Anil Kumar Mishra
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization Brig, Delhi, India
| |
Collapse
|
34
|
Sheena Mary Y, Shyma Mary Y, Krátký M, Vinsova J, Baraldi C, Gamberini MC. DFT, molecular docking and SERS (concentration and solvent dependant) investigations of a methylisoxazole derivative with potential antimicrobial activity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
35
|
Mary YS, Mary YS, Rad AS, Yadav R, Celik I, Sarala S. Theoretical investigation on the reactive and interaction properties of sorafenib – DFT, AIM, spectroscopic and Hirshfeld analysis, docking and dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115652] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
36
|
Al-Otaibi JS, Mary YS, Mary YS, Kaya S, Serdaroglu G. DFT computational study of trihalogenated aniline derivative's adsorption onto graphene/fullerene/fullerene-like nanocages, X 12Y 12 (X = Al, B, and Y = N, P). J Biomol Struct Dyn 2021; 40:8630-8643. [PMID: 33876711 DOI: 10.1080/07391102.2021.1914172] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Adsorption of 2,4,6-tribromoaniline (BA), 2,4,6-trifluoroaniline (FA) and 2,4,6-trichloroaniline (CA) onto the surface of coronene/fullerene/fullerene-like nanocages was investigated by theoretical calculations. Due to the adsorption of BA/FA/CA, there are significant changes in chemical descriptors and nonlinear optical properties. Energy gap values of all nanoclusters are lowered, giving an increase in conductivity of complexes except for fullerene. All complex's ultraviolet visible wavenumber is blue-shifted and especially for fullerene complex, the values are very high. The enhancement of Raman intensities shows that it is possible to design a nanocage sensor for detecting these compounds by surface-enhanced Raman scattering (SERS).Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | | | | | - Savaş Kaya
- Health Services Vocational School, Department of Pharmacy, Sivas Cumhuriyet University, Sivas, Turkey
| | - Goncagül Serdaroglu
- Faculty of Education, Math. and Sci. Edu, Sivas Cumhuriyet University, Sivas, Turkey
| |
Collapse
|
37
|
Synthesis, in vitro evaluation and molecular docking of new pyrazole derivatives bearing 1,5,10,10a-tetrahydrobenzo[g]quinoline-3-carbonitrile moiety as potent antibacterial agents. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2021. [DOI: 10.1007/s13738-020-02086-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
38
|
Mary YS, Mary YS, Krátký M, Vinsova J, Baraldi C, Cristina Gamberini M. Concentration dependent SERS, DFT and molecular docking studies of a ureido derivative with antitubercular properties. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119329. [PMID: 33360209 DOI: 10.1016/j.saa.2020.119329] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/03/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering (SERS) of antimycobactetial 4-[3-(4-acetylphenyl)ureido]-2-hydroxybenzoic acid (AUHB) have been studied on different silver sols. For Raman and SERS wavenumbers, very large changes are observed. Observed variations in the modes of ring may be due to surface π-electron interactions and presence of this indicated that poly substituted ring is more inclined than para substituted phenyl ring and assumes a inclined position for concentration 10-3 M. Changes in orientation are seen in SERS spectra depending on concentration. In order to find electron-rich and poor sites of AUHB, molecular electrostatic potential was also constructed. The molecular docking results show that binding affinity and interactions with the receptor DprE1 may be supporting evidence for further studies in design further AUHB pharmaceutical applications. Based on antitubercular activity of 4-aminosalicylic acid (PAS) and urea derivatives we designed, synthesized and investigated mutual PAS-urea derivatives as potential antimycobacterial agents.
Collapse
Affiliation(s)
- Y Sheena Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India.
| | - Y Shyma Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India
| | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Jarmila Vinsova
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103 41125, Modena, Italy
| | - Maria Cristina Gamberini
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103 41125, Modena, Italy
| |
Collapse
|
39
|
Gamberini MC, Mary YS, Mary YS, Krátký M, Vinsova J, Baraldi C. Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a benzoic acid derivative. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119265. [PMID: 33316651 DOI: 10.1016/j.saa.2020.119265] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering of 4-((3-bromo-5-chloro-2-hydroxybenzylidene)amino)benzoic acid (BCHB) have been studied on different silver colloids concentrations in order to know the particular chemical species responsible for the spectra. For Raman and surface enhanced Raman scattering (SERS) wavenumbers, changes are observed. Observed variations in the modes of ring may be due to interaction of the π-electrons and presence of this indicated that RingII is more inclined than RingI and the BCHB assumes inclined orientation for concentration 10-3 M. Changes in orientation are seen in SERS spectra depending on concentration. In order to determine the electron-rich and poor sites of BCHB, the molecular electrostatic potential was also constructed. The molecular docking studies show that the bindings and interactions with the receptors may be supporting evidence for further studies in design further BCHB pharmaceutical applications.
Collapse
Affiliation(s)
- Maria Cristina Gamberini
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Y Shyma Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India
| | - Y Sheena Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India.
| | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Jarmila Vinsova
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| |
Collapse
|
40
|
Sheena Mary Y, Shyma Mary Y, Krátký M, Vinsova J, Baraldi C, Gamberini MC. DFT, SERS-concentration and solvent dependent and docking studies of a bioactive benzenesulfonamide derivative. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129680] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
41
|
Kumar VS, Mary YS, Mary YS, Krátký M, Vinsova J, Baraldi C, Roxy MS, Gamberini MC. Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a hydroxybenzylidene derivative. J Biomol Struct Dyn 2021; 40:6952-6964. [PMID: 33645445 DOI: 10.1080/07391102.2021.1891971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering (SERS) of (E)-N'-(5-chloro-2-hydroxybenzylidene)-4-trifluoromethyl) benzohydrazide (CHTB) have been studied on different silver colloids in order to know the particular chemical species responsible for the spectra. Very significant shifts are observed for Raman and SERS wavenumbers. Observed changes in the υ-ring modes may be due to surface interaction of the π-electrons and the presence of this suggested that RingII is more tilted in both cases than RingI and the molecule assumes a tilted orientation for the concentration 10-3 M. Orientation changes are seen in concentration dependent SERS spectra. The molecular electrostatic potential has also been constructed to determine the electron rich and poor site of CHTB. The molecular docking studies indicate that the binding affinity and hydrogen bond interactions with the receptors may be supporting evidence for further studies in designing other pharmaceutical applications of CHTB.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Veena S Kumar
- Department of Physics, SN College, Kollam, Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | | | | | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Jarmila Vinsova
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - M S Roxy
- Department of Physics, SN College, Kollam, Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | | |
Collapse
|
42
|
Synthesis, Cytotoxic Activity, Crystal Structure, DFT Studies and Molecular Docking of 3-Amino-1-(2,5-dichlorophenyl)-8-methoxy-1H-benzo[f]chromene-2-carbonitrile. CRYSTALS 2021. [DOI: 10.3390/cryst11020184] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The target compound 3-amino-1-(2,5-d ichlorophenyl)-8-methoxy-1H-benzo[f]-chromene-2-carbonitrile (4) was synthesized via a reaction of 6-methoxynaphthalen-2-ol (1), 2,5-dichlorobenzaldehyde (2), and malononitrile (3) in ethanolic piperidine solution under microwave irradiation. The newly synthesized β-enaminonitrile was characterized by FT-IR, 1H NMR, 13C NMR, mass spectroscopy, elemental analysis and X-ray diffraction data. Its cytotoxic activity was evaluated against three different human cancer cell lines MDA-MB-231, A549, and MIA PaCa-2 in comparison to the positive controls etoposide and camptothecin employing the XTT cell viability assay. The analysis of the Hirshfeld surface was utilized to visualize the reliability of the crystal package. The obtained results confirmed that the tested molecule revealed promising cytotoxic activities against the three cancer cell lines. Furthermore, theoretical calculations (DFT) were carried out with the Becke3-Lee-Yang-parr (B3LYP) level using 6-311++G(d,p) basis. The optimization geometry for molecular structures was in agreement with the X-ray structure data. The HOMO-LUMO energy gap of the studied system was discussed. The intermolecular-interactions were studied through analysis of the topological-electron-density(r) using the QTAIM and NCI methods. The novel compound exhibited favorable ADMET properties and its molecular modeling analysis showed strong interaction with DNA methyltransferase 1.
Collapse
|
43
|
Almuqrin AH, Al-Otaibi JS, Mary YS, Mary YS. DFT computational study towards investigating psychotropic drugs, promazine and trifluoperazine adsorption on graphene, fullerene and carbon cyclic ring nanoclusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 246:119012. [PMID: 33039847 DOI: 10.1016/j.saa.2020.119012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/05/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Detection and qualification process related to impurities assume importance in pharmacological drug development programmes and the present article gives the structural and spectral characterisation of phenothiazine derivatives, promazine (PME) and trifluoperazine (TPE) and their self-assembly with graphene/fullerene/carbon ring (CG/CF/CR) systems theoretically. The investigation of adsorption behaviour of these compounds can provide valuable information about its reactivity, electronic and structural properties. Three-dimensional electrostatic potential diagrams were mapped. The frontier orbital energies and energy band gaps of the molecules were computed. Delocalization of charge density between the bonding or lone pair and antibonding orbitals is calculated by NBO analysis. Docking was executed to investigate binding areas of chemical compounds. Bioactivity scores show that the pharmacokinetic and pharmacological properties of the ligands are appropriate leading to be considered potential drug agents. The obtained theoretical wavenumber results of the present study were fully compatible with the experimental results.
Collapse
Affiliation(s)
- Aljawhara H Almuqrin
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India.
| | - Y Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| |
Collapse
|
44
|
Matada BS, Pattanashettar R, Yernale NG. A comprehensive review on the biological interest of quinoline and its derivatives. Bioorg Med Chem 2020; 32:115973. [PMID: 33444846 DOI: 10.1016/j.bmc.2020.115973] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022]
Abstract
Amongst heterocyclic compounds, quinoline is an advantaged scaffold that appears as a significant assembly motif for the development of new drug entities. Quinoline and its derivatives tested with diverse biological activity constitute an important class of compounds for new drug development. Therefore, many scientific communities have developed these compounds as intent structure and evaluated their biological activities. The present, review provides brief natural sources of quinoline and including a new extent of quinoline-based marketed drugs. This review also confers information about the biological activities of quinoline derivatives such as antibacterial, antifungal, antimycobacterial, antiviral, anti-protozoal, antimalarial, anticancer, cardiovascular, CNS effects, antioxidant, anticonvulsant, analgesic, anti-inflammatory, anthelmintic and miscellaneous activities.
Collapse
Affiliation(s)
| | | | - Nagesh Gunavanthrao Yernale
- Department of Chemistry, Guru Nanak First Grade Science, Commerce and Post Graduate College, Bidar 585 403, Karnataka, India.
| |
Collapse
|
45
|
Mary YS, Kumar VS, Mary YS, K. S. R, Thomas R. Detailed Quantum Mechanical Studies on Three Bioactive Benzimidazole Derivatives and Their Raman Enhancement on Adsorption over Graphene Sheets. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1852267] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Y. Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Veena S. Kumar
- Department of Physics, SN College, Kollam, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Resmi K. S.
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| |
Collapse
|
46
|
Al-Otaibi JS, Almuqrin AH, Sheena Mary Y, Mary YS, Thomas R. Modeling the Conformational Preference, Spectral Analysis and Other Quantum Mechanical Studies on Three Bioactive Aminobenzoate Derivatives and Their SERS Active Graphene Complexes. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1827270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Aljawhara H. Almuqrin
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, India
| | - Y. Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, India
| |
Collapse
|
47
|
Al-Otaibi JS, Almuqrin AH, Mary YS, Mary YS. Comprehensive quantum mechanical studies on three bioactive anastrozole based triazole analogues and their SERS active graphene complex. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128388] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
48
|
DFT and molecular docking studies of self-assembly of sulfone analogues and graphene. J Mol Model 2020; 26:273. [DOI: 10.1007/s00894-020-04546-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/14/2020] [Indexed: 01/30/2023]
|
49
|
Cocrystals of hydrochlorothiazide with picolinamide, tetramethylpyrazine and piperazine: quantum mechanical studies, docking and modelling of the photovoltaic efficiency for DSSC. J Mol Model 2020; 26:256. [PMID: 32885337 DOI: 10.1007/s00894-020-04528-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/31/2020] [Indexed: 01/06/2023]
Abstract
Cocrystals are of immense applications in crystal engineering and pharmaceutical chemistry. Hydrochlorothiazide is found to form cocrystals with picolinamide (H1), tetramethylpyrazine (H2) and piperazine (H3). It was characterized using IR spectra, and quantum mechanical calculations for geometry and other properties. Frontier orbital energies are used to predict the energy properties and model the possible charge transfer between the constituents of the cocrystal. The frontier molecular orbital analysis indicates chemical reactivity and bioactivity of the cocrystals. The MEP surface reveals the various reactive surfaces in the cocrystal system, which is very important in deciding various biological activities. The UV-Vis spectra show the possible electronic transitions of the molecules. Simulated electronic spectra using TDDFT method with CAM-B3LYP functional were used to investigate the suitability of the cocrystals to be used in DSSC. Moreover, the molecular docking analysis proves that the cocrystals can act as potential inhibitors and paves the way for developing effective drugs.
Collapse
|
50
|
DFT and MD simulations and molecular docking of co-crystals of octafluoro-1,4-diiodobutane with phenazine and acridine. Struct Chem 2020. [DOI: 10.1007/s11224-020-01616-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|