1
|
Xu B, Zhang Z, Tantillo DJ, Dai M. Concise Total Syntheses of ( -)-Crinipellins A and B Enabled by a Controlled Cargill Rearrangement. J Am Chem Soc 2024; 146:21250-21256. [PMID: 39052841 PMCID: PMC11311239 DOI: 10.1021/jacs.4c07900] [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: 06/11/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Herein, we report concise total syntheses of diterpene natural products (-)-crinipellins A and B with a tetraquinane skeleton, three adjacent all-carbon quaternary centers, and multiple oxygenated and labile functional groups. Our synthesis features a convergent Kozikowski β-alkylation to unite two readily available building blocks with all the required carbon atoms, an intramolecular photochemical [2 + 2] cycloaddition to install three challenging and adjacent all-carbon quaternary centers and a 5-6-4-5 tetracyclic skeleton, and a controlled Cargill rearrangement to rearrange the 5-6-4-5 tetracyclic skeleton to the desired tetraquinane skeleton. These strategically enabling transformations allowed us to complete total syntheses of (-)-crinipellins A and B in 12 and 13 steps, respectively. The results of quantum chemical computations revealed that the Bronsted acid-catalyzed Cargill rearrangements likely involve stepwise paths to products and the AlR3-catalyzed Cargill rearrangements likely involve a concerted path with asynchronous alkyl shifting events to form the desired product.
Collapse
Affiliation(s)
- Bo Xu
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ziyao Zhang
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California—Davis, Davis, California 95616, United States
| | - Mingji Dai
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Pharmacology and Chemical Biology, Emory
University, Atlanta, Georgia 30322, United States
| |
Collapse
|
2
|
Ahmed M, Gupta MK, Ansari A. DFT and TDDFT exploration on the role of pyridyl ligands with copper toward bonding aspects and light harvesting. J Mol Model 2023; 29:358. [PMID: 37919553 DOI: 10.1007/s00894-023-05765-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
CONTEXT Schiff base-containing metal complexes have been the subject of extensive research. In this work, a coordination polymer-derived complex called [Cu(L)] that is solution-stable (L = 2-(2-hydroxybenzylidene-amino)phenol) has been explored theoretically with five different pyridyl-based ligands using DFT/TDDFT in order to understand the structural-functional and electronic transitions of these five complexes. Frontier molecular orbital (FMO) analysis was carried out to assess the reactivity behavior of all five complexes. For the purpose of studying the charge energy distribution over complexes, electrostatic potential maps were also drawn. Furthermore, in order to identify any stabilizing interactions that may be present in the given complexes, an NBO analysis was studied. To learn more about any potential correlations between the properties of these five complexes, a comparative analysis was explored. Our calculations demonstrate that complex 3 having pyridine-4-carboxamide as a ligand has a lower energy gap and a higher negative electrostatic potential which may indicate its higher reactivity and this may be due to the electron withdrawing group (carboxamide). TDDFT results show that the highest light harvesting efficiency (LHE) of all the studied complexes is found in the range of 440-448 nm. Complexes 1, 2, and 4 show the higher light harvesting efficiency as compared to complexes 3 and 5. Our findings are in good accordance with the available experimental data. METHODS All DFT computations were performed using the Gaussian16 with unrestricted B3LYP-D2 functional with the basis sets 6-31G(d,p) for O, N, C, and H while LanL2DZ for Cu. The polarized continuum model (PCM) was used for the solvation. The software GaussView6.1 was utilized for the modeling of initial geometries and the plotting of MEP maps. The NBO6.0 program which is incorporated in Gaussian16 was utilized to investigate the bonding nature and stabilization energies of the complexes. The ORCA program was used to simulate the absorption spectra.
Collapse
Affiliation(s)
- Mukhtar Ahmed
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Manoj Kumar Gupta
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana, 123031, India.
| |
Collapse
|
3
|
Gurushankar K, Jeyaseelan SC, Grishina M, Siswanto I, Tiwari R, Puspaningsih NNT. Density Functional Theory, Molecular Dynamics and AlteQ Studies Approaches of Baimantuoluoamide A and Baimantuoluoamide B to Identify Potential Inhibitors of M pro Proteins: a Novel Target for the Treatment of SARS COVID-19. JETP LETTERS 2023; 117:1-10. [PMID: 37360903 PMCID: PMC10184967 DOI: 10.1134/s0021364023600039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 06/28/2023]
Abstract
COVID-19 has resulted in epidemi conditions over the world. Despite efforts by scientists from all over the world to develop an effective va ine against this virus, there is presently no recognized cure for COVID-19. The most succeed treatments for various ailments come from natural components found in medicinal plants, which are also rucial for the development of new medications. This study intends to understand the role of the baimantuoluoamide A and baimantuoluoamide B molecules in the treatment of Covid19. Initially, density functional theory (DFT) used to explore their electronic potentials along with the Becke3-Lee-Yang-Parr (B3LYP) 6-311 + G(d, p) basis set. A number of characteristics, including the energy gap, hardness, local softness, electronegativity, and electrophilicity, have also been calculated to discuss the reactivity of mole ules. Using natural bond orbital, the title compound's bioactive nature and stability were investigated. Further, both compounds potential inhibitors with main protease (Mpro) proteins, molecular dynamics simulations and AlteQ investigations also studied. Supplementary Information The online version contains supplementary material available at 10.1134/S0021364023600039.
Collapse
Affiliation(s)
- K. Gurushankar
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080 Chelyabinsk, Russia
- Department of Physics, Kalasalingam Academy of Research and Education, 626126 Krishnankoil, Tamilnadu India
| | - S. Ch. Jeyaseelan
- Post Graduate & Research Department of Physics, N.M.S.S.V.N. College, 625019 Madurai, Tamilnadu India
- Post Graduate Department of Physics, Mannar Thirumalai Naciker College, 625004 Madurai, Tamilnadu India
| | - M. Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080 Chelyabinsk, Russia
| | - I. Siswanto
- Bioinformati Laboratory, UCoE Research Center for Bio-Molecule Engineering Universitas Airlangga, 60115 Surabaya, Indonesia
| | - R. Tiwari
- Department of Physics, Coordinator Research and Development Cell, Dr CV Raman University, 495113 Kargi Kota, Bilaspur CG India
| | - N. N. T. Puspaningsih
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, 60115 Surabaya, Indonesia
| |
Collapse
|
4
|
Saloni, Kumari D, Ranjan P, Chakraborty T. A computational study of potential therapeutics for COVID-19 invoking conceptual density functional theory. Struct Chem 2022; 33:2195-2204. [PMID: 36097582 PMCID: PMC9452875 DOI: 10.1007/s11224-022-02048-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/28/2022] [Indexed: 01/18/2023]
Abstract
The pandemic, COVID-19, has caused social and economic disruption at a larger pace all over the world. Identification of an effective drug for the deadliest disease is still an exigency. One of the most promising approaches to combat the lethal disease is use of repurposed drugs. This study provides insights into some of the potential repurposed drugs viz. camostat mesylate, hydroxychloroquine, nitazoxanide, and oseltamivir in terms of the computational quantum chemical method. Properties of these compounds have been elucidated in terms of Conceptual Density Functional Theory (CDFT)-based descriptors, IR spectra, and thermochemical properties. Computed results specify that hydroxychloroquine is the most reactive drug among them. Thermochemical data reveals that camostat mesylate has the utmost heat capacity, entropy, and thermal energy. Our findings indicate that camostat mesylate and hydroxychloroquine may be investigated further as potential COVID-19 therapeutics. We anticipate that the current study will aid the scientific community to design and develop viable therapeutics against COVID-19.
Collapse
Affiliation(s)
- Saloni
- Department of Chemistry and Biochemistry, School of Basic Sciences and Research, Sharda University, 201310, Greater Noida, UP India
| | - Dimple Kumari
- Department of Chemistry and Biochemistry, School of Basic Sciences and Research, Sharda University, 201310, Greater Noida, UP India
| | - Prabhat Ranjan
- Department of Mechatronics Engineering, Manipal University Jaipur, Dehmi Kalan-303007, Rajasthan, India
| | - Tanmoy Chakraborty
- Department of Chemistry and Biochemistry, School of Basic Sciences and Research, Sharda University, 201310, Greater Noida, UP India
| |
Collapse
|
5
|
Mohapatra RK, Azam M, Mohapatra PK, Sarangi AK, Abdalla M, Perekhoda L, Yadav O, Al-Resayes SI, Jong-Doo K, Dhama K, Ansari A, Seidel V, Verma S, Raval MK. Computational studies on potential new anti-Covid-19 agents with a multi-target mode of action. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2022; 34:102086. [PMID: 35582633 PMCID: PMC9101701 DOI: 10.1016/j.jksus.2022.102086] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 05/28/2023]
Abstract
A compound that could inhibit multiple targets associated with SARS-CoV-2 infection would prove to be a drug of choice against the virus. Human receptor-ACE2, receptor binding domain (RBD) of SARS-CoV-2 S-protein, Papain-like protein of SARS-CoV-2 (PLpro), reverse transcriptase of SARS-CoV-2 (RdRp) were chosen for in silico study. A set of previously synthesized compounds (1-5) were docked into the active sites of the targets. Based on the docking score, ligand efficiency, binding free energy, and dissociation constants for a definite conformational position of the ligand, inhibitory potentials of the compounds were measured. The stability of the protein-ligand (P-L) complex was validated in silico by using molecular dynamics simulations using the YASARA suit. Moreover, the pharmacokinetic properties, FMO and NBO analysis were performed for ranking the potentiality of the compounds as drug. The geometry optimizations and electronic structures were investigated using DFT. As per the study, compound-5 has the best binding affinity against all four targets. Moreover, compounds 1, 3 and 5 are less toxic and can be considered for oral consumption.
Collapse
Affiliation(s)
- Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, Odisha 758002, India
| | - Mohammad Azam
- Department of Chemistry, College of Science, King Saud University, PO BOX 2455, Riyadh 11451, Saudi Arabia
| | - Pranab K Mohapatra
- Department of Chemistry, C. V. Raman Global University, Bidyanagar, Mahura, Janla, Bhubaneswar, Odisha 752054, India
| | - Ashish K Sarangi
- Department of Chemistry, School of Applied Sciences, Centurion University of Technology and Management, Odisha, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province 250012, PR China
| | - Lina Perekhoda
- Department of Medicinal Chemistry, National University of Pharmacy, Pushkinska Str. 53, Kharkiv 61002, Ukraine
| | - Oval Yadav
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Saud I Al-Resayes
- Department of Chemistry, College of Science, King Saud University, PO BOX 2455, Riyadh 11451, Saudi Arabia
| | - Kim Jong-Doo
- Buddhist Culture College, Dongguk University, Gyeongju-si, Gyeongsangbuk-do 780-714, South Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Veronique Seidel
- Natural Products Research Laboratory, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Sarika Verma
- Council of Scientific and Industrial Research-Advanced Materials and Processes Research Institute, Bhopal, MP 462026, India
- Academy of Council Scientific and Industrial Research - Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, M.P 462026, India
| | - Mukesh K Raval
- Department of Chemistry, G. M. University, Sambalpur, Odisha, India
| |
Collapse
|
6
|
Mohamed GG, Omar MM, Ahmed YM. Metal complexes of Tridentate Schiff base: Synthesis, Characterization, Biological Activity and Molecular Docking Studies with COVID-19 Protein Receptor. Z Anorg Allg Chem 2021; 647:2201-2218. [PMID: 34908618 PMCID: PMC8662136 DOI: 10.1002/zaac.202100245] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/18/2021] [Indexed: 02/05/2023]
Abstract
Mononuclear chelates of Cr(III), Mn(II), Fe(III), Ni(II), Cu(II), Zn(II) and Cd(II) resulted from new tridentate Schiff base ligand, 4-((1-(5-acetyl-2,4-dihydroxyphenyl)ethylidene)amino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one, were synthesized. Metal to ligand ratio was found to be1 : 1, which was revealed via elemental analysis and characterized via various spectroscopic tools. IR has point out that the coordination of the ligand towards the metal ions was carried out via NOO donor atoms. UV-Vis, 1H NMR spectral data, molar conductivity measurements, BET surface area, melting points and theoretically through density function theory were used such as characterizing techniques in supporting further interpretation of the complexes structures. The complexes were octahedral except Cu(II) and Ni(II) complexes were tetrahedral as suggested from the magnetic moment measurement. The complexes were found to have surface area, pore volume and particle radius of 23-176 m2 g-1, 0.02-0.33 cc/g and 8.71-4.32 nm, respectively, as pointed out from BET measurement. Schiff base ligand and metal complexes were tested in vitro to estimate their antimicrobial activity opposed to Gram-negative and Gram-positive bacterial and fungal organisms. MOE 2008 was used headed for screen potential drugs with molecular docking by the protein sites of new coronavirus and the study was constructed to molecular docking without validation through MD simulations.
Collapse
Affiliation(s)
- Gehad G. Mohamed
- Chemistry DepartmentFaculty of ScienceCairo UniversityGiza12613Egypt
| | - M. M. Omar
- Chemistry DepartmentFaculty of ScienceCairo UniversityGiza12613Egypt
| | - Yasmin M. Ahmed
- Chemistry DepartmentFaculty of ScienceCairo UniversityGiza12613Egypt
| |
Collapse
|
7
|
Enhancement of Molecular imprinted polymer as organic fillers on bagasse cellulose fibers with biological evaluation and computational calculations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130660] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|