1
|
Zulfiqar A, Akhter MS, Waqas M, Bhatti IA, Imran M, Shawky AM, Shaban M, Alotaibi HF, Mahal A, Ashour A, Duan M, S Alshomrany A, Khera RA. Engineering of the Central Core on DBD-Based Materials with Improved Power-Conversion Efficiency by Using the DFT Approach. ACS OMEGA 2024; 9:29205-29225. [PMID: 39005764 PMCID: PMC11238312 DOI: 10.1021/acsomega.3c09215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/27/2024] [Accepted: 02/20/2024] [Indexed: 07/16/2024]
Abstract
Developing proficient organic solar cells with improved optoelectronic properties is still a matter of concern. In the current study, with an aspiration to boost the optoelectronic properties and proficiency of organic solar cells, seven new small-molecule acceptors (Db1-Db7) are presented by altering the central core of the reference molecule (DBD-4F). The optoelectronic aspects of DBD-4F and Db1-Db7 molecules were explored using the density functional theory (DFT) approach, and solvent-state calculations were assessed utilizing TD-SCF simulations. It was noted that improvement in photovoltaic features was achieved by designing these molecules. The results revealed a bathochromic shift in absorption maxima (λmax) of designed molecules reaching up to 776 nm compared to 736 nm of DBD-4F. Similarly, a narrow band gap, low excitation energy, and reduced binding energy were also observed in newly developed molecules in comparison with the pre-existing DBD-4F molecule. Performance improvement can be indicated by the high light-harvesting efficiency (LHE) of designed molecules (ranging from 0.9992 to 0.9996 eV) compared to the reference having a 0.9991 eV LHE. Db4 and Db5 exhibited surprisingly improved open-circuit voltage (V OC) values up to 1.64 and 1.67 eV and a fill factor of 0.9198 and 0.9210, respectively. Consequently, these newly designed molecules can be considered in the future for practical use in manufacturing OSCs with improved optoelectronic and photovoltaic attributes.
Collapse
Affiliation(s)
- Aamna Zulfiqar
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Salim Akhter
- Department of Chemistry, College of Science, University of Bahrain, Sakhir 32028, Bahrain
| | - Muhammad Waqas
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Ijaz Ahmad Bhatti
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Imran
- Chemistry Department, College of Science, King Khalid University (KKU), P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohamed Shaban
- Department of Physics, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
- Nanophotonics and Applications (NPA) Lab, Physics Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Hadil Faris Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint AbdulRahman University, Riyadh 11671, Saudi Arabia
| | - Ahmed Mahal
- Department of Medical Biochemical Analysis, College of Health Technology, Cihan University-Erbil, Erbil 44001, Kurdistan Region, Iraq
| | - Adel Ashour
- Department of Physics, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
| | - Meitao Duan
- School of Pharmacy, Xiamen Medical College, Xiamen 361023, P. R. China
- Research Center for Sustained and Controlled Release Agents, Xiamen Medical College, Xiamen 361023, P. R. China
- Key Laboratory of Functional and Clinical Translational Medicine, Fujian Province University, Xiamen Medical College, Xiamen 361023, P. R. China
| | - Ali S Alshomrany
- Department of Physics, College of Sciences, Umm Al-Qura University, Al Taif HWY, Mecca 24381, Saudi Arabia
| | - Rasheed Ahmad Khera
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| |
Collapse
|
2
|
Tue-Ngeun P, Rakitikul W, Thinkumrob N, Hannongbua S, Meelua W, Jitonnom J. Binding interactions and in silico ADME prediction of isoconessimine derivatives as potent acetylcholinesterase inhibitors. J Mol Graph Model 2024; 129:108746. [PMID: 38401250 DOI: 10.1016/j.jmgm.2024.108746] [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: 02/10/2023] [Revised: 12/25/2023] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
In pursuit of new acetylcholinesterase (AChE) inhibitors for treating Alzheimer's disease (AD), a series of ten previously synthesized isoconessimine compounds (7a-7j) was in silico investigated for their binding interactions with AChE and pharmacokinetics based on absorption, distribution, metabolism, and excretion (ADME) properties using molecular docking, ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) method and SwissADME tools. Docking experiments showed that all compounds bind within the active site gorge of AChE (PDB entry 1C2B), posing its aryloxy-substitutional ethyl group to catalytic site and conessine skeleton to peripheral anionic site. ONIOM interaction energy was used as an ONIOM score to improve docking score, and it ranked 7b as the most potent AChE inhibitor, in agreement with previous experiment. Residues, ASP74, TRP86, GLY122, GLU202, TRP286, GLU292, SER293, ILE294, TYR337, TYR341, and HIS447 were identified as important for the binding of the AChE-isoconessimine complex. The SwissADME investigation suggested that four compounds (7a, 7c, 7d and 7f) agree with the rules of drug-likeness. The steric and electronic effects on the aryloxy-substitutional ethyl group as important factors in the AChE inhibition were also discussed, which brings a better understanding of Alzheimer's disease drug development.
Collapse
Affiliation(s)
- Panthip Tue-Ngeun
- Program in Chemistry, Faculty of Science and Technology, Uttaradit Rajabhat University, Uttaradit, 53000, Thailand; Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand
| | - Waleepan Rakitikul
- Program of Chemical Technology, Faculty of Science and Technology, Chiang Rai Rajabhat University, Chiang Rai, 57100, Thailand; Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand
| | - Natechanok Thinkumrob
- Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Wijitra Meelua
- Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand; Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand; Demonstration School, University of Phayao, Phayao, 56000, Thailand
| | - Jitrayut Jitonnom
- Unit of Excellence in Computational Molecular Science and Catalysis, University of Phayao, Phayao, 56000, Thailand; Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand.
| |
Collapse
|
3
|
Kamal IM, Chakrabarti S. MetaDOCK: A Combinatorial Molecular Docking Approach. ACS OMEGA 2023; 8:5850-5860. [PMID: 36816658 PMCID: PMC9933224 DOI: 10.1021/acsomega.2c07619] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Molecular docking plays a major role in academic and industrial drug screening and discovery processes. Despite the availability of numerous docking software packages, there is a lot of scope for improvement for the docking algorithms in terms of becoming more reliable to replicate the experimental binding results. Here, we propose a combinatorial or consensus docking approach where complementary powers of the existing methods are captured. We created a meta-docking protocol by combining the results of AutoDock4.2, LeDock, and rDOCK programs as these are freely available, easy to use, and suitable for large-scale analysis and produced better performance on benchmarking studies. Rigorous benchmarking analyses were undertaken to evaluate the scoring, posing, and screening capability of our approach. Further, the performance measures were compared against one standard state-of-the-art commercial docking software, GOLD, and one freely available software, PLANTS. Performances of MetaDOCK for scoring, posing, and screening the protein-ligand complexes were found to be quite superior compared to the reference programs. Exhaustive molecular dynamics simulation and molecular mechanics Poisson-Boltzmann and surface area-based free energy estimation also suggest better energetic stability of the docking solutions produced by our meta-approach. We believe that the MetaDOCK approach is a useful packaging of the freely available software and provides a better alternative to the scientific community who are unable to afford costly commercial packages.
Collapse
Affiliation(s)
- Izaz Monir Kamal
- Division
of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Salt Lake, Sector V, Kolkata 700032, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Saikat Chakrabarti
- Division
of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Salt Lake, Sector V, Kolkata 700032, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
4
|
Computational Screening of Phenylamino-Phenoxy-Quinoline Derivatives against the Main Protease of SARS-CoV-2 Using Molecular Docking and the ONIOM Method. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061793. [PMID: 35335157 PMCID: PMC8955101 DOI: 10.3390/molecules27061793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 01/02/2023]
Abstract
In the search for new anti-HIV-1 agents, two forms of phenylamino-phenoxy-quinoline derivatives have been synthesized, namely, 2-phenylamino-4-phenoxy-quinoline and 6-phenylamino-4-phenoxy-quinoline. In this study, the binding interactions of phenylamino-phenoxy-quinoline derivatives and six commercially available drugs (hydroxychloroquine, ritonavir, remdesivir, S-217622, N3, and PF-07321332) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) were investigated using molecular docking and the ONIOM method. The molecular docking showed the hydrogen bonding and hydrophobic interactions of all the compounds in the pocket of SARS-CoV-2 main protease (Mpro), which plays an important role for the division and proliferation of the virus into the cell. The binding free energy values between the ligands and Mpro ranged from −7.06 to −10.61 kcal/mol. The molecular docking and ONIOM results suggested that 4-(2′,6′-dimethyl-4′-cyanophenoxy)-2-(4″-cyanophenyl)-aminoquinoline and 4-(4′-cyanophenoxy)-2-(4″-cyanophenyl)-aminoquinoline have low binding energy values and appropriate molecular properties; moreover, both compounds could bind to Mpro via hydrogen bonding and Pi-Pi stacking interactions with amino acid residues, namely, HIS41, GLU166, and GLN192. These amino acids are related to the proteolytic cleavage process of the catalytic triad mechanisms. Therefore, this study provides important information for further studies on synthetic quinoline derivatives as antiviral candidates in the treatment of SARS-CoV-2.
Collapse
|
5
|
Monteiro AFM, de Oliveira Viana J, Muratov E, Scotti MT, Scotti L. In Silico Studies against Viral Sexually Transmitted Diseases. Curr Protein Pept Sci 2020; 20:1135-1150. [PMID: 30854957 DOI: 10.2174/1389203720666190311142747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/02/2023]
Abstract
Sexually Transmitted Diseases (STDs) refer to a variety of clinical syndromes and infections caused by pathogens that can be acquired and transmitted through sexual activity. Among STDs widely reported in the literature, viral sexual diseases have been increasing in a number of cases globally. This emphasizes the need for prevention and treatment. Among the methods widely used in drug planning are Computer-Aided Drug Design (CADD) studies and molecular docking which have the objective of investigating molecular interactions between two molecules to better understand the three -dimensional structural characteristics of the compounds. This review will discuss molecular docking studies applied to viral STDs, such as Ebola virus, Herpes virus and HIV, and reveal promising new drug candidates with high levels of specificity to their respective targets.
Collapse
Affiliation(s)
- Alex F M Monteiro
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, Joao Pessoa-PB, Brazil
| | - Jessika de Oliveira Viana
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, Joao Pessoa-PB, Brazil
| | - Engene Muratov
- Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina, Beard Hall 301, CB#7568, Chapel Hill, NC, 27599, United States
| | - Marcus T Scotti
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, Joao Pessoa-PB, Brazil
| | - Luciana Scotti
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, Joao Pessoa-PB, Brazil.,Teaching and Research Management - University Hospital, Federal University of Paraíba, Campus I, 58051-900, João Pessoa-PB, Brazil
| |
Collapse
|
6
|
Yadav R, Selvaraj C, Aarthy M, Kumar P, Kumar A, Singh SK, Giri R. Investigating into the molecular interactions of flavonoids targeting NS2B-NS3 protease from ZIKA virus through in-silico approaches. J Biomol Struct Dyn 2020; 39:272-284. [PMID: 31920173 DOI: 10.1080/07391102.2019.1709546] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Zika virus (ZIKV), belongs to the flavivirus genus and Flaviviridae family that associated with serious diseased conditions like microcephaly and other neurological disorders (Guillan-Barré syndrome). As there is no vaccine or therapies available against ZIKV to date. Hence, it is an unmet need to find potential drug candidates and target sites against Zika virus infection. NS2B-NS3 protease making an attractive target for therapeutic intervention in ZIKV infections because of its critical role in hydrolysis of a single polyprotein encoded by Zika virus. Recently, there are some experimental evidence about the flavonoids as Zika virus NS2B-NS3 protease inhibitors. However, molecular interaction between protease complex and inhibitors at atomic levels has not been explored. Here, we have taken the experimentally validated thirty-eight flavonoids inhibitors against NS2B-NS3 protease to examine the molecular interaction using molecular docking and molecular dynamics simulations. We found out few flavonoids such as EGCG and its two derivatives, isoquercetin, rutin and sanggenon O showing interaction with catalytic triad (His51, Asp75, and Ser135) of the active site of NS2B-NS3 protease and found to be stable throughout the simulation. Therefore it is evident that interaction with the catalytic triad playing a vital role in the inhibition of the enzyme activity as a result inhibition of the virus propagation. However these compounds can be explored further for understanding the mechanism of action of these compounds targeting NS2B-NS3 protease for inhibition of Zika virus.
Collapse
Affiliation(s)
- Rakhi Yadav
- School of Basic Science, Indian Institute of Technology Mandi, Mandi, India
| | - Chandrabose Selvaraj
- School of Basic Science, Indian Institute of Technology Mandi, Mandi, India.,Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab, Alagappa University, Karaikudi, India
| | - Murali Aarthy
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab, Alagappa University, Karaikudi, India
| | - Prateek Kumar
- School of Basic Science, Indian Institute of Technology Mandi, Mandi, India
| | - Ankur Kumar
- School of Basic Science, Indian Institute of Technology Mandi, Mandi, India
| | - Sanjeev Kumar Singh
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab, Alagappa University, Karaikudi, India
| | - Rajanish Giri
- School of Basic Science, Indian Institute of Technology Mandi, Mandi, India
| |
Collapse
|
7
|
Tarasova O, Poroikov V, Veselovsky A. Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review. Molecules 2018; 23:molecules23051233. [PMID: 29883406 PMCID: PMC6100360 DOI: 10.3390/molecules23051233] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 02/05/2023] Open
Abstract
Currently, millions of people are living with human immunodeficiency virus type 1 (HIV-1), which causes acquired immunodeficiency syndrome. However, the spread of the HIV-1 resistance to antiviral agents is the major problem in the antiretroviral therapy and medical management of HIV-infected patients. HIV-1 reverse transcriptase (RT) is one of the key viral targets for HIV-1 inhibition. Therefore, the studies on the combatting the HIV resistance that occurs due to the structural changes in RT, are in great demand. This work aims to provide an overview of the state-of-the-art molecular docking approaches applied to the studies of the HIV-1 resistance, associated with RT structure changes. We have reviewed recent studies using molecular docking with mutant forms of RT. The work discusses the modifications of molecular docking, which have been developed to find the novel molecules active against resistance mutants of RT and/or recombinant strains of HIV-1. The perspectives of the existing algorithms of molecular docking to the studies on molecular mechanisms of resistance and selection of the correct binding poses for the reverse transcriptase inhibitors are discussed.
Collapse
Affiliation(s)
- Olga Tarasova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya st., Moscow 119121, Russia.
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya st., Moscow 119121, Russia.
| | - Alexander Veselovsky
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya st., Moscow 119121, Russia.
| |
Collapse
|
8
|
Talevi A. Drug repositioning: current approaches and their implications in the precision medicine era. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2018. [DOI: 10.1080/23808993.2018.1424535] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Alan Talevi
- Laboratory of Research and Development of Bioactive Compounds – Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences, University of La Plata, La Plata, Argentina
| |
Collapse
|