Carbohydrate-Based Derivatives Act as Potential Antimicrobial and Influenza Virus Inhibitors: In vitro and In silico Approaches | Chapter 3 | Chemistry and Biochemistry: Research Progress Vol. 9

 

A wide range of carbohydrate-derived drugs are currently utilised worldwide as antifungal, antibacterial and anticancer drugs. In this context, our research group focused on designing and synthesising new derivatives of methyl α-D-mannopyranoside (1, MDM) and exploring its antiviral and antibacterial properties through both experimental and computational approaches.

 

Seven MDM derivatives (2–7) were synthesised via selective acylation and fully characterised using spectroscopic techniques. In vitro antibacterial activity was evaluated by MIC and MBC assays, while in silico analyses included PASS prediction, density functional theory calculations, molecular docking, and molecular dynamics simulations against influenza A neuraminidase (H1N1, PDB ID: 7XGC). Compounds 3 and 5 exhibited the most significant antibacterial activity against both Gram-positive and Gram-negative strains, with compound 5 showing superior MIC and MBC values. Computational studies revealed favourable electronic properties for the active compounds. Docking and molecular dynamics analyses identified compounds 6 and 7 as the most potent neuraminidase binders, forming stable interactions with key catalytic residues commonly involved in known neuraminidase inhibitors. The combined in vitro and in silico findings highlight acylated MDM derivatives as promising dual-action antibacterial and antiviral scaffolds, with compound 5 emerging as a potential antibacterial lead and compounds 6 and 7 as promising candidates for anti-influenza drug development.

 

 

Author(s) Details

 

Sarkar M. A. Kawsar
Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong-4331, Bangladesh.

 

Md. Farhan Labib
Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong-4331, Bangladesh.

 

S. M. Sajid Hasan Shammo
Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong-4331, Bangladesh.

 

Nazia Islam
Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong-4331, Bangladesh.

 

Please see the book here :- https://doi.org/10.9734/bpi/cbrp/v9/6927

The Use of Computational Tools to Investigate the Impact of SARS-CoV2 Spike Protein Variants on Human Antibodies | Chapter 10 | Research Perspectives of Microbiology and Biotechnology Vol. 4

 

Understanding the process of formation of the complexes between Spike protein variants that make up the structure of the SARS-CoV2 virus and human antibodies, brings light into how variations have an impact on this complex formation. In this work, databases such as CoV3D, PDB and pyDockWEB were used to collect sequencing results and structures of SARS-CoV2 variants. Finally, molecular docking was also used in order to predict the interaction between the virus' Spike protein and antibodies. These results were then made available on a website produced exclusively for public dissemination of these analyses. Among other answers, this work serves as a guideline for molecular docking studies of the interaction between Spike protein variants and human antibodies.

 

 

Author(s) Details

Sérgio Amorim de Alencar

Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília-DF, Brazil.

Rickson Passos Campoe

Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília-DF, Brazil.

Yasmin Rezende

Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília-DF, Brazil.

Rute Pereira de Souza

Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília-DF, Brazil.

 

Please see the link:- https://doi.org/10.9734/bpi/rpmab/v4/1106

Spasmolytic Activity, Anti-Inflammatory Potential, and Molecular Docking Studies of Anthranilic Acid Hybrids | Chapter 8| Chemical and Materials Sciences - Developments and Innovations Vol. 3

Anthranilic acid and its analogs have an impressive biological profile; its structural nucleus has been thoroughly studied for the development of pharmaceuticals. Due to the predicted in silico methods spasmolytic activity, we synthesized a hybrid molecule of anthranilic acid and substituted 2-phenylethylamines. Phenylethylamines are serotonin agonists and are building blocks of isoquinoline alkaloids. Therefore, the synthesis of a new hybrid molecule of anthranilic acid and substituted 2-phenylethylamines, is extremely interesting in view of what properties the newly obtained molecule would inherit from both fragments. The current study has shifted towards the synthesis of novel hybrids as spasmolytic and anti-inflammatory agents. DFT calculations and docking simulations were performed on the synthesized compounds. The obtained results from all the experiments demonstrate that the hybrid molecule and its diamides inherit spasmolytic, antimicrobial, and anti-inflammatory capabilities, making them excellent candidates for future medications. Based on the experimental data, we can conclude that a collection of Novel 2-phenylethylamine hybrids were successfully synthesized and they can be considered as antispasmodics and anti-inflammatory drug candidates – alternatives to current therapeutics.

 

 

Author(s) Details

 

Miglena Milusheva

Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria and Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria.

Vera Gledacheva

Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria.

Iliyana Stefanova

Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria.

Mehran Feizi-Dehnayebi

Department of Organic Chemistry, Faculty of Chemistry, Alzahra University, Tehran, Iran.

Mina Todorova

Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria.

Yulian Tumbarski

Department of Microbiology, Technological Faculty, University of Food Technologies, 4002 Plovdiv, Bulgaria.

Ghodsi Mohammadi Ziarani

Department of Organic Chemistry, Faculty of Chemistry, Alzahra University, Tehran, Iran.

Stoyanka Nikolova

Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria.

 

Please see the link:- https://doi.org/10.9734/bpi/cmsdi/v3/11872F

The Use of Computational Tools to Investigate the Impact of SARS-CoV2 Spike Protein Variants on Human Antibodies | Chapter 10 | Research Perspectives of Microbiology and Biotechnology Vol. 4

 

Understanding the process of formation of the complexes between Spike protein variants that make up the structure of the SARS-CoV2 virus and human antibodies, brings light into how variations have an impact on this complex formation. In this work, databases such as CoV3D, PDB and pyDockWEB were used to collect sequencing results and structures of SARS-CoV2 variants. Finally, molecular docking was also used in order to predict the interaction between the virus' Spike protein and antibodies. These results were then made available on a website produced exclusively for public dissemination of these analyses. Among other answers, this work serves as a guideline for molecular docking studies of the interaction between Spike protein variants and human antibodies.

 

 

Author(s) Details

 

Sérgio Amorim de Alencar

Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília-DF, Brazil.

Rickson Passos Campoe

Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília-DF, Brazil.

Yasmin Rezende

Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília-DF, Brazil.

Rute Pereira de Souza

Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília-DF, Brazil.

 

Please see the link:- https://doi.org/10.9734/bpi/rpmab/v4/1106

Synthesis and Characterization of N,N-Dimethyl Aminophenyl Schiff’s Base-Chalcone Hybrid by In-silico and In-vitro Studies | Chapter 8 | Current Research Progress in Physical Science Vol. 3

The two biological active scaffolds (chalcone and Schiff base) were combined in a single compound by the simple synthetic methodology. Nuclear Magnetic Resonance (NMR), Fourier Transform – Infra Red (FT-IR), Ultraviolet (UV)-visible spectroscopy, and mass spectrophotometer techniques were used to characterize the synthesised compound. The reactivity of these compounds was theoretically revealed using Density Functional Theory (DFT) calculations such as Frontier Molecular Orbital (FMO), Mullikan charge distribution and molecular electrostatic potential (MEP) mapping studies by the use of Density Functional Theory (DFT) calculations, such as Frontier Molecular Orbital (FMO), Mullikan charge distribution, and molecular electrostatic potential (MEP) mapping studies, was revealed the reactivity of these compounds theoretically. Furthermore, the enzymes such as 1PGG.pdb, 4COX.pdb, and 1HNY.pdb which cause inflammation and diabetes were also carried out by molecular docking studies. In addition to that in-vitro activity of the inflammation and diabetes was also executed and results were compared with standard drug molecules. Schiff base ligands and their metal complexes have a wide range of applications reported so far. These complete theoretical and experimental studies could provide more functional details of the compounds in the wide applications of biological studies.

 

Author(s) Details

 

Rajendran Nithyabalaji
Department of Physics, SRM Valliammai Engineering College, Kattankulathur, Kanchepuram Dt., Tamil Nadu, India.

 

Ramya Rajan M. P.
Department of Physics, SRM Valliammai Engineering College, Kattankulathur, Kanchepuram Dt., Tamil Nadu, India.

 

Rengarajan Kavitha
Department of Physics, Rajalakshmi Institute of Technology, Poonathamalee, Chennai, Tamil Nadu-6000124, India.

 

Please see the book here:- https://doi.org/10.9734/bpi/crpps/v3/2021

 

Synthesis of Putrescine Bisamides as Antimicrobial and Anti-Inflammatory Agents with Molecular Docking Studies | Chapter 2 | Science and Technology: Developments and Applications Vol. 9

Putrescine bis amides are one of the subclasses of naturally occurring polyamides. During the last two decades, several symmetrical and unsymmetrical putrescine bisamides have been isolated from Aglaia, Liberica, and Carydalis species. In this study, a new naturally occurring N1, N6-dihydrocinnamyl putrescine bisamide, JBIR-94, along with nine structural analogs and a series of substituted phenyl and alkyl putrescine bisamides have been synthesized from putrescine and appropriately substituted carboxylic acids, through carboxylic acid chlorides. Antimicrobial, 5-Lipooxygenase enzyme inhibitory, and antioxidant studies were performed for all synthesized compounds. Antimicrobial assay performed against human pathogenic bacteria and fungi. Zone of inhibition was determined using agar well diffusion method, and minimum inhibitory concentration (MIC) was determined by broth dilution assay. The 5-Lipoxygenase (PDB ID 308Y) X-Ray crystal structure was obtained from the Protein Data Bank and used in docking studies. Antioxidant activities of putrescine bisamides were performed through radical scavenging assay using DPPH and Superoxide radicals. Dihydrocinnamyl series of putrescine bisamides (4a-4i) showed good bioactivities compared to substituted phenyl (6a-6g) and diakyl (6h-6j) series of compounds. Among all compounds, 4h (methylenedioxy analog) and 4a (JBIR-94) showed good antimicrobial, anti-inflammatory, and antioxidant activities.

 

Author (s) Details

Siddaiah Vidavalur
Department of Chemistry, Andhra University, Visakhapatnam, India.

 

Sunanda Kumari Kadiri
Department of Microbiology, Andhra University, Visakhapatnam, India.

 

Kumari Yettula
Department of Chemistry, Andhra University, Visakhapatnam, India.

 

Srinuvasarao Rayavarapu
Department of Chemistry, Andhra University, Visakhapatnam, India.

 

Mahaboob Basha Gajula
Department of Chemistry, Andhra University, Visakhapatnam, India.

 

Mangarao Nakka
Department of Chemistry, Andhra University, Visakhapatnam, India.

Ramu Tadikonda
Department of Chemistry, Andhra University, Visakhapatnam, India.

 

Please see the book here:- https://doi.org/10.9734/bpi/stda/v9/4995

Spasmolytic Activity, Anti-Inflammatory Potential, and Molecular Docking Studies of Anthranilic Acid Hybrids | Chapter 8| Chemical and Materials Sciences - Developments and Innovations Vol. 3

 Anthranilic acid and its analogs have an impressive biological profile, its structural nucleus has been thoroughly studied for the development of pharmaceuticals. Due to the predicted in silico methods spasmolytic activity, we synthesized a hybrid molecule of anthranilic acid and substituted 2-phenylethylamines. Phenylethylamines are serotonin agonists and are building blocks of isoquinoline alkaloids. Therefore, the synthesis of a new hybrid molecule of anthranilic acid and substituted 2-phenylethylamines, is extremely interesting in view of what properties the newly obtained molecule would inherit from both fragments. The current study has shifted towards the synthesis of novel hybrids as spasmolytic and anti-inflammatory agents. DFT calculations and docking simulations were performed on the synthesized compounds. The obtained results from all the experiments demonstrate that the hybrid molecule and its diamides inherit spasmolytic, antimicrobial, and anti-inflammatory capabilities, making them excellent candidates for future medications. Based on the experimental data, we can conclude that a collection of Novel 2-phenylethylamine hybrids were successfully synthesized and they can be considered as antispasmodics and anti-inflammatory drug candidates – alternatives to current therapeutics.

 

Author (s) Details

Miglena Milusheva,
Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria and Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria.

Vera Gledacheva,
Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria.

Iliyana Stefanova,
Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria.

Mehran Feizi-Dehnayebi,,
Department of Organic Chemistry, Faculty of Chemistry, Alzahra University, Tehran, Iran.

Mina Todorova
Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria.

Yulian Tumbarsk,
Department of Microbiology, Technological Faculty, University of Food Technologies, 4002 Plovdiv, Bulgaria.

Ghodsi Mohammadi Ziarani,
Department of Organic Chemistry, Faculty of Chemistry, Alzahra University, Tehran, Iran.

Stoyanka Nikolova,
Department of Organic Chemistry, Faculty of Chemistry, Alzahra University, Tehran, Iran.

 

Please see the book here:-  https://doi.org/10.9734/bpi/cmsdi/v3/11872F

Molecular Docking Tool: General Concept and Recent Advances | Chapter 9 | Recent Developments in Chemistry and Biochemistry Research Vol. 1

This study explores about general concept and recent advances of molecular docking. Molecular docking is a computational method used to predict the interaction of two molecules generating a binding model. In many drug discovery applications, docking is done between a small molecule and a macromolecule for example, protein-ligand docking. The molecular docking approach can be used to model the interaction between a small molecule and a protein at the atomic level, which allow us to characterize the behavior of small molecules in the binding site of target proteins as well as to elucidate fundamental biochemical processes. The simulation of the docking process as such is a much more complicated process in this approach, the protein and the ligand are separated by some physical distance, and the ligand finds its position into the protein’s active site after a certain number of “moves” in its conformational space. The present Review focus Concept, Strategy, Types and other Aspects with Recent Advances of Molecular Docking. It is concluded that molecular docking has been able to identify promising compounds that might represent future solutions in critical areas of human health.

Author(s) Details:

Biswaranjan Ray,
PG Department, College of Pharmaceutical Sciences, Puri, Odisha, India.

Amiyakanta Mishra,
PG Department, College of Pharmaceutical Sciences, Puri, Odisha, India.

Chinmaya Kesari Sahoo,
PG Department, College of Pharmaceutical Sciences, Puri, Odisha, India.

Please see the link here: https://stm.bookpi.org/RDCBR-V1/article/view/13640

Molecular Docking of Secondary Metabolites from Lichens Targeting Sars-CoV-2 Main Protease (Mpro) and Spike Protein Receptors | Chapter 5 | Novel Aspects on Pharmaceutical Research Vol. 7

 This episode aimed to screen the flowerless plant substances to label the potential drug to inhibit SARS-CoV-2 main protease and spike protein by microscopic docking system.COVID-19 (Coronavirus disease) is induced by severe severe respiratory disease coronavirus (SARS-CoV)-2. It is a deadly pathogenic and transmissible bacterium. Since there is no particular antiviral treatment against COVID-19, labeling new therapeutics is a important need. Plant natural wealthes represent the rich source of alive molecules that can find many uses in the field of plant structure, pharmacy, and cure including oncology. The COVID-19 main protease (Mpro) and pierce proteins (S protein) were selected as target proteins. A total of 108 flowerless plant compounds were subjected to ADMET reasoning and 14 compounds were selected established the ADMET properties and Lipinski’s rule of five. The Schrodinger Glide piece software was used to act molecular docking for protect of chosen individual flowerless plant metabolites against the primary protease and pierce protein receptors of SARS-CoV-2.  Molecular docking studies of flowerless plant secondary metabolites (14 compounds) were completed activity with SARS-CoV-2 proteins. The interactions of flowerless plant metabolites with main protease and pierce protein of SARS-CoV-2 tabulated accompanying G-Score, number of hydrogen bonds, bond length, and the communicating residues. Among the lead compounds, fallacinol (1,8-dihydroxy-3-(hydroxymethyl)-6 methoxyanthracene - 9,10-dione) showed the topmost binding energy value of -11.83 kcal/mol against pierce protein, and 4-O-Demethyl barbatic acid (4-(2,4-dihydroxy-3,6-dimethylbenzoyl)oxy-2-hydroxy-3,6-dimethylbenzoic acid ) exhibited the chief dock score of -11.67 kcal/mol against main protease. This study finding desires that lichen wealthes may potential inhibitors of receptors of  SARS-CoV-2.

Author(s) Details:

S. Senthil Prabhu,
Department of Microbiology, Dr. N.G.P. Arts and Science College, Coimbatore, Tamil Nadu, India.

R. Sathish Kumar,
Department of Biotechnology, Kongunadu Arts and Science College, Coimbatore, Tamil Nadu, India.

J. Rengaramanujam,
Department of Microbiology, Dr. N.G.P. Arts and Science College, Coimbatore, Tamil Nadu, India.

Please see the link here: https://stm.bookpi.org/NAPR-V7/article/view/11435

Molecular Docking: Concept and Application | Chapter 3 | Novel Aspects on Pharmaceutical Research Vol. 1

 Molecular tying up is a computational method that create a binding model by predicting the interplay of two molecules. Molecular anchoring can demonstrate the practicability of any biochemical response as it is accomplished former than experimental indiscriminate any research. In many uses for drug discovery, rendezvousing is carried out middle from two points a small particle and a macromolecule, for instance, protein-ligand mooring. The simulation of the hooking up process as such is a much more difficult process in this plan, the protein and the ligand are separated by few physical distance, and the ligand finds allure position into the protein’s active location after the number of “moves” in its conformational scope. The current Review concentrates on the Concept, Strategy, Types and other Aspects accompanying Recent Advances of Molecular Docking.

Author(s) Details:

Sanjaya Kumar Nayak,
P.G. Department, College of Pharmaceutical Sciences, Puri, Odisha, India.

B. Ray,
Institute of Pharmaceutical Science, Jaleswar, Odisha, India.

Please see the link here: https://stm.bookpi.org/NAPR-V1/article/view/10301

Isatin Derivatives as Human Intestinal Carboxylesterase Inhibitors: An Approach towards 3D-QSAR, Pharmacophore and Molecular Docking | Chapter 1 | Current Aspects in Pharmaceutical Research and Development Vol. 2

 Carboxylesterases (CEs) metabolise a variety of medications, and inhibiting them can increase the bioactivity or reduce the toxicity of substances activated by these enzymes. Isatin derivatives that were previously described as carboxylesterase inhibitors were chosen to develop a quantitative structure-activity link using k-nearest neighbour molecular field analysis (kNN MFA). The dataset consisted of 49 chemicals, and the data set was divided into training and test sets using the sphere exclusion (SE) technique. The models were created using various dissimilarity levels, and the best model (dissimilarity value 3.75) had a cross verified correlation coefficient (q2) of 0.8594 and a predicted correlation coefficient (pred r2) of 0.8106 with a test set of 9 chemicals. The QSAR models were built using the kNN-MFA methodology with stepwise (SW) forward-backward. The kNN-MFA contour plots revealed a link between the structural properties of substituted isatin derivatives and their actions, which could be exploited to develop novel CE inhibitors. Molsign and Pharmagist techniques demonstrate common two aromatic (AroC) and two hydrogen bond acceptors (HAc) properties in pharmacophore investigations. The results of this study could help with lead optimization and the development of potent carboxylesterase inhibitors. To discover probable interactions of the chemicals with the carboxylesterase active site, a molecular docking research was conducted. The pdb id 2hrq (crystal structure of human carboxylesterase with soman) was chosen for this purpose. Compound 62 has a similar docking score and binds to the enzyme's active site.

Author(s) Details

Sanmati K. Jain
Drug Discovery and Research Laboratory, SLT Institute of Pharmaceutical Sciences, Guru Ghasidas Vishwavidyalaya, Bilaspur, 495009, India.

Piyush Ghode
Drug Discovery and Research Laboratory, SLT Institute of Pharmaceutical Sciences, Guru Ghasidas Vishwavidyalaya, Bilaspur, 495009, India.

Achal Mishra
Faculty of Pharmaceutical Sciences, Shri Shankaracharya Group of Institutions, Junwani, Bhilai, India.

View Book :- https://stm.bookpi.org/CAPRD-V2/article/view/3949

Study on Isolation, Characterization, and Docking Studies of Isolated Compounds as Antidiabetic Molecules from Cressa cretica | Chapter 16 | Technological Innovation in Pharmaceutical Research Vol. 9

 The goal of this work was to use spectroscopic analysis and molecular docking investigations to examine the diabetic effect of phytocompounds derived from Cressa cretica Linn. Methods: 2-Isopropyl-4-(1-methyl-dodeca-2,4-dienyloxy)-benzene-1,3,5-triol (Compound CN-01) and 11-Methyl-dodeca-2,4,6,8,10-pentenoic acid 2,3-dihydroxy-5-methyl-phenyl ester (Compound CN-02) were obtained in pure form from a coarse powder of the complete plant of C. cretica. The target protein's three-dimensional structure was retrieved from the Protein Data Bank (www.rcsb.org), and the ligand files CN-01 and CN-02 were converted to MDL Molfile (V2000) format using Chem Sketch 2017.2.1. Because these files couldn't be directly used in AutoDock 4.0 tools, they had to be converted to PDB files using an open babel tool. Spectroscopic investigation yielded compounds, which were then screened using AutoDock 4.0 techniques. An existing phytochemical from the plant C. cretica, CN-01 and CN-02, had the greatest fitness docking score and hence potentially be an effective antidiabetic medication, according to a docking research. Conclusion: Based on molecular docking research, we found that the receptor (glycogen phosphorylase protein) holds a promising lead target formation against diabetes (minimum hydrogen bond length and maximum docked score). As a result, these molecules can be employed effectively as medications to treat diabetes, as indicated by docking scores.

Author(s) Details

Dr. Sangeeta Rani
Department of Pharmacognosy, S.D. College of Pharmacy and Vocational Studies, Muzaffarnagar, Uttar Pradesh, India.

Dr. Kavita Gahlot
Department of Pharmacognosy, IFTM University, Moradabad, Uttar Pradesh, India.

Dr. Arvind Kumar
Department of Pharmaceutical Chemistry and Drug Design, S.D. College of Pharmacy and Vocational Studies, Muzaffarnagar, Uttar Pradesh, India.

View Book :-  https://stm.bookpi.org/TIPR-V9/article/view/2529