Saleh Alarfaji - Academia.edu (original) (raw)
Papers by Saleh Alarfaji
Materials Today Communications
Open Chemistry
A donor–acceptor substituted derivative 2,6-diamino-4-(3,4,5-trimethoxy-phenyl)-pyridine-3,5-dica... more A donor–acceptor substituted derivative 2,6-diamino-4-(3,4,5-trimethoxy-phenyl)-pyridine-3,5-dicarbonitrile (DTPP) has been synthesized and its photophysical properties have been studied. Effect of solvent on the photophysical features of DTPP has been undertaken by steady state absorption and emission techniques. Strong solvatochromic emission has been observed due to intramolecular charge transfer characteristics, upon changing the solvent polarity, revealing the highly polar character of the excited state. Dipole moment changes between the excited and ground state have been estimated by using the theory of solvatochromism from Lippert–Mataga and Reichardt’s correlations. The geometrical parameters for ground and excited states, conformational flexibility, and NLO behavior of the molecule have been theoretically investigated. The electronic distributions of DTPP in HOMO and LUMO were also investigated using density functional theory (DFT) methods at B3LYP/6-31 G** level. The corre...
Computational and Theoretical Chemistry
Materials Science and Engineering: B
International Journal of Hydrogen Energy
Chemical Papers
The world is now facing intolerable damage in all sectors of life because of the deadly COVID-19 ... more The world is now facing intolerable damage in all sectors of life because of the deadly COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2. The discovery and development of anti-SARS-CoV-2 drugs have become pragmatic in the time needed to fight against this pandemic. The non-structural protein 3 is essential for the replication of transcriptase complex (RTC) and may be regarded as a possible target against SARS-CoV-2. Here, we have used a comprehensive in silico technique to find potent drug molecules against the NSP3 receptor of SARS-CoV-2. Virtual screening of 150 Isatin derivatives taken from PubChem was performed based on their binding affinity estimated by docking simulations, resulting in the selection of 46 ligands having binding energy greater than −7.1 kcal/mol. Moreover, the molecular interactions of the nine best-docked ligands having a binding energy of ≥ −8.5 kcal/mol were analyzed. The molecular interactions showed that the three ligands (S5, S16, and S42) were stabilized by forming hydrogen bonds and other significant interactions. Molecular dynamic simulations were performed to mimic an in vitro protein-like aqueous environment and to check the stability of the best three ligands and NSP3 complexes in an aqueous environment. The binding energy of the S5, S16, and S42 systems obtained from the molecular mechanics Poisson-Boltzmann surface area also favor the system's stability. The MD and MM/PBSA results explore that S5, S16, and S42 are more stable and can be considered more potent drug candidates against COVID-19 disease.
Journal of Computational Biophysics and Chemistry
SARS-CoV-2, which causes COVID-19 disease, has proven to be a disastrous pandemic due to its cont... more SARS-CoV-2, which causes COVID-19 disease, has proven to be a disastrous pandemic due to its contagious nature. This study has been planned to theoretically explore some antidotes against this virus from natural compounds. A total of 150 compounds from the shogaol class and shogaol derivatives (SDs) have been screened whereas 50 among those, which obeyed Lipinski’s Rule of Five (Ro5), have further been investigated using molecular docking techniques. Furthermore, reference antiviral drug chloroquine (ChQ) and Co-Crystallized inhibitor have also been studied against Mpro of SARS-CoV-2 for comparing the potential of our docked ligands. Surprisingly, 78% of our docked ligands have shown binding energies and inhibition constants lower than ChQ and all ligands showed these values lower than an inhibitor. We further visualized the nature of intermolecular interactions for the best docked six ligands, which have shown higher binding affinities. We have also assessed ADMET properties for th...
Chemical Papers
The current study reveals the inhibitory potential of novel bioactive compounds of mangrove actin... more The current study reveals the inhibitory potential of novel bioactive compounds of mangrove actinomycetes against nsp10 of SARS-CoV-2. A total of fifty (50) novel bioactive (antibacterial, antitumor, antiviral, antioxidant, and anti-inflammatory) compounds of mangrove actinomycetes from different chemical classes such as alkaloids, dilactones, sesquiterpenes, macrolides, and benzene derivatives are used for interaction analysis against nsp10 of SARS-CoV-2. The six antiviral agents sespenine, xiamycin c, xiamycin d, xiamycin e, xiamycin methyl ester, and xiamycin A (obeyed RO5 rule) are selected based on higher binding energy, low inhibition constant values, and better-docked positions. The effective hydrogen and hydrophobic (alkyl,-sigma,-T shaped and-alkyl) interaction analysis reveals the four antivirals sespenine, xiamycin C, xiamycin methyl ester, and xiamycin A are supposed to be the most auspicious inhibitors against nsp10 of SARS-CoV-2. Quantum chemistry methods such as frontier molecular orbitals and molecular electrostatic potential are used to explain the thermal stability and chemical reactivity of ligands. The toxicity profile shows that selected ligands are safe by absorption, distribution, metabolism, excretion, and toxicity profiling and also effective for inhibition of nsp10 protein of SARS-CoV-2. The molecular dynamic simulation investigation of apo and halo forms of nsp10 done by RMSD of C atoms of nsp10, all amino acid residues RMSF, count total number of hydrogen bonds and radius of gyration (R g). MD simulations reveal the complexes are stable and increase the structural compactness of nsp10 in the binding pocket. The lead antiviral compounds sespenine, xiamycin C, xiamycin methyl ester, and xiamycin A are recommended as the most promising inhibitors against nsp10 of SARS-CoV-2 pathogenicity.
Journal of Computational Biophysics and Chemistry, 2022
The ongoing eruption of the COVID-19 pandemic instigated by severe-acute-respiratory-syndrome-cor... more The ongoing eruption of the COVID-19 pandemic instigated by severe-acute-respiratory-syndrome-coronavirus 2 (SARS-CoV-2) has produce enormous damage to the world. The need of the hour is to stop this pandemic by inhibiting the main protease (MPro) of SARS-CoV-2, which is primarily involved in viral replication. Our study aims to find potential inhibitors for MPro by docking marine fungi-based 90 antiviral compounds against SARS-CoV-2. Among these, 11 antiviral compounds (obeying Lipinski RO5) are selected from 90 docked antiviral compounds on the basis of binding energy range ([Formula: see text]6.4[Formula: see text]kcal/mol to [Formula: see text]9[Formula: see text]kcal/mol) and low inhibition constant values (0.23[Formula: see text][Formula: see text]M to 2.5[Formula: see text][Formula: see text]M) as compared with remdesivir (reference compound) toward MPro of SARS-CoV-2. Tryptoquivaline F, arisugacin B, and arisugacin A antiviral compounds exhibited effective hydrogen and hydro...
Journal of Computational Biophysics and Chemistry, 2022
Breast cancer is the most common cancer among women worldwide. Breast cancer is caused by the ove... more Breast cancer is the most common cancer among women worldwide. Breast cancer is caused by the overexpression of genes that facilitate breast cell proliferation. Estrogen receptor alpha (ER[Formula: see text]) mediation is mostly responsible for the development of malignant tumors by regulating the transcription of various genes as a transcription factor. ER[Formula: see text] is regarded as an important receptor for the proliferation of this disease and its inhibition is necessary for the treatment of breast cancer. In our study, the aim is to find out potential inhibitors for ER[Formula: see text] by docking 100 anticancer constituents of different halogen-based derivatives against ER[Formula: see text]. Among the 100 [Formula: see text]-based derivatives, 20 ligands were selected based on the interaction energy ranging from [Formula: see text]6.7[Formula: see text]kcal/mol to [Formula: see text]8.2[Formula: see text]kcal/mol and lower values of inhibition constant (0.92–11.77[Form...
Chemistry & Biodiversity, 2022
In our continuous screening for bioactive microbial natural products, the culture extracts of a t... more In our continuous screening for bioactive microbial natural products, the culture extracts of a terrestrial Actinomycetes sp. GSCW‐51 yielded two new metabolites, i. e., 5‐hydroxymethyl‐3‐(1‐hydroxy‐6‐methyl‐7‐oxooctyl)dihydrofuran‐2(3H)‐one (1), 5‐hydroxymethyl‐3‐(1,7‐dihydroxy‐6‐methyloctyl)dihydrofuran‐2(3H)‐one (2), and two known compounds; 5′‐methylthioinosine (3), and 5′‐methylthioinosine sulfoxide (4), which are isolated first time from any natural source, along with four known compounds (5–8). The structures of the new compounds were deduced by HR‐ESI‐MS, 1D and 2D NMR data, and in comparison with related compounds from the literature. Additionally, owing to the current COVID‐19 pandemic situation, we also computationally explored the therapeutic potential of our isolated compounds against SARS‐CoV‐2. Compound 4 showed the best binding energies of −6.2 and −6.6 kcal/mol for Mpro and spike proteins, respectively. The intermolecular interactions were also studied using 2‐D and...
ACS Omega, 2022
Two imine compounds named as (E)-2-(((3,4dichlorophenyl)imino)methyl)phenol (DC2H) and (E)-4-(((2... more Two imine compounds named as (E)-2-(((3,4dichlorophenyl)imino)methyl)phenol (DC2H) and (E)-4-(((2,4dimethylphenyl)imino)methyl)phenol (DM4H) are synthesized, and their crystal structures are verified using the single-crystal X-ray diffraction (XRD) technique. The crystal structures of the compounds are compared with the closely related crystal structures using the Cambridge Structural Database (CSD). The crystal packing in terms of intermolecular interactions is fully explored by Hirshfeld surface analysis. Void analysis is carried out for both compounds to check the strength of the crystal packing. Furthermore, a state-of-the-art dual computational technique consisting of quantum chemical and molecular docking methods is used to shed light on the molecular structure, optoelectronic properties, and bioactivity of indigenously synthesized compounds. The optimized molecular geometries are compared with their counterpart experimental values. Based on previous reports of biofunctions of the indigenously synthesized imine derivatives, they are explored for their potential inhibition properties against two very crucial proteins (main protease (M pro) and nonstructural protein 9 (NSP9)) of SARS-CoV-2. The calculated interaction energy values of DC2H and DM4H with M pro are found to be −6.3 and −6.6 kcal/mol, respectively, and for NSP9, the calculated interaction energy value is found to be −6.5 kcal/mol. We believe that the current combined study through experiments and computational techniques will not only pique the interest of the broad scientific community but also evoke interest in their further in vitro and in vivo investigations.
Journal of Nonlinear Optical Physics & Materials, 2020
In this study, density functional theory is used to examine the electronic and nonlinear optical ... more In this study, density functional theory is used to examine the electronic and nonlinear optical properties of a narrative class boron nitride (B[Formula: see text]N[Formula: see text]) doped with super alkali OLi3. From the computational investigations, these complexes are highly stable and superalkali prefer a cubic position of the nanocage energetically to be chemisorbed. When superalkali doped on B[Formula: see text]N[Formula: see text], a significant decrease in the HOMO–LUMO energy gap was observed and this shifted the B[Formula: see text]N[Formula: see text] nanocage from insulator to n-type semiconductor. The HOMO–LUMO energy gap of pure B[Formula: see text]N[Formula: see text] was 6.84[Formula: see text]eV and when superalkali (OLi3) is doped on it, the HOMO–LUMO energy gap was changed in the range of 3.94–0.42[Formula: see text]eV. BNM2b showed a HOMO–LUMO energy gap of 3.94[Formula: see text]eV, while BNM4a showed a minimum HOMO–LUMO energy gap (0.42[Formula: see text]eV)...
Materials Today Communications
Open Chemistry
A donor–acceptor substituted derivative 2,6-diamino-4-(3,4,5-trimethoxy-phenyl)-pyridine-3,5-dica... more A donor–acceptor substituted derivative 2,6-diamino-4-(3,4,5-trimethoxy-phenyl)-pyridine-3,5-dicarbonitrile (DTPP) has been synthesized and its photophysical properties have been studied. Effect of solvent on the photophysical features of DTPP has been undertaken by steady state absorption and emission techniques. Strong solvatochromic emission has been observed due to intramolecular charge transfer characteristics, upon changing the solvent polarity, revealing the highly polar character of the excited state. Dipole moment changes between the excited and ground state have been estimated by using the theory of solvatochromism from Lippert–Mataga and Reichardt’s correlations. The geometrical parameters for ground and excited states, conformational flexibility, and NLO behavior of the molecule have been theoretically investigated. The electronic distributions of DTPP in HOMO and LUMO were also investigated using density functional theory (DFT) methods at B3LYP/6-31 G** level. The corre...
Computational and Theoretical Chemistry
Materials Science and Engineering: B
International Journal of Hydrogen Energy
Chemical Papers
The world is now facing intolerable damage in all sectors of life because of the deadly COVID-19 ... more The world is now facing intolerable damage in all sectors of life because of the deadly COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2. The discovery and development of anti-SARS-CoV-2 drugs have become pragmatic in the time needed to fight against this pandemic. The non-structural protein 3 is essential for the replication of transcriptase complex (RTC) and may be regarded as a possible target against SARS-CoV-2. Here, we have used a comprehensive in silico technique to find potent drug molecules against the NSP3 receptor of SARS-CoV-2. Virtual screening of 150 Isatin derivatives taken from PubChem was performed based on their binding affinity estimated by docking simulations, resulting in the selection of 46 ligands having binding energy greater than −7.1 kcal/mol. Moreover, the molecular interactions of the nine best-docked ligands having a binding energy of ≥ −8.5 kcal/mol were analyzed. The molecular interactions showed that the three ligands (S5, S16, and S42) were stabilized by forming hydrogen bonds and other significant interactions. Molecular dynamic simulations were performed to mimic an in vitro protein-like aqueous environment and to check the stability of the best three ligands and NSP3 complexes in an aqueous environment. The binding energy of the S5, S16, and S42 systems obtained from the molecular mechanics Poisson-Boltzmann surface area also favor the system's stability. The MD and MM/PBSA results explore that S5, S16, and S42 are more stable and can be considered more potent drug candidates against COVID-19 disease.
Journal of Computational Biophysics and Chemistry
SARS-CoV-2, which causes COVID-19 disease, has proven to be a disastrous pandemic due to its cont... more SARS-CoV-2, which causes COVID-19 disease, has proven to be a disastrous pandemic due to its contagious nature. This study has been planned to theoretically explore some antidotes against this virus from natural compounds. A total of 150 compounds from the shogaol class and shogaol derivatives (SDs) have been screened whereas 50 among those, which obeyed Lipinski’s Rule of Five (Ro5), have further been investigated using molecular docking techniques. Furthermore, reference antiviral drug chloroquine (ChQ) and Co-Crystallized inhibitor have also been studied against Mpro of SARS-CoV-2 for comparing the potential of our docked ligands. Surprisingly, 78% of our docked ligands have shown binding energies and inhibition constants lower than ChQ and all ligands showed these values lower than an inhibitor. We further visualized the nature of intermolecular interactions for the best docked six ligands, which have shown higher binding affinities. We have also assessed ADMET properties for th...
Chemical Papers
The current study reveals the inhibitory potential of novel bioactive compounds of mangrove actin... more The current study reveals the inhibitory potential of novel bioactive compounds of mangrove actinomycetes against nsp10 of SARS-CoV-2. A total of fifty (50) novel bioactive (antibacterial, antitumor, antiviral, antioxidant, and anti-inflammatory) compounds of mangrove actinomycetes from different chemical classes such as alkaloids, dilactones, sesquiterpenes, macrolides, and benzene derivatives are used for interaction analysis against nsp10 of SARS-CoV-2. The six antiviral agents sespenine, xiamycin c, xiamycin d, xiamycin e, xiamycin methyl ester, and xiamycin A (obeyed RO5 rule) are selected based on higher binding energy, low inhibition constant values, and better-docked positions. The effective hydrogen and hydrophobic (alkyl,-sigma,-T shaped and-alkyl) interaction analysis reveals the four antivirals sespenine, xiamycin C, xiamycin methyl ester, and xiamycin A are supposed to be the most auspicious inhibitors against nsp10 of SARS-CoV-2. Quantum chemistry methods such as frontier molecular orbitals and molecular electrostatic potential are used to explain the thermal stability and chemical reactivity of ligands. The toxicity profile shows that selected ligands are safe by absorption, distribution, metabolism, excretion, and toxicity profiling and also effective for inhibition of nsp10 protein of SARS-CoV-2. The molecular dynamic simulation investigation of apo and halo forms of nsp10 done by RMSD of C atoms of nsp10, all amino acid residues RMSF, count total number of hydrogen bonds and radius of gyration (R g). MD simulations reveal the complexes are stable and increase the structural compactness of nsp10 in the binding pocket. The lead antiviral compounds sespenine, xiamycin C, xiamycin methyl ester, and xiamycin A are recommended as the most promising inhibitors against nsp10 of SARS-CoV-2 pathogenicity.
Journal of Computational Biophysics and Chemistry, 2022
The ongoing eruption of the COVID-19 pandemic instigated by severe-acute-respiratory-syndrome-cor... more The ongoing eruption of the COVID-19 pandemic instigated by severe-acute-respiratory-syndrome-coronavirus 2 (SARS-CoV-2) has produce enormous damage to the world. The need of the hour is to stop this pandemic by inhibiting the main protease (MPro) of SARS-CoV-2, which is primarily involved in viral replication. Our study aims to find potential inhibitors for MPro by docking marine fungi-based 90 antiviral compounds against SARS-CoV-2. Among these, 11 antiviral compounds (obeying Lipinski RO5) are selected from 90 docked antiviral compounds on the basis of binding energy range ([Formula: see text]6.4[Formula: see text]kcal/mol to [Formula: see text]9[Formula: see text]kcal/mol) and low inhibition constant values (0.23[Formula: see text][Formula: see text]M to 2.5[Formula: see text][Formula: see text]M) as compared with remdesivir (reference compound) toward MPro of SARS-CoV-2. Tryptoquivaline F, arisugacin B, and arisugacin A antiviral compounds exhibited effective hydrogen and hydro...
Journal of Computational Biophysics and Chemistry, 2022
Breast cancer is the most common cancer among women worldwide. Breast cancer is caused by the ove... more Breast cancer is the most common cancer among women worldwide. Breast cancer is caused by the overexpression of genes that facilitate breast cell proliferation. Estrogen receptor alpha (ER[Formula: see text]) mediation is mostly responsible for the development of malignant tumors by regulating the transcription of various genes as a transcription factor. ER[Formula: see text] is regarded as an important receptor for the proliferation of this disease and its inhibition is necessary for the treatment of breast cancer. In our study, the aim is to find out potential inhibitors for ER[Formula: see text] by docking 100 anticancer constituents of different halogen-based derivatives against ER[Formula: see text]. Among the 100 [Formula: see text]-based derivatives, 20 ligands were selected based on the interaction energy ranging from [Formula: see text]6.7[Formula: see text]kcal/mol to [Formula: see text]8.2[Formula: see text]kcal/mol and lower values of inhibition constant (0.92–11.77[Form...
Chemistry & Biodiversity, 2022
In our continuous screening for bioactive microbial natural products, the culture extracts of a t... more In our continuous screening for bioactive microbial natural products, the culture extracts of a terrestrial Actinomycetes sp. GSCW‐51 yielded two new metabolites, i. e., 5‐hydroxymethyl‐3‐(1‐hydroxy‐6‐methyl‐7‐oxooctyl)dihydrofuran‐2(3H)‐one (1), 5‐hydroxymethyl‐3‐(1,7‐dihydroxy‐6‐methyloctyl)dihydrofuran‐2(3H)‐one (2), and two known compounds; 5′‐methylthioinosine (3), and 5′‐methylthioinosine sulfoxide (4), which are isolated first time from any natural source, along with four known compounds (5–8). The structures of the new compounds were deduced by HR‐ESI‐MS, 1D and 2D NMR data, and in comparison with related compounds from the literature. Additionally, owing to the current COVID‐19 pandemic situation, we also computationally explored the therapeutic potential of our isolated compounds against SARS‐CoV‐2. Compound 4 showed the best binding energies of −6.2 and −6.6 kcal/mol for Mpro and spike proteins, respectively. The intermolecular interactions were also studied using 2‐D and...
ACS Omega, 2022
Two imine compounds named as (E)-2-(((3,4dichlorophenyl)imino)methyl)phenol (DC2H) and (E)-4-(((2... more Two imine compounds named as (E)-2-(((3,4dichlorophenyl)imino)methyl)phenol (DC2H) and (E)-4-(((2,4dimethylphenyl)imino)methyl)phenol (DM4H) are synthesized, and their crystal structures are verified using the single-crystal X-ray diffraction (XRD) technique. The crystal structures of the compounds are compared with the closely related crystal structures using the Cambridge Structural Database (CSD). The crystal packing in terms of intermolecular interactions is fully explored by Hirshfeld surface analysis. Void analysis is carried out for both compounds to check the strength of the crystal packing. Furthermore, a state-of-the-art dual computational technique consisting of quantum chemical and molecular docking methods is used to shed light on the molecular structure, optoelectronic properties, and bioactivity of indigenously synthesized compounds. The optimized molecular geometries are compared with their counterpart experimental values. Based on previous reports of biofunctions of the indigenously synthesized imine derivatives, they are explored for their potential inhibition properties against two very crucial proteins (main protease (M pro) and nonstructural protein 9 (NSP9)) of SARS-CoV-2. The calculated interaction energy values of DC2H and DM4H with M pro are found to be −6.3 and −6.6 kcal/mol, respectively, and for NSP9, the calculated interaction energy value is found to be −6.5 kcal/mol. We believe that the current combined study through experiments and computational techniques will not only pique the interest of the broad scientific community but also evoke interest in their further in vitro and in vivo investigations.
Journal of Nonlinear Optical Physics & Materials, 2020
In this study, density functional theory is used to examine the electronic and nonlinear optical ... more In this study, density functional theory is used to examine the electronic and nonlinear optical properties of a narrative class boron nitride (B[Formula: see text]N[Formula: see text]) doped with super alkali OLi3. From the computational investigations, these complexes are highly stable and superalkali prefer a cubic position of the nanocage energetically to be chemisorbed. When superalkali doped on B[Formula: see text]N[Formula: see text], a significant decrease in the HOMO–LUMO energy gap was observed and this shifted the B[Formula: see text]N[Formula: see text] nanocage from insulator to n-type semiconductor. The HOMO–LUMO energy gap of pure B[Formula: see text]N[Formula: see text] was 6.84[Formula: see text]eV and when superalkali (OLi3) is doped on it, the HOMO–LUMO energy gap was changed in the range of 3.94–0.42[Formula: see text]eV. BNM2b showed a HOMO–LUMO energy gap of 3.94[Formula: see text]eV, while BNM4a showed a minimum HOMO–LUMO energy gap (0.42[Formula: see text]eV)...