In-silico strategies for probing chloroquine based inhibitors against SARS-CoV-2

Understanding selective sensing of human serum albumin using a D-π-A probe: a photophysical and computational approach

The human serum albumin (HSA) level is a valuable indicator of an individual's health status. Therefore, its detection/estimation can be used to diagnose several diseases. In this work, we have developed a series of donor-π-acceptor probes, which were found to selectively detect HSA over BSA (bovine serum albumin). Among these probes, A4, which bears the trifluoroacetyl group, showed the highest selectivity for HSA, with limits of detection and quantification being 1.36 nM and 2.59 nM, respectively. CD spectroscopy of the HSA-A4 ensemble indicated an increase in the α-helicity of the protein, while the displacement assays revealed the localization of the probe in the hemin site of HSA. The probe works on the principle of excited state intramolecular charge transfer (ICT). Its selectivity was also validated computationally. Docking experiments confirmed the preference of the probe for the hemin binding IB site of HSA, as observed from the fluorescence displacement assay results, and a comparison of docking scores demonstrated the greater preference of A4 for HSA compared to BSA. Computational experiments also showed a change in preference for HSA amino acid residues exhibited by the excited state of probe A4 (Tyr161, Met123, Pro118, and Leu115) when compared to its ground state (Arg186 and His146). Hydrophobic interactions dominated the excited state protein-probe ensemble, whereas there was significant involvement of the water bridges along with the hydrophobic interactions in the ground state ensemble. Probe A4 was also assessed for its practical utility and found to successfully sense HSA in urine at extremely low concentrations. Moreover, the A4-HSA ensemble was employed for hemin sensing with a detection limit of 0.23 μM.

In silico design and ADMET evaluation of new inhibitors for PIM1 kinase using QSAR studies, molecular docking, and molecular dynamic simulation

The proviral Integration site of Moloney (PIM) kinase is highly expressed in various diseases, including cancer, making the development of selective inhibitors for this protein important. A series of PIM1 inhibitors, triazolo [4, 3-b] pyridazin-3-yl-quinoline derivatives, have been studied to design new inhibitors. The activity and structural features of these derivatives were investigated to understand their interactions with PIM1 using molecular docking, molecular dynamic simulation, and QSAR techniques. In a study of 30 compounds using the structure-activity technique and the MLR method, a linear model with R2 train = 0.91 and R2 test = 0.96 was obtained. The model utilized descriptors such as RDF080v, RDF105v, RDF135v, Mor03v, and H046 to express the structural characteristics of the inhibitors. To enhance the model, the SVR non-linear method with the RBF function was also used, resulting in an improved model with R2 train = 0.98 and R2 test = 0.98. Furthermore, the molecular docking technique was employed to investigate the interaction of compounds with high (compound 25) and low (compound 13) inhibitory activity. It was observed that the rings with nitrogen atoms interacted with the protein. The molecular binding results indicate that groups such as OMe and rings with Nitrogen can enhance the inhibitory activity of the compounds. Additionally, oxygen and nitrogen atoms contribute to an increased number of hydrogen bonds, thereby increasing the inhibitory activity of the compounds. Additionally, the stability and bonding modes of active and inactive compounds were studied using molecular dynamic simulation. Based on the results, four new inhibitors were designed, demonstrating better inhibition efficiency with the PIM1 kinase compared to the reference compounds. Moreover, the designed compounds underwent evaluation for ADMET, yielding promising results.

Unveiling promising phytocompounds from Moringa oleifera as dual inhibitors of EGFR(T790M/C797S) and VEGFR-2 in non-small cell lung cancer through in silico screening, ADMET, dynamics simulation, and DFT analysis

Non-small cell lung cancer (NSCLC) is among the main causes of mortality from cancer around the globe, affecting all genders. Current treatments mainly focus on tyrosine kinase inhibitors (TKIs) targeting the epidermal growth factor receptor (EGFR). However, resistance mechanisms, such as the emergence of T790M and C797S EGFR mutations and upregulation of VEGFR-2, often hinder the effectiveness of TKIs. Thereby, EGFR and VEGFR-2 present an intriguing opportunity for the treatment of NSCLC by developing dual-acting drugs. This research aims to evaluate prospective Moringa oleifera L. (MO)-originated compounds to efficiently block both of these receptors. In our research, we screened a library of 200 compounds sourced from MO, a plant known for its remarkable therapeutic potential. We identified five intriguing phytocompounds: hesperetin, gossypetin, quercetin, gallocatechin, and epigallocatechin, as potential anti-cancer agents. The compounds have demonstrated notable binding affinity in virtual screening and multi-stage molecular docking analysis, surpassing the controls, Erlotinib and Bevacizumab + Rituximab. In addition, these compounds demonstrate top-notch drug-likeness and ADMET properties. The five promising drug candidates also had a strong ability to bind to receptors and stayed stable with them during the 200 ns molecular dynamics (MD) simulation and MM-GBSA calculation. Furthermore, DFT analysis indicates that hesperetin, gossypetin, and quercetagetin stand out as the most promising drug candidates among all others. The findings of our study suggest that these three therapeutic candidates can precisely target both EGFR and VEGFR-2 and can potentially act on both of these pathways as a single agent.

In silico screening of a series of 1,6-disubstituted 1H-pyrazolo[3,4-d]pyrimidines as potential selective inhibitors of the Janus kinase 3

Rheumatoid arthritis is a common chronic disabling inflammatory disease that is characterized by inflammation of the synovial membrane and leads to discomfort. In the current study, twenty-seven 1,6-disubstituted 1H-pyrazolo[3,4-d]pyrimidines were tested as potential selective inhibitors of the tyrosine-protein kinase JAK3 using a number of molecular modeling methods. The activity of the screened derivatives was statistically quantified using multiple linear regression and artificial neural networks. To assess the quality, robustness, and predictability of the generated models, the leave-one-out cross-validation method was applied with favorable results (Q2 = 0.75) and Y-randomization. In addition, the evaluation of the predictive ability of the established model was confirmed by means of an external validation using a composite test set and an applicability domain approach. The covalent docking indicated that the tested 1H-pyrazolo[3,4-d]pyrimidines containing the acrylic aldehyde moiety had irreversible interaction with the residue Cys909 in the active sites of the tyrosine-protein kinase JAK3 by Michael addition. The molecular dynamics for three selected derivatives (compounds 9, 12, and 18) were used to verify the covalent docking by determining the stability of hydrogen bonding interactions with active sites, which are needed to stop tyrosine-protein kinase JAK3. The results obtained showed that the tested compounds containing acrylic aldehyde moiety had favorable binding free energies, indicating a strong affinity for the JAK3 enzyme. Overall, this current study suggests that the tested compounds containing the acrylic aldehyde moiety have the potential to act as anti-JAK3 inhibitors. They could be explored further to be used as treatment options for rheumatoid arthritis.Communicated by Ramaswamy H. Sarma.

Discovery of anti-colon cancer agents targeting wild-type and mutant p53 using computer-aided drug design

Mutations in the p53 gene are common and occur in over 50% of all cancers, as it is involved in DNA damage repair, cell cycle regulation and apoptosis. Moreover, the p53 gene is mutated in 70% of colon cancers. Therefore, the development of drugs to combat this mutation requires urgent attention. With this in mind, in silico drug design approaches were applied on quinoline derivatives with anticancer activity. In 3D-QSAR study, steric, electrostatic, hydrophobic and H-bond acceptor fields (SEHA) play an important role in prediction and design of new colon cancer compounds. Indeed, the two best CoMSIA/SEHA models with (Q2 = 0.737, R2 = 0.914, R pred 2 = 0.720) and (Q2 = 0.738, R2 = 0.919, R pred 2 = 0.739) show good prediction of human colon carcinoma HCT 116 (p53+/+) and (p53-/-) activities, respectively. Furthermore, the predictive ability and robustness of these models were tested by several validation methods. Molecular docking analyses reveal crucial interactions with the active sites of the p53 protein in both wild type and mutant. Based on these theoretical studies, we designed 10 new compounds with good anticancer activity potential, which were evaluated using ADMET properties. Molecular dynamics simulations were performed to confirm the detailed binding mode of the docking results. Finally, the MM-GBSA based on molecular dynamics simulation confirmed that the designed compounds were able to form stable hydrogen bonding interactions with the crucial residues, which are essential to overcome the p53 mutation in colon cancer.Communicated by Ramaswamy H. Sarma.

Synthesis, crystal structure, spectroscopic characterization, DFT calculations, Hirshfeld surface analysis, molecular docking, and molecular dynamics simulation investigations of novel pyrazolopyranopyrimidine derivatives

A series of new pyrazolopyranopyrimidine derivatives (3-9) were synthesized from 5-amino-2,4-dihydro-3-methyl-4-phenylpyrano-[2,3-c]pyrazole-5-carbonitrile (2) by multicomponent reactions (MCR) involving malononitrile, benzaldehyde, and pyrazolone under refluxing ethanol in the presence of piperidine. Compound (2) was then converted to 2-acetylpyrazolopyranopyrimidine (3) through a reaction with acetic anhydride. The deprotection of 3 using ammonium hydroxide in ethanol, leads to 4. Subsequent chlorination of 4 by phosphorus oxychloride affords 5 which was alkylated using methyl iodide and ethyl bromoacetate in DMF, leading to regioisomers 6-9. The products were characterized by spectroscopic techniques (1H and 13C NMR) and confirmed by single crystal X-ray diffraction (XRD) studies for 2, 5, 6, and 9. Moreover, the geometrical parameters, molecular orbital calculations, and spectral data of 2, 5, 6, and 9 were compared by DFT at the B3LYP/6-311G(d,p) level of theory. There is good agreement between the calculated results and the experimental data. The intermolecular contacts for 2, 5, 6, and 9 were studied by Hirshfeld surface analysis. In addition, the molecular docky study was conducted to investigate the binding patterns of 2, 5, 6, and 9 within the binding site of cyclin-dependent kinase 2 (CDK2) and penicillin-binding protein 1 A. After the docking process, molecular dynamics (MD) simulations for 100 ns were performed on CDK2 and PBP 1 A proteins in the complex with 5.Communicated by Ramaswamy H. Sarma.

Threat of respiratory syncytial virus infection knocking the door: a proposed potential drug candidate through molecular dynamics simulations, a future alternative

The discovery of antiviral approaches to prevent or cure respiratory syncytial virus (RSV) infections is critical, particularly because RSV is one of the most common causes of infant respiratory problems. There is currently no approved vaccination available to treat RSV infections. FDA has approved the drug ribavirin, but it is not sufficient to treat RSV. This work aimed to find and study in silico anti-RSV drugs that target matrix protein and nucleoprotein. In this study, we have identified five drug candidates that had better binding energies than ribavirin. Garenoxacin appeared as top lead compounds between them. AutoDock Vina was used to execute molecular docking of a library of chosen chemicals. The high-score compound was then confirmed using the Maestro 12.3 module's molecular dynamics simulation and the binding energies derived using Prime/Molecular Mechanics Generalized Born Surface Area (Prime/MM-GBSA). Comparative molecular dynamics simulations revealed that garenoxacin has better stability and high residue contacts with high binding affinity than ribavirin. This study showed garenoxacin could prevent RSV infection better than ribavirin. In pursuing a more effective RSV control drug, additional research into these chemicals in vitro and in vivo is essential.

Phytochemical rich Himalayan Rhododendron arboreum petals inhibit SARS-CoV-2 infection in vitro

Phytochemicals with potential to competitively bind to the host receptors or inhibit SARS-CoV-2 replication, may prove to be useful as adjunct therapeutics for COVID-19. We profiled and investigated the phytochemicals of Rhododendron arboreum petals sourced from Himalayan flora, undertook in vitro studies and found it as a promising candidate against SARS-CoV-2. The phytochemicals were reported in various scientific investigations to act against a range of virus in vitro and in vivo, which prompted us to test against SARS-CoV-2. In vitro assays of R. arboreum petals hot aqueous extract confirmed dose dependent reduction in SARS-CoV-2 viral load in infected Vero E6 cells (80% inhibition at 1 mg/ml; IC50 = 173 µg/ml) and phytochemicals profiled were subjected to molecular docking studies against SARS CoV-2 target proteins. The molecules 5-O-Feruloyl-quinic acid, 3-Caffeoyl-quinic acid, 5-O-Coumaroyl-D-quinic acid, Epicatechin and Catechin showed promising binding affinity with SARS-CoV-2 Main protease (M^Pro; PDB ID: 6LU7; responsible for viral replication) and Human Angiotensin Converting Enzyme-2 (ACE2; PDB ID: 1R4L; mediate viral entry in the host). Molecular dynamics (MD) simulation of 5-O-Feruloyl-quinic acid, an abundant molecule in the extract complexed with the target proteins showed stable interactions. Taken together, the phytochemical profiling, in silico analysis and in vitro anti-viral assay revealed that the petals extract act upon M^Pro and may be inhibiting SARS-CoV-2 replication. This is the first report highlighting R. arboreum petals as a reservoir of antiviral phytochemicals with potential anti-SARS-CoV-2 activity using an in vitro system.

Discovery of potential FGFR3 inhibitors via QSAR, pharmacophore modeling, virtual screening and molecular docking studies against bladder cancer

BACKGROUND

Fibroblast growth factor receptor 3 is known as a favorable aim in vast range of cancers, particularly in bladder cancer treatment. Pharmacophore and QSAR modeling approaches are broadly utilized for developing novel compounds for the determination of inhibitory activity versus the biological target. In this study, these methods employed to identify FGFR3 potential inhibitors.

METHODS

To find the potential compounds for bladder cancer targeting, ZINC and NCI databases were screened. Pharmacophore and QSAR modeling of FGFR3 inhibitors were utilized for dataset screening. Then, with regard to several factors such as Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties and Lipinski's Rule of Five, the recognized compounds were filtered. In further step, utilizing the flexible docking technique, the obtained compounds interactions with FGFR3 were analyzed.

RESULTS

The best five compounds, namely ZINC09045651, ZINC08433190, ZINC00702764, ZINC00710252 and ZINC00668789 were selected for Molecular Dynamics (MD) studies. Off-targeting of screened compounds was also investigated through CDD search and molecular docking. MD outcomes confirmed docking investigations and revealed that five selected compounds could make steady interactions with the FGFR3 and might have effective inhibitory potencies on FGFR3.

CONCLUSION

These compounds can be considered as candidates for bladder cancer therapy with improved therapeutic properties and less adverse effects.

Strategic analyses to identify key structural features of antiviral/antimalarial compounds for their binding interactions with 3CLpro, PLpro and RdRp of SARS-CoV-2: in silico molecular docking and dynamic simulation studies

Severe acute respiratory syndrome coronavirus (SARS-CoV-2), a novel member of the betacoronavirus family is a single-stranded RNA virus that has spread worldwide prompting the World Health Organization to declare a global pandemic. This creates an alarming situation and generates an urgent need to develop innovative therapeutic agents. In this context, an in silico molecular docking and molecular dynamics (MD) simulation study on the existing 58 antiviral and antimalarial compounds was performed on 3CLpro, PLpro and RdRp SARS-CoV-2 proteins. The antiviral compounds are best fitted in the binding pockets and interact more profoundly with the amino acid residues compared to antimalarial compounds. An HIV protease inhibitor, saquinavir showed a good dock score and binding free energy with varied binding interactions against 3CLpro and PLpro. While, adefovir, a nucleotide HBV DNA polymerase inhibitor exhibited good dock score and binding interactions against RdRp. Although, the antimalarial compounds showed relatively less dock score but were found to be crucial in displaying essential binding interactions with these proteins. The MD simulation runs for 100 ns on 3CLpro-saquinavir, PLpro-saquinavir and RdRp-adefovir complexes using Desmond revealed fairly stable nature of interactions. This study helped in understanding the key interactions of the vital functionalities that provide a concrete base to develop lead molecules effective against SARS-CoV-2.

Ebselen suitably interacts with the potential SARS-CoV-2 targets: an in-silico approach

Ebselen (SPI-1005) is an active selenoorganic compound that can be found potential inhibitory activity against different types of viral infections such as zika virus, influenza A virus, HCV, and HIV-1; and also be found to exhibit promising antiviral activity against SARS-CoV-2 in cell-based assays but its particular target action against specific non-structural and structural proteins of SARS-CoV-2 is unclear to date. The purpose of this study is to evaluate the anti-SARS-CoV-2 efficacy of Ebselen along with the determination of the specific target among the 12 most common target proteins of SARS-CoV-2. AutoDock Vina in PyRx platform was used for docking analysis against the 12 selected SARS-CoV-2 encoded drug targets. ADME profiling was examined by using SwissADME online server. The stability of binding mode in the target active sites was evaluated using molecular dynamics (MD) simulation studies through NAMD and Desmond package software application. In this docking study, we recognized that Ebselen possesses the highest affinity to N protein (C domain) (PDB ID: 6YUN) and PLpro (PDB ID: 6WUU) among the selected SARS-CoV-2 targets showing -7.4 kcal/mol binding energy. The stability of Ebselen-6YUN and Ebselen-6WUU was determined by a 100 ns trajectory of all-atom molecular dynamics simulation. Structural conformation of these two complexes displayed stable root mean square deviation (RMSD), while root mean square fluctuations (RMSF) were also found to be consistent. This molecular docking study may propose the efficiency of Ebselen against SARS-CoV-2 to a significant extent which makes it a candidature of COVID-19 treatment.

In Vitro, In Silico and Network Pharmacology Mechanistic Approach to Investigate the α-Glucosidase Inhibitors Identified by Q-ToF-LCMS from Phaleria macrocarpa Fruit Subcritical CO2 Extract

The fruit of Phaleria macrocarpa have been traditionally used as an antidiabetic remedy in Malaysia and neighbouring countries. Despite its potential for diabetes treatment, no scientific study has ever been conducted to predict the inhibitor interaction of the protein α-glucosidase identified in an extract prepared with a non-conventional extraction technique. Hence, the major aim of this research was to evaluate the in vitro antioxidant, the α-glucosidase inhibitors, and the molecular dynamic simulations of the α-glucosidase inhibitors identified by Quadrupole Time-of-Flight Liquid Chromatography Mass Spectrometry (Q-ToF-LCMS) analysis. Initially, dry fruit were processed using non-conventional and conventional extraction methods to obtain subcritical carbon dioxide extracts (SCE-1 and SCE-2) and heating under reflux extract (HRE), respectively. Subsequently, all extracts were evaluated for their in vitro antioxidative and α-glucosidase inhibitory potentials. Subsequently, the most bioactive extract (SCE-2) was subjected to Q-ToF-LCMS analysis to confirm the presence of α-glucosidase inhibitors, which were then analysed through molecular dynamic simulations and network pharmacology approaches to confirm their possible mechanism of action. The highest inhibitory effects of the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and α-glucosidase on SCE-2 was found as 75.36 ± 0.82% and 81.79 ± 0.82%, respectively, compared to the SCE-1 and HRE samples. The Q-ToF-LCMS analysis tentatively identified 14 potent α-glucosidase inhibitors. Finally, five identified compounds, viz., lupenone, swertianolin, m-coumaric acid, pantothenic acid, and 8-C-glucopyranosyleriodictylol displayed significant stability, compactness, stronger protein-ligand interaction up to 100 ns further confirming their potential as α-glucosidase inhibitors. Consequently, it was concluded that the SCE-2 possesses a strong α-glucosidase inhibitory effect due to the presence of these compounds. The findings of this study might prove useful to develop these compounds as alternative safe α-glucosidase inhibitors to manage diabetes more effectively.

Evaluation of flavonoids as potential inhibitors of the SARS-CoV-2 main protease and spike RBD: Molecular docking, ADMET evaluation and molecular dynamics simulations

The 3CLpro main protease and the RDB spike (s) protein of SARS-CoV-2 are critical targets in the treatment of coronavirus 19 disease (COVID-19), as they are responsible for the COVID-19 replication and infection. With this in mind, Molecular docking of 26 natural compounds belonging to the flavonoid family with the 3CLpro and RBD sites of SARS-CoV-2 has been performed. The docking results revealed that the ligands Silibinin, Tomentin A, Tomentin B, 4′-O-methyldiplacone, Hesperidin Amentoflavone and Bilobetin act as a potential inhibitor of SARS-CoV-2 3CLpro, and that the ligands Herbacetin, Morin, Silibinin, Tomentin E, Amentoflavone, Bilobetin, Baicalein and Quercetin can be potential inhibitors of SARS-CoV-2 RBD. It has been noticed that three ligands can inhibit both sites of SARS-CoV-2, indicating a great potential of these compounds to combat COVID-19. Moreover, molecular docking has been validated by a new validation method based on visual inspiration. Evaluation of ADMET pharmacokinetic properties and the drug likeness in silico revealed that six compounds could be effective drugs against COVID-19. Finally, the docking results were verified by molecular dynamics simulations and MM-GBSA calculation to confirm the stability of hydrogen bonding interactions with crucial residues, which are essential to overcome SARS-CoV-2. These results could direct researchers toward plant-derived compounds that could be further investigated as therapeutic targets against COVID-19 replication and infection.

Deep learning-based molecular dynamics simulation for structure-based drug design against SARS-CoV-2

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), has led to a global pandemic. Deep learning (DL) technology and molecular dynamics (MD) simulation are two mainstream computational approaches to investigate the geometric, chemical and structural features of protein and guide the relevant drug design. Despite a large amount of research papers focusing on drug design for SARS-COV-2 using DL architectures, it remains unclear how the binding energy of the protein-protein/ligand complex dynamically evolves which is also vital for drug development. In addition, traditional deep neural networks usually have obvious deficiencies in predicting the interaction sites as protein conformation changes. In this review, we introduce the latest progresses of the DL and DL-based MD simulation approaches in structure-based drug design (SBDD) for SARS-CoV-2 which could address the problems of protein structure and binding prediction, drug virtual screening, molecular docking and complex evolution. Furthermore, the current challenges and future directions of DL-based MD simulation for SBDD are also discussed.

Developing New Treatments for COVID-19 through Dual-Action Antiviral/Anti-Inflammatory Small Molecules and Physiologically Based Pharmacokinetic Modeling

Broad-spectrum antiviral agents that are effective against many viruses are difficult to develop, as the key molecules, as well as the biochemical pathways by which they cause infection, differ largely from one virus to another. This was more strongly highlighted by the COVID-19 pandemic, which found health systems all over the world largely unprepared and proved that the existing armamentarium of antiviral agents is not sufficient to address viral threats with pandemic potential. The clinical protocols for the treatment of COVID-19 are currently based on the use of inhibitors of the inflammatory cascade (dexamethasone, baricitinib), or inhibitors of the cytopathic effect of the virus (monoclonal antibodies, molnupiravir or nirmatrelvir/ritonavir), using different agents. There is a critical need for an expanded armamentarium of orally bioavailable small-molecular medicinal agents, including those that possess dual antiviral and anti-inflammatory (AAI) activity that would be readily available for the early treatment of mild to moderate COVID-19 in high-risk patients. A multidisciplinary approach that involves the use of in silico screening tools to identify potential drug targets of an emerging pathogen, as well as in vitro and in vivo models for the determination of a candidate drug’s efficacy and safety, are necessary for the rapid and successful development of antiviral agents with potentially dual AAI activity. Characterization of candidate AAI molecules with physiologically based pharmacokinetics (PBPK) modeling would provide critical data for the accurate dosing of new therapeutic agents against COVID-19. This review analyzes the dual mechanisms of AAI agents with potential anti-SARS-CoV-2 activity and discusses the principles of PBPK modeling as a conceptual guide to develop new pharmacological modalities for the treatment of COVID-19.

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.

Therapeutic role of traditionally used Indian medicinal plants and spices in combating COVID-19 pandemic situation

The coronavirus disease (COVID-19) caused by SARS-CoV-2 is a big challenge and burning issue to the scientific community and doctors worldwide. Globally, COVID-19 has created a health disaster and adversely affects the economic growth. Although some vaccines have already emerged, no therapeutic medication has yet been approved by FDA for the treatment of COVID-19 patients. Traditionally, we have been using different medicinal plants like neem, tulsi, tea, and many spices like garlic, ginger, turmeric, black seed, onion, etc. for the treatment of flu-like diseases. In this paper, we are highlighting the recent research progress in the identification of natural products from the Indian medicinal plants and spices that have potential inhibition properties against SARS-CoV-2. This study will provide an initiative to stimulate further research by providing useful guidance to the medicinal chemists for designing new protease inhibitors effective against SARS-CoV-2 in future.

Point-specific interactions of isovitexin with the neighboring amino acid residues of the hACE2 receptor as a targeted therapeutic agent in suppressing the SARS-CoV-2 influx mechanism

Objective:

Despite the development of several vaccines against severe acute respiratory syndrome coronavirus-2, the need for an additional prophylactic agent is evident. In recent in silico studies, isovitexin exhibited a higher binding affinity against the human angiotensin converting-enzyme 2 (hACE2) receptor than existing antiviral drugs. The research aimed to find out the point specificity of isovitexin for the hACE2 receptor and to assess its therapeutic potential, depending on the stability of the isovitexin–hACE2 complex.

Materials and Methods:

The pharmacokinetic profile of isovitexin was analyzed. The crystal structure of the hACE2 receptor and the ligand isovitexin were docked to form a ligand–protein complex following molecular optimization. To determine the isovitexin–hACE2 complex stability, their binding affinity, hydrogen bonding, and hydrophobic interactions were studied. Lastly, the root mean square deviation (RMSD), root mean square fluctuation, solvent accessible surface area, molecular surface area, radius of gyration (Rg), polar surface area, and principal component analysis values were found by simulating the complex with molecular dynamic (MD).

Results:

The predicted Lethal dose₅₀ for isovitexin was 2.56 mol/kg, with an acceptable maximum tolerated dose and no hepatotoxicity or AMES toxicity. Interactions with the amino acid residues Thr371, Asp367, Glu406, Pro346, His345, Phe274, Tyr515, Glu375, Thr347, Glu402, and His374 of the hACE2 protein were required for the high binding affinity and specificity of isovitexin. Based on what was learned from the MD simulation, the hACE2 receptor-blocking properties of isovitexin were looked at.

Conclusions:

Isovitexin is a phytochemical with a reasonable bioactivity and safety profile for use in humans, and it can potentially be used as a hACE2-specific therapeutic to inhibit COVID-19 infection.

Active site-specific quantum tunneling of hACE2 receptor to assess its complexing poses with selective bioactive compounds in co-suppressing SARS-CoV-2 influx and subsequent cardiac injury

Objective:

This research aims to study the target specificity of selective bioactive compounds in complexing with the human angiotensin-converting enzyme (hACE2) receptor to impede the severe acute respiratory syndrome coronavirus 2 influx mechanism resulting in cardiac injury and depending on the receptor’s active site properties and quantum tunneling.

Materials and Methods:

A library of 120 phytochemical ligands was prepared, from which 5 were selected considering their absorption, distribution, metabolism, and excretion (ADMET) and quantitative structure–activity relationship (QSAR) profiles. The protein active sites and belonging quantum tunnels were defined to conduct supramolecular docking of the aforementioned ligands. The hydrogen bond formation and hydrophobic interactions between the ligand–receptor complexes were studied following the molecular docking steps. A comprehensive molecular dynamic simulation (MDS) was conducted for each of the ligand–receptor complexes to figure out the values – root mean square deviation (RMSD) (Å), root mean square fluctuation (RMSF) (Å), H-bonds, Cα, solvent accessible surface area (SASA) (Ų), molecular surface area (MolSA) (Ų), Rg (nm), and polar surface area (PSA) (Å). Finally, computational programming and algorithms were used to interpret the dynamic simulation outputs into their graphical quantitative forms.

Results:

ADMET and QSAR profiles revealed that the most active candidates from the library to be used were apigenin, isovitexin, piperolactam A, and quercetin as test ligands, whereas serpentine as the control. Based on the binding affinities of supramolecular docking and the parameters of molecular dynamic simulation, the strength of the test ligands can be classified as isovitexin > quercetin > piperolactam A > apigenin when complexed with the hACE2 receptor. Surprisingly, serpentine showed lower affinity (−8.6 kcal/mol) than that of isovitexin (−9.9 kcal/mol) and quercetin (−8.9 kcal/mol). The MDS analysis revealed all ligands except isovitexin having a value lower than 2.5 Ǻ. All the test ligands exhibited acceptable fluctuation ranges of RMSD (Å), RMSF (Å), H-bonds, Cα, SASA (Ų), MolSA (Ų), Rg (nm), and PSA (Å) values.

Conclusion:

Considering each of the parameters of molecular optimization, docking, and dynamic simulation interventions, all of the test ligands can be suggested as potential targeted drugs in blocking the hACE2 receptor.

DK, Ragunathan V, Tiwari P, A. S, P BD. Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease

The study aims to evaluate the potency of two hundred natural antiviral phytocompounds against the active site of the Severe Acquired Respiratory Syndrome - Coronavirus - 2 (SARS-CoV-2) Main-Protease (Mpro) using AutoDock 4.2.6. The three- dimensional crystal structure of the Mpro (PDB Id: 6LU7) was retrieved from the Protein Data Bank (PDB), the active site was predicted using MetaPocket 2.0. Food and Drug Administration (FDA) approved viral protease inhibitors were used as standards for comparison of results. The compounds theaflavin-3-3'-digallate, rutin, hypericin, robustaflavone, and (-)-solenolide A with respective binding energy of -12.41 (Ki = 794.96 pM); -11.33 (Ki = 4.98 nM); -11.17 (Ki = 6.54 nM); -10.92 (Ki = 9.85 nM); and -10.82 kcal/mol (Ki = 11.88 nM) were ranked top as Coronavirus Disease - 2019 (COVID-19) Mpro inhibitors. The interacting amino acid residues were visualized using Discovery Studio 3.5 to elucidate the 2-dimensional and 3-dimensional interactions. The study was validated by i) re-docking the N3-peptide inhibitor-Mpro and superimposing them onto co-crystallized complex and ii) docking decoy ligands to Mpro. The ligands that showed low binding energy were further predicted for and pharmacokinetic properties and Lipinski's rule of 5 and the results are tabulated and discussed. Molecular dynamics simulations were performed for 50 ns for those compounds using the Desmond package, Schrödinger to assess the conformational stability and fluctuations of protein-ligand complexes during the simulation. Thus, the natural compounds could act as a lead for the COVID-19 regimen after in-vitro and in- vivo clinical trials.Communicated by Ramaswamy H. Sarma.

Newly Identified COVID-19 Drug Candidates Based on Computational Strategies

The COVID-19 has raised a public health catastrophe in early 2020 worldwide. Despite several approved vaccines that have repressed the pandemic and decreased the mortality rate since then, attempts to discover an effective antiviral drug have not indicated reliable results. In this research, in silico studies (virtual screening and molecular docking) were performed based on quinoline structure to identify novel drug candidates against SARS-CoV-2 before laboratory evaluations. A chemical library consisting of 548 compounds was collected from literature mining of five databases to select the best ligands interacting with three target proteins of SARS-CoV-2, including the main protease, spike protein, and chimeric receptor-binding domain in a complex of human angiotensin-converting enzyme 2. The top five compounds that presented suitable binding energy against each target protein are reported in detail for the first time. Notably, new compound N-4-(6-methyl-3-pyridinyl) phenyl)-9-acridinamine showed high affinity to all selected proteins. These identified compounds will help in speeding up the drug development against COVID-19.

Current status and strategic possibilities on potential use of combinational drug therapy against COVID-19 caused by SARS-CoV-2

The spread of new coronavirus infection starting December 2019 as novel SARS-CoV-2, identified as the causing agent of COVID-19, has affected all over the world and been declared as pandemic. Approximately, more than 8,807,398 confirmed cases of COVID-19 infection and 464,483 deaths have been reported globally till the end of 21 June 2020. Until now, there is no specific drug therapy or vaccine available for the treatment of COVID-19. However, some potential antimalarial drugs like hydroxychloroquine and azithromycin, antifilarial drug ivermectin and antiviral drugs have been tested by many research groups worldwide for their possible effect against the COVID-19. Hydroxychloroquine and ivermectin have been identified to act by creating the acidic condition in cells and inhibiting the importin (IMPα/β1) mediated viral import. There is a possibility that some other antimalarial drugs/antibiotics in combination with immunomodulators may help in combatting this pandemic disease. Therefore, this review focuses on the current use of various drugs as single agents (hydroxychloroquine, ivermectin, azithromycin, favipiravir, remdesivir, umifenovir, teicoplanin, nitazoxanide, doxycycline, and dexamethasone) or in combinations with immunomodulators additionally. Furthermore, possible mode of action, efficacy and current stage of clinical trials of various drug combinations against COVID-19 disease has also been discussed in detail.Communicated by Ramaswamy H. Sarma.

Inhibitory activity of FDA-approved drugs cetilistat, abiraterone, diiodohydroxyquinoline, bexarotene, remdesivir, and hydroxychloroquine on COVID-19 main protease and human ACE2 receptor: A comparative in silico approach

By September 1, 2021, SARS-CoV-2, a respiratory virus that prompted Coronavirus Disease in 2019, had infected approximately 218,567,442 patients and claimed 4,534,151 lives. There are currently no specific treatments available for this lethal virus, although several drugs, including remdesivir and hydroxychloroquine, have been tested. The purpose of this study is to assess the activity of FDA-approved drugs cetilistat, abiraterone, diiodohydroxyquinoline, bexarotene, remdesivir, and hydroxychloroquine as potential SARS-CoV-2 main protease inhibitors. Additionally, this study aims to provide insight into the development of potential inhibitors that may inhibit ACE2, thereby preventing SARS-CoV-2 entry into the host cell and infection. To this end, remdesivir and hydroxychloroquine were used as comparator drugs. The calculations revealed that cetilistat, abiraterone, diiodohydroxyquinoline, and bexarotene inhibit main protease and ACE2 receptors more effectively than the well-known drug hydroxychloroquine when used against COVID-19. Meanwhile, bexarotene and cetilistat bind more tightly to the SARS-CoV-2 main protease and the ACE2 receptor, respectively, than remdesivir, a potential treatment for COVID-19 that is the first FDA-approved drug against this virus. As a result, the molecular dynamic simulations of these two drugs in the presence of proteins were investigated. The MD simulation results demonstrated that these drugs interact to stabilize the systems, allowing them to be used as effective inhibitors of these proteins. Meanwhile, bexarotene, abiraterone, cetilistat, and diiodohydroxyquinoline's systemic effects should be further investigated in suitable ex vivo human organ culture or organoids, animal models, or clinical trials.

Synthesis, X-ray crystal structure, IR and Raman spectroscopic analysis, quantum chemical computational and molecular docking studies on hydrazone-pyridine compound: As an insight into the inhibitor capacity of main protease of SARS-CoV2

The characterization and synthesis of 3-chloro-2-{(2E)-2-[1-(4-chlorophenyl)ethylidene]hydrazinyl}pyridine (CCPEHP) was investigated in our study. Mass and UV-visible spectra were recorded in chloroform solvent. The CCPEHP molecule containing pyridine and chlorophenyl rings and hydrazone group crystallized in the triclinic system and P-1 space group. FTRaman and FTIR spectra were performed in the solid state. The optimized geometry of CCPEHP was computed by DFT/B3LYP method with 6-311 G (d, p) and 6-31 G (d, p) levels. The computed vibrational analysis, electronic absorption spectrum, electronic properties, molecular electrostatic potential, natural bond orbitals analysis and other calculated structural parameters were determined by using the DFT/B3LYP/6-31 G (d, p) basis set. The correlation of fundamental modes of the compound and the complete vibrational assignments analysis were studied. The strong and weak contacts were identified by using Hirshfeld surface analysis. The molecular modeling results showed that CCPEHP structure strongly binds to COVID-19 main protease by relative binding affinity of -6.4 kcal/mol.

Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CLpro)

The COVID-19 pandemic has been responsible for several deaths worldwide. The causative agent behind this disease is the Severe Acute Respiratory Syndrome - novel Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 belongs to the category of RNA viruses. The main protease, responsible for the cleavage of the viral polyprotein is considered as one of the hot targets for treating COVID-19. Earlier reports suggest the use of HIV anti-viral drugs for targeting the main protease of SARS-CoV, which caused SARS in the year 2002-2003. Hence, drug repurposing approach may prove to be useful in targeting the main protease of SARS-CoV-2. The high-resolution crystal structure of the main protease of SARS-CoV-2 (PDB ID: 6LU7) was used as the target. The Food and Drug Administration approved and SWEETLEAD database of drug molecules were screened. The apo form of the main protease was simulated for a cumulative of 150 ns and 10 μs open-source simulation data was used, to obtain conformations for ensemble docking. The representative structures for docking were selected using RMSD-based clustering and Markov State Modeling analysis. This ensemble docking approach for the main protease helped in exploring the conformational variation in the drug-binding site of the main protease leading to the efficient binding of more relevant drug molecules. The drugs obtained as top hits from the ensemble docking possessed anti-bacterial and anti-viral properties. This in silico ensemble docking approach would support the identification of potential candidates for repurposing against COVID-19.Communicated by Ramaswamy H. Sarma.

Immunobiology and nanotherapeutics of severe acute respiratory syndrome 2 (SARS-CoV-2): a current update

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) constitutes the most significant global public health challenge in a century. It has reignited research interest in coronavirus. While little information is available, research is currently in progress to comprehensively understand the general biology and immune response mechanism against SARS-CoV-2. The spike proteins (S protein) of SARS-CoV-2 perform a crucial function in viral infection establishment. ACE2 and TMPRSS2 play a pivotal role in viral entry. Upon viral entry, the released pro-inflammatory proteins (cytokines and chemokines) cause the migration of the T cells, monocytes, and macrophages to the infection site. IFNϒ released by T cells initiates a loop of pro-inflammatory feedback. The inflammatory state may further enhance with an increase in immune dysfunction responsible for the infection's progression. A treatment approach that prevents ACE2-mediated viral entry and reduces inflammatory response is a crucial therapeutic intervention strategy, and nanomaterials and their conjugates are promising candidates. Nanoparticles can inhibit viral entry and replication. Nanomaterials have also found application in targeted drug delivery and also in developing a vaccine against SARS-CoV-2. Here, we briefly summarize the origin, transmission, and clinical features of SARS-CoV-2. We then discussed the immune response mechanisms of SARS-CoV-2. Finally, we further discussed nanotechnology's potentials as an intervention strategy against SARS-CoV-2 infection. All these understandings will be crucial in developing therapeutic strategies against SARS-CoV-2.

Promising inhibitors of main protease of novel corona virus to prevent the spread of COVID-19 using docking and molecular dynamics simulation

Coronavirus disease-2019 (COVID-19) is a global health emergency and the matter of serious concern, which has been declared a pandemic by WHO. Till date, no potential medicine/ drug is available to cure the infected persons from SARS-CoV-2. This deadly virus is named as novel 2019-nCoV coronavirus and caused coronavirus disease, that is, COVID-19. The first case of SARS-CoV-2 infection in human was confirmed in the Wuhan city of the China. COVID-19 is an infectious disease and spread from man to man as well as surface to man . In the present work, in silico approach was followed to find potential molecule to control this infection. Authors have screened more than one million molecules available in the ZINC database and taken the best two compounds based on binding energy score. These lead molecules were further studied through docking against the main protease of SARS-CoV-2. Then, molecular dynamics simulations of the main protease with and without screened compounds were performed at room temperature to determine the thermodynamic parameters to understand the inhibition. Further, molecular dynamics simulations at different temperatures were performed to understand the efficiency of the inhibition of the main protease in the presence of the screened compounds. Change in energy for the formation of the complexes between the main protease of novel coronavirus and ZINC20601870 as well ZINC00793735 at room temperature was determined on applying MM-GBSA calculations. Docking and molecular dynamics simulations showed their antiviral potential and may inhibit viral replication experimentally. Communicated by Ramaswamy H. Sarma.

An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19

The recent outbreak of the deadly coronavirus disease 19 (COVID-19) pandemic poses serious health concerns around the world. The lack of approved drugs or vaccines continues to be a challenge and further necessitates the discovery of new therapeutic molecules. Computer-aided drug design has helped to expedite the drug discovery and development process by minimizing the cost and time. In this review article, we highlight two important categories of computer-aided drug design (CADD), viz., the ligand-based as well as structured-based drug discovery. Various molecular modeling techniques involved in structure-based drug design are molecular docking and molecular dynamic simulation, whereas ligand-based drug design includes pharmacophore modeling, quantitative structure-activity relationship (QSARs), and artificial intelligence (AI). We have briefly discussed the significance of computer-aided drug design in the context of COVID-19 and how the researchers continue to rely on these computational techniques in the rapid identification of promising drug candidate molecules against various drug targets implicated in the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The structural elucidation of pharmacological drug targets and the discovery of preclinical drug candidate molecules have accelerated both structure-based as well as ligand-based drug design. This review article will help the clinicians and researchers to exploit the immense potential of computer-aided drug design in designing and identification of drug molecules and thereby helping in the management of fatal disease.

In silico inquest reveals the efficacy of Cannabis in the treatment of post-Covid-19 related neurodegeneration

Coronavirus (SARS-CoV-2), the causative agent of the Covid-19 pandemic has proved itself as the deadliest pathogen. A major portion of the population has become susceptible to this strain. Scientists are pushing their limits to formulate a vaccine against Covid-19 with the least side effects. Although the recent discoveries of vaccines have shown some relief from the covid infection rate, however, physical fatigue, mental abnormalities, inflammation and other multiple organ damages are arising as post-Covid symptoms. The long-term effects of these symptoms are massive. Patients with such symptoms are known as long-haulers and treatment strategy against this condition is still unknown. In this study, we tried to explore a strategy to deal with the post-Covid symptoms. We targeted three human proteins namely ACE2, Interleukin-6, Transmembrane serine protease and NRP1 which are already reported to be damaged via Covid-19 proteins and upregulated in the post-Covid stage. Our target plant in this study is Cannabis (popularly known as 'Ganja' in India). The molecular docking and simulation studies revealed that Cannabidiol (CBD) and Cannabivarin (CVN) obtained from Cannabis can bind to post-Covid symptoms related central nervous system (CNS) proteins and downregulate them which can be beneficial in post-covid symptoms treatment strategy. Thus we propose Cannabis as an important therapeutic plant against post-Covid symptoms.Communicated by Ramaswamy H. Sarma.

The situation of small molecules targeting key proteins to combat SARS-CoV-2: Synthesis, metabolic pathway, mechanism of action, and potential therapeutic applications

Due to the global epidemic and high mortality of 2019 coronavirus disease (COVID-19), there is an immediate need to discover drugs that can help before a vaccine becomes available. Given that the process of producing new drugs is so long, the strategy of repurposing existing drugs is one of the promising options for the urgent treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19 disease. Although FDA has approved Remdesivir for the use in hospitalized adults and pediatric patients suffering from COVID-19, no fully effective and reliable drug has been yet identified worldwide to treat COVID-19 specifically. Thus, scientists are still trying to find antivirals specific to COVID-19. This work reviews the chemical structure, metabolic pathway, mechanism of action of existing drugs with potential therapeutic applications for COVID-19. Further, we summarized the molecular docking stimulation of the medications related to key protein targets. These already drugs could be developed for further clinical trials to supply suitable therapeutic options for patients suffering from COVID-19.

Exploring potential inhibitor of SARS-CoV2 replicase from FDA approved drugs using insilico drug discovery methods

Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV2) is responsible for fetal pneumonia called COVID19. SARS-CoV2 emerged in Wuhan, Hubei Province of China in December 2019. The COVID19 pandemic has now gripped the entire world with more than 70 million cases and over 1.5 million deaths so far. There no treatment option for COVID19 is in term of a drug or vaccine is currently available. Therefore drug repurposing may only provide a quick method for utilizing existing drugs for a therapeutic option. The virus genome contains several non-structural proteins (NSP) which serve as target for designing of antiviral agents. NSP9 of SARS-CoV2 encodes for a replicase enzyme which is essential for the virus replication in the host cell. In search of potent inhibitors, we have screened FDA approved drugs against NSP9 using in silico methods. Five drugs fluspirilene, troglitazone, alvesco, dihydroergotoxine and avodart were found to have highest affinities with the replicase. The molecular dynamics simulation (MDS) studies demonstrated strong drugs binding and stable NSP9-drugs complexes formation. The findings are also strongly supported by root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and hydrogen bond analysis of the complexes. Principal component analysis showed the stable conformation of NSP9 upon drug binding. It could be inferred that these five drugs individually or in combinations may be used as potential inhibitors of NSP9 of SARS-CoV-2 after exploring their in vivo antiviral potential.Communicated by Ramaswamy H. Sarma.

Identification of a repurposed drug as an inhibitor of Spike protein of human coronavirus SARS-CoV-2 by computational methods

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is an emerging new viral pathogen that causes severe respiratory disease. SARS-CoV-2 is responsible for the outbreak of COVID-19 pandemic worldwide. As there are no confirmed antiviral drugs or vaccines currently available for the treatment of COVID-19, discovering potent inhibitors or vaccines are urgently required for the benefit of humanity. The glycosylated Spike protein (S-protein) directly interacts with human angiotensin-converting enzyme 2 (ACE2) receptor through the receptor-binding domain (RBD) of S-protein. As the S-protein is exposed to the surface and is essential for entry into the host, the S-protein can be considered as a first-line therapeutic target for antiviral therapy and vaccine development. In silico screening, docking, and molecular dynamics simulation studies were performed to identify repurposing drugs using DrugBank and PubChem library against the RBD of S-protein. The study identified a laxative drug, Bisoxatin (DB09219), which is used for the treatment of constipation and preparation of the colon for surgical procedures. It binds nicely at the S-protein–ACE2 interface by making substantial π-π interactions with Tyr505 in the ‘Site 1’ hook region of RBD and hydrophilic interactions with Glu406, Ser494, and Thr500. Bisoxatin consistently binds to the protein throughout the 100 ns simulation. Taken together, we propose that the discovered molecule, Bisoxatin may be a promising repurposable drug molecule to develop new chemical libraries for inhibiting SARS-CoV-2 entry into the host.

Hydroxychloroquine in COVID-19: Potential Mechanism of Action Against SARS-CoV-2

PURPOSE OF REVIEW

The rapid spread of virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has turned out to be a global emergency. Symptoms of this viral infection, coronavirus disease 2019 (COVID-19), include mild infections of the upper respiratory tract, viral pneumonia, respiratory failure, multiple organ failure and death. Till date, no drugs have been discovered to treat COVID-19 patients, and therefore, a considerable amount of interest has been shown in repurposing the existing drugs.

RECENT FINDINGS

Out of these drugs, chloroquine (CQ) and hydroxychloroquine (HCQ) have demonstrated positive results indicating a potential antiviral role against SARS-CoV-2. Its mechanism of action (MOA) includes the interference in the endocytic pathway, blockade of sialic acid receptors, restriction of pH mediated spike (S) protein cleavage at the angiotensin-converting enzyme 2 (ACE2) binding site and prevention of cytokine storm. Unfortunately, its adverse effects like gastrointestinal complications, retinopathy and QT interval prolongation are evident in treated COVID-19 patients. Yet, multiple clinical trials have been employed in several countries to evaluate its ability in turning into a needed drug in this pandemic.

SUMMARY

This review attempts to summarize the MOA of CQ/HCQ and its side effects. The existing literature hints that till date, the role of CQ/HCQ in COVID-19 may be sceptical, and further studies are warranted for obtaining a therapeutic option that could be effectively used across the world to rise out from this pandemic.

New Anti SARS-Cov-2 Targets for Quinoline Derivatives Chloroquine and Hydroxychloroquine

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a severe global health crisis. In this paper, we used docking and simulation methods to identify potential targets and the mechanism of action of chloroquine (CQ) and hydroxychloroquine (HCQ) against SARS-CoV-2. Our results showed that both CQ and HCQ influenced the functionality of the envelope (E) protein, necessary in the maturation processes of the virus, due to interactions that modify the flexibility of the protein structure. Furthermore, CQ and HCQ also influenced the proofreading and capping of viral RNA in SARS-CoV-2, performed by nsp10/nsp14 and nsp10/nsp16. In particular, HCQ demonstrated a better energy binding with the examined targets compared to CQ, probably due to the hydrogen bonding of the hydroxyl group of HCQ with polar amino acid residues.

Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study

The spread of novel coronavirus strain, Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) causes Coronavirus disease (COVID-19) has now spread worldwide and effecting the entire human race. The viral genetic material is transcripted and replicated by 3 C-like protease, as a result, it is an important drug target for COVID-19. Hydroxychloroquine (HCQ) report promising results against this drug target so, we perform molecular docking followed by MD-simulation studies of HCQ and modelled some ligand (Mod-I and Mod-II) molecules with SARS-CoV-2-main protease which reveals the structural organization of the active site residues and presence of a conserve water-mediated catalytic triad that helps in the recognition of Mod-I/II ligand molecules. The study may be helpful to gain a detailed structural insight on the presence of water-mediated catalytic triad which could be useful for inhibitor modelling. Communicated by Ramaswamy H. Sarma.

Sars-cov-2 host entry and replication inhibitors from Indian ginseng: an in-silico approach

COVID-19 has ravaged the world and is the greatest of pandemics in modern human history, in the absence of treatment or vaccine, the mortality and morbidity rates are very high. The present investigation identifies potential leads from the plant Withania somnifera (Indian ginseng), a well-known antiviral, immunomodulatory, anti-inflammatory and a potent antioxidant plant, using molecular docking and dynamics studies. Two different protein targets of SARS-CoV-2 namely NSP15 endoribonuclease and receptor binding domain of prefusion spike protein from SARS-CoV-2 were targeted. Molecular docking studies suggested Withanoside X and Quercetin glucoside from W. somnifera have favorable interactions at the binding site of selected proteins, that is, 6W01 and 6M0J. The top-ranked phytochemicals from docking studies, subjected to 100 ns molecular dynamics (MD) suggested Withanoside X with the highest binding free energy (ΔG_bind = -89.42 kcal/mol) as the most promising inhibitor. During MD studies, the molecule optimizes its conformation for better fitting with the receptor active site justifying the high binding affinity. Based on proven therapeutic, that is, immunomodulatory, antioxidant and anti-inflammatory roles and plausible potential against n-CoV-2 proteins, Indian ginseng could be one of the alternatives as an antiviral agent in the treatment of COVID 19. Communicated by Ramaswamy H. Sarma.