Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review

Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-clinical drug discovery, and various computational techniques and software programs are typically used in combination, in a bid to achieve the desired outcome. Several approved drugs have been developed with the aid of CADD. On SciFinder®, we evaluated more than 600 publications through systematic searching and refining, using the terms, virtual screening; software methods; computational studies and publication year, in order to obtain data concerning particular aspects of CADD. The primary focus of this review was on the databases screened, virtual screening and/or molecular docking software program used. Furthermore, we evaluated the studies that subsequently performed molecular dynamics (MD) simulations and we reviewed the software programs applied, the application of density functional theory (DFT) calculations and experimental assays. To represent the latest trends, the most recent data obtained was between 2015 and 2020, consequently the most frequently employed techniques and software programs were recorded. Among these, the ZINC database was the most widely preferred with an average use of 31.2%. Structure-based virtual screening (SBVS) was the most prominently used type of virtual screening and it accounted for an average of 57.6%, with AutoDock being the preferred virtual screening/molecular docking program with 41.8% usage. Following the screening process, 38.5% of the studies performed MD simulations to complement the virtual screening and GROMACS with 39.3% usage, was the popular MD software program. Among the computational techniques, DFT was the least applied whereby it only accounts for 0.02% average use. An average of 36.5% of the studies included reports on experimental evaluations following virtual screening. Ultimately, since the inception and application of CADD in pre-clinical drug discovery, more than 70 approved drugs have been discovered, and this number is steadily increasing over time.

Calendulaglycoside A showing potential activity against SARS-CoV-2 main protease: Molecular docking, molecular dynamics, and SAR studies

BACKGROUND AND AIM

The discovery of drugs capable of inhibiting SARS-CoV-2 is a priority for human beings due to the severity of the global health pandemic caused by COVID-19. To this end, natural products can provide therapeutic alternatives that could be employed as an effective safe treatment for COVID-19.

EXPERIMENTAL PROCEDURE

Twelve compounds were isolated from the aerial parts of C. officinalis L. and investigated for their inhibitory activities against SARS-CoV-2 Mpro compared to its co-crystallized N3 inhibitor using molecular docking studies. Furthermore, a 100 ns MD simulation was performed for the most active two promising compounds, Calendulaglycoside A (SAP5) and Osteosaponin-I (SAP8).

RESULTS AND CONCLUSION

At first, molecular docking studies showed interesting binding scores as compared to the N3 inhibitor. Calendulaglycoside A (SAP5) achieved a superior binding than the co-crystallized inhibitor indicating promising affinity and intrinsic activity towards the Mpro of SARS-CoV-2 as well. Moreover, findings illustrated preferential stability for SAP5 within the Mpro pocket over that of N3 beyond the 40 ns MD simulation course. Structural preferentiality for triterpene-Mpro binding highlights the significant role of 17β-glucosyl and carboxylic 3α-galactosyl I moieties through high electrostatic interactions across the MD simulation trajectories. Furthermore, this study clarified a promising SAR responsible for the antiviral activity against the SARS-CoV-2 Mpro and the design of new drug candidates targeting it as well. The above findings could be promising for fast examining the previously isolated triterpenes both pre-clinically and clinically for the treatment of COVID-19.

Synthesis and biological evaluation of a new series of benzimidazole derivatives as antimicrobial, antiquorum-sensing and antitumor agents

New benzimidazole derivatives were synthesized and assessed for antimicrobial efficacy toward Escherichia coli, Bacillus cereus, Staphylococcus aureus, Candida albicans and Aspergillus fumigatus 293. Results indicated that compounds 3c and 3n have promising activity toward S. aureus, whereas 3i exhibited remarkable efficacy toward B. cereus. Moreover, compound 3c was proved to be the most active antifungal analog toward C. albicans. On the other hand, 3n displayed the highest activity against A. fumigatus 293. Antiquorum-sensing activity of the same compounds was also tested against Chromobacterium violacium ATCC 12472, whereas compounds 3c-f, 3i-k and 3m-o showed acceptable activity. In vitro antitumor testing of these compounds toward liver cancer (HepG2), colon cancer (HCT-116) and breast cancer (MCF-7) cell lines revealed that compound 3p has the highest potency against the three tested cell lines. Moreover, 3f, 3m and 3n displayed promising activity toward all tested cell lines. Compounds 3f, 3m, 3n and 3p were esteemed for in vivo antitumor activity against EAC cells. The active antimicrobial and antitumor analogs, 3a, 3c, 3f, 3i-k, 3m, 3n and 3p were assessed for DNA-binding affinity, and results indicated that 3c, 3f, 3i, 3k and 3n have strong DNA-binding affinity. The computational studies affirmed that almost all of the inspected compounds meet the optimal requirements for good absorption and oral bioavailability.

In vitro and computational insights revealing the potential inhibitory effect of Tanshinone IIA against influenza A virus

Seasonal human influenza is a serious respiratory infection caused by influenza viruses that can be found all over the world. Type A influenza is a contagious viral infection that, if left untreated, can lead to life-threatening consequences. Fortunately, the plant kingdom has many potent medicines with broad-spectrum antiviral activity. Herein, six plant constituents, namely Tanshinone IIA 1, Carnosic acid 2, Rosmarinic acid 3, Glycyrrhetinic acid 4, Baicalein 5, and Salvianolic acid B 6, were screened for their antiviral activities against H1N1 virus using in vitro and in silico approaches. Hence, their anti-influenza activities were tested in vitro to determine inhibitory concentration 50 (IC50) values after measuring their CC50 values using MTT assay on MDCK cells. Interestingly, Tanshinone IIA (TAN) 1 was the most promising member with CC50 = 9.678 μg/ml. Moreover, the plaque reduction assay carried on TAN 1 revealed promising viral inhibition percentages of 97.9%, 95.8%, 94.4%, and 91.7% using concentrations 0.05 μg/μl, 0.025 μg/μl, 0.0125 μg/μl, and 0.006 μg/μl, respectively. Furthermore, in silico molecular docking disclosed the superior affinities of Salvianolic acid B (SAL) 6 towards both surface glycoproteins of influenza A virus (namely, hemagglutinin (HA) and neuraminidase (NA)). The docked complexes of both SAL and TAN inside HA and NA receptor pockets were selected for 100 ns MD simulations followed by MM-GBSA binding free energy calculation to confirm the docking results and give more insights regarding the stability of both compounds inside influenza mentioned receptors, respectively. The selection criteria of the previously mentioned complexes were based on the fact that SAL showed the highest docking scores on both viral HA and NA glycoproteins whereas TAN achieved the best inhibitory activity on the other hand. Finally, we urge more advanced preclinical and clinical research, particularly for TAN, which could be used to treat the human influenza A virus effectively.

Gemcitabine anticancer activity enhancement by water soluble celecoxib/sulfobutyl ether-β-cyclodextrin inclusion complex

We investigated the complexation of celecoxib (CCB) into sulfobuthyl-ether-β-cyclodextrin (SBE-β-CD) for the realization of an inhalable dry-powder formulation containing gemcitabine (GEM) for lung anticancer therapy. Complexation increased the water solubility of CCB (0.003 mg/mL and 0.834 mg/mL for CCB free and complexed, respectively) and produced a quantitative dissolution of the drug within 15 min. The CCB/SBE-β-CD inclusion complex showed a high stability constant (8131 M-1) not influenced by the presence of GEM in solution. Two-dimensional NMR experiments and computational studies demonstrated that the pyrazole ring of CCB penetrates deeper into SBE-β-CD from the secondary rim. The aromatic rings are positioned at the edge of the cavity, establishing hydrogen bonds with the SBE-β-CD that stabilized the complex. CCB showed limited cytotoxic activity on A549 cell lines. Complexation significantly increased activity passing from 30% to 45% cell mortality. Moreover, CCB/SBE-β-CD strongly improved the cytotoxicity of GEM, observing about 60% of cell mortality for the combined formulation.

Molecularly imprinted polymers for selective extraction of rosmarinic acid from Rosmarinus officinalis L

This study provides a robust and reproducible approach for selective extraction of rosmarinic acid (RA) using molecularly imprinted polymers (MIPs). Computational modeling and UV spectroscopic analysis were performed to optimize MIP synthesis. Consequently, six different bulk and surface imprinted polymers were generated using RA as the template. Binding performance of the imprinted polymers was evaluated using static equilibrium and complementary dynamic rebinding experiments. Despite the high selectivity of thus generated surface imprinted polymers, the corresponding bulk polymers exhibited better binding performance when serving as sorbents during solid phase extraction (SPE). An optimized molecularly imprinted solid phase extraction (MISPE) protocol was developed in respect to loaded amount of RA, composition of the loading solution, washing solvent, and elution volume. Thereby, a remarkably selective extraction of RA from real-world Rosmarinus officinalis L. extract with a recovery rate and purity of 81.96 ± 6.33% and 80.59 ± 0.30%, respectively, was achieved.

A new approach for antimicrobial and antiviral activities of biocompatible nanocomposite based on cellulose, amino acid and graphene oxide

In this work, biocompatible, antimicrobial, and antiviral nanocomposites were prepared through two steps. In the first step, periodate oxidation of cellulose was performed to get dialdehyde cellulose (DAC). The second step included the reaction of DAC with sulfur-containing amino acids included Cysteine (Cys) and Methionine (Meth) in the presence of graphene oxide (GO). The prepared nanocomposites were characterized via FT-IR, SEM, TEM, and TGA. Antimicrobial and antiviral activities for all designed nanocomposites besides DAC were carried out. Both DAC/GO/Cys and DAC/GO/Meth exhibited a promising antimicrobial activity against Gram-negative (E. coli and P. aeruginosa), Gram-positive (B. subtilis and S. aureus), and unicellular fungi (C. Albicans and C. neoformans), while the DAC/GO/Cys/Meth nanocomposite was the lowest. Moreover, all designed nanocomposites have a strong antiviral activity against Herpes simplex virus 1(HSV-1) at minimum nontoxic concentration. Additionally, Computational procedures and Molecular docking showed the reactivity and stability of the molecules that have biological activity against Gram-positive, Gram-negative, and HSV-1. As well as DAC incorporation with amino acid enhanced their reactivity and their interaction.

A multi-targeted approach to identify potential flavonoids against three targets in the SARS-CoV-2 life cycle

The advent and persistence of the Severe Acute Respiratory Syndrome Coronavirus - 2 (SARS-CoV-2)-induced Coronavirus Disease (COVID-19) pandemic since December 2019 has created the largest public health emergency in over a century. Despite the administration of multiple vaccines across the globe, there continues to be a lack of approved efficacious non-prophylactic interventions for the disease. Flavonoids are a class of phytochemicals with historically established antiviral, anti-inflammatory and antioxidative properties that are effective against cancers, type 2 diabetes mellitus, and even other human coronaviruses. To identify the most promising bioactive flavonoids against the SARS-CoV-2, this article screened a virtual library of 46 bioactive flavonoids against three promising targets in the SARS-CoV-2 life cycle: human TMPRSS2 protein, 3CLpro, and PLpro. By examining the effects of glycosylation and other structural-activity relationships, the presence of sugar moiety in flavonoids significantly reduces its binding energy. It increases the solubility of flavonoids leading to reduced toxicity and higher bioavailability. Through protein-ligand contact profiling, it was concluded that naringin formed more hydrogen bonds with TMPRSS2 and 3CLpro. In contrast, hesperidin formed a more significant number of hydrogen bonds with PLpro. These observations were complimented by the 100 ns molecular dynamics simulation and binding free energy analysis, which showed a considerable stability of docked bioflavonoids in the active site of SARS-CoV-2 target proteins. Finally, the binding affinity and stability of the selected docked complexes were compared with the reference ligands (camostat for TMPRSS2, GC376 for 3CLpro, and GRL0617 for PLpro) that strongly inhibit their respective SARS-COV-2 targets. Overall analysis revealed that the selected flavonoids could be potential therapeutic agents against SARS-CoV-2. Naringin showed better affinity and stability for TMPRSS2 and 3CLpro, whereas hesperidin showed a better binding relationship and stability for PLpro.

Microwave assisted synthesis and docking study of N-(2-oxo-2-(4-oxo-2-substituted thiazolidin-3ylamino)ethyl)benzamide derivatives as anticonvulsant agents

Herewith, we report the design and synthesis of a series of N-(2-oxo-2((4-oxo-2-substituted thiazolidin-3yl)amino)ethyl) benzamide derivatives 7(a-j) under microwave irradiation, based on four component pharmacophoric model to get structural prerequisite indispensable for anticonvulsant activity. The synthesized derivatives were investigated in maximal electroshock seizure (MES), subcutaneous pentylenetetrazole (sc-PTZ) induced seizure and neurotoxicity screening. All the test compounds were administered at a dose of 30, 100 and 300 mg/kg body weight at the time interval of 0.5 h and 4 h. The compounds were also evaluated for behavioral activity and toxicity study. The compound 7 h was found to be most active in MES model. The anticonvulsant screening data shows that 65% of the compounds were found active against MES model when compared to 35% sc-PTZ model. The computational parameter such as docking study, logP determination and ADME prediction were performed to exploit the results.

Molecular docking, molecular modeling, vibrational and biological studies of some new heterocyclic α-aminophosphonates

A new diphenyl (aryl) (Ǹ-quinazolin-4-yl-hydrazino) methylphosphonates 3a-3d was synthesized via anhydrous zinc chloride catalyzed Kabachnic-Fields reaction. The structure of the synthesized compounds was confirmed by elemental analysis, FT-IR, ¹H NMR, ¹³C NMR, ³¹P NMR and MS spectral data. The synthesized compounds showed significant antimicrobial and also remarkable cytotoxicity anticancer activities against breast carcinoma cell line (MCF7). The quantum chemical calculations were performed using density functional theory (DFT) to study the effect of the changes of molecular and electronic structures on the biological activity of the investigated compounds. Also, NBO and theoretical FT-IR were calculated. The experimental results were validated by molecular docking simulation of compound 3b in the active pocket of the enzyme. The important binding interactions with the key residues in the active site were revealed. A good correlation was found between the quantum chemical parameters and experimental data.

Microwave-assisted synthesis of a new Piperonal-Chitosan Schiff base as a bio-inspired corrosion inhibitor for oil-well acidizing

A new Schiff base of chitosan, namely Piperonal-chitosan (Pip-Cht), was synthesized for the first time, using a microwave irradiation method and characterized using spectroscopic techniques. The corrosion inhibition behavior of the new Schiff base was evaluated on carbon steel in 15% HCl medium via gravimetric and electrochemical techniques. This is the first work on the application of chemically functionalized chitosan as a corrosion inhibitor in the oil-well acidizing environment. The Pip-Cht inhibitor exhibited a high corrosion inhibition efficiency of 85.16% at a moderate dose of 600 mg L-1. Further, the addition of potassium iodide as a synergistic agent to the corrosive electrolyte produced a significant improvement in the inhibition efficiency to 91.15% at a low dosage of 10 mM of KI. At a higher temperature of 65 °C, the combination of both the inhibitor and KI yielded a high inhibition efficiency. The results of the gravimetric and electrochemical experiments were corroborated using AFM and SEM studies. The DFT calculations indicated that corrosion inhibition behavior of the Schiff base mainly occurs in the protonated form.

Potential RNA-dependent RNA polymerase (RdRp) inhibitors as prospective drug candidates for SARS-CoV-2

The SARS-CoV-2 pandemic is considered as one of the most disastrous pandemics for human health and the world economy. RNA-dependent RNA polymerase (RdRp) is one of the key enzymes that control viral replication. RdRp is an attractive and promising therapeutic target for the treatment of SARS-CoV-2 disease. It has attracted much interest of medicinal chemists, especially after the approval of Remdesivir. This study highlights the most promising SARS-CoV-2 RdRp repurposed drugs in addition to natural and synthetic agents. Although many in silico predicted agents have been developed, the lack of in vitro and in vivo experimental data has hindered their application in drug discovery programs.

Validation of Computational Studies for Electrical Brain Stimulation With Phantom Head Experiments

BACKGROUND

Although computational studies of electrical brain stimulation (EBS) have received attention as a cost-effective tool, few studies have validated the technique, particularly in invasive cortical stimulation.

OBJECTIVE

In order to validate such studies, we used EBS to compare electric potential distributions generated by both numerical simulations and empirical measurements in three phantom head models (one-/three-layered spherical heads and MRI-based head).

METHODS

We constructed spherical phantom heads that consisted of one or three layers, and an anatomical, MRI-based phantom that consisted of three layers and represented the brain or brain/skull/scalp in order to perform both numerical simulations using the finite element method (FEM) and experimental measurements. Two stimulation electrodes (cathode and anode) were implanted in the phantoms to inject regulated input voltage, and the electric potential distributions induced were measured at various points located either on the surface or deep within the phantoms.

RESULTS

We observed that both the electric potential distributions from the numerical simulations and experiments behaved similarly and resulted in average relative differences of 5.4% (spherical phantom) and 10.3% (MRI-based phantom).

CONCLUSIONS

This study demonstrated that numerical simulation is reasonably consistent with actual experimental measurements; thus, because of its cost-effectiveness, EBS computational studies may be an attractive approach for necessary intensive/extensive studies.

New Pyrazine Conjugates: Synthesis, Computational Studies, and Antiviral Properties against SARS-CoV-2

Currently, limited therapeutic options are available for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). We have developed a set of pyrazine-based small molecules. A series of pyrazine conjugates was synthesized by microwave-assisted click chemistry and benzotriazole chemistry. All the synthesized conjugates were screened against the SAR-CoV-2 virus and their cytotoxicity was determined. Computational studies were carried out to validate the biological data. Some of the pyrazine-triazole conjugates (5 d-g) and (S)-N-(1-(benzo[d]thiazol-2-yl)-2-phenylethyl)pyrazine-2-carboxamide 12 i show significant potency against SARS-CoV-2 among the synthesized conjugates. The selectivity index (SI) of potent conjugates indicates significant efficacy compared to the reference drug (Favipiravir).

Exploration of docetaxel palmitate and its solid lipid nanoparticles as a novel option for alleviating the rising concern of multi-drug resistance

Docetaxel (DTX), a widely prescribed anticancer agent, is now associated with increased instances of multidrug resistance. Also, being a problematic BCS class IV drug, it poses challenges for the formulators. Henceforth, it was envisioned to synthesize an analogue of DTX with a biocompatible lipid, i.e., palmitic acid. The in-silico studies (molecular docking and simulation) inferred lesser binding of docetaxel palmitate (DTX-PL) with P-gp vis-à-vis DTX and paclitaxel, indicating it to be a poor substrate for P-gp efflux. Solid lipid nanoparticles (SLNs) of the conjugate were prepared using various lipids, viz. palmitic acid, stearic acid, cetyl palmitate and glyceryl monostearate. The characterization studies for the nanocarrier were performed for the surface charge, drug payload, micromeritics, release pattern of drug and surface morphology. From the cytotoxicity assays on resistant MCF-7 cells, it was established that the new analogue offered substantially decreased IC₅₀ to that of DTX. Further, apoptosis assay also corroborated the results obtained in IC₅₀ determination wherein, SA-SLNs showed the highest apoptotic index than free DTX. The conjugate not only enhanced the solubility but also offered lower plasma protein binding and improved pharmacokinetic and pharmacodynamic effect for DTX loaded SA-SLNs in apt animal models, and lower affinity to P-gp efflux. The studies provide preliminary evidence and a ray of hope for a better candidate in its nano version for safer and effective cancer chemotherapy.

Design, synthesis and biological evaluation of new series of hexahydroquinoline and fused quinoline derivatives as potent inhibitors of wild-type EGFR and mutant EGFR (L858R and T790M)

New series of hexahydroquinoline and fused quinoline derivatives were designed and synthesized. The thirty seven new compounds were screened for in vitro antitumor activity against HepG2, HCT-116 and MCF-7 cancer cells. Results indicated that compounds 2e, 2h, 5b, 5c, 6a, 7d and 9b have the strongest potency against the three cancer cells, and they were further screened for in vitro cytotoxicity against A431 and H1975 cancer cells, as well as WI38 and WISH normal cells. Results revealed that 7d potently inhibited the growth of H1975 cells harboring EGFRT790M mutation (IC50 = 1.32 ± 0.2 µM) over A431 cells overexpressing EGFRWT (IC50 = 4.96 ± 0.3 µM). Moreover, the seven compounds displayed low cytotoxicity against the tested normal cells. The seven potent antitumor compounds were examined for their ability to inhibit the activity of EGFRWT. The attained data manifested that 7d has remarkable EGFRWT inhibitory activity (IC50 = 0.083 ± 0.002 μM) compared to erlotinib (IC50 = 0.067 ± 0.002 μM). Compound 7d was further studied for its enzymatic inhibitory activity against other eight human kinases, and it displayed outstanding inhibitory activity against EGFRL858R and EGFRT790M mutants (IC50 = 0.053 ± 0.002, 0.026 ± 0.001 μM, respectively), as well as JAK3 (IC50 = 0.069 ± 0.003 μM). Analysis of cell cycle evidenced that 7d induces cell cycle arrest in G2/M and pre-G1 phases in the tested cancer cells. In addition, cancer cell death induced by 7d was proved to take place via apoptosis supported by elevated Bax/Bcl-2 ratio in the tested cancer cells. Moreover, docking results confirmed the good binding interactions of 7d with EGFRWT, EGFRL858R, EGFRT790M and JAK3, which came in agreement with the results of in vitro enzyme assay. Further, 7d is predicted to have good oral absorption, good drug-likeness properties and low toxicity risks in human.

Exploring a potential palonosetron allosteric binding site in the 5-HT(3) receptor

Palonosetron (Aloxi) is a potent second generation 5-HT(3) receptor antagonist whose mechanism of action is not yet fully understood. Palonosetron acts at the 5-HT(3) receptor binding site but recent computational studies indicated other possible sites of action in the extracellular domain. To test this hypothesis we mutated a series of residues in the 5-HT3A receptor subunit (Tyr(73), Phe(130), Ser(163), and Asp(165)) and in the 5-HT3B receptor subunit (His(73), Phe(130), Glu(170), and Tyr(143)) that were previously predicted by in silico docking studies to interact with palonosetron. Homomeric (5-HT(3)A) and heteromeric (5-HT(3)AB) receptors were then expressed in HEK293 cells to determine the potency of palonosetron using both fluorimetric and radioligand methods to test function and ligand binding, respectively. The data show that the substitutions have little or no effect on palonosetron inhibition of 5-HT-evoked responses or binding. In contrast, substitutions in the orthosteric binding site abolish palonosetron binding. Overall, the data support a binding site for palonosetron at the classic orthosteric binding pocket between two 5-HT3A receptor subunits but not at allosteric sites previously identified by in silico modelling and docking.

Molecular mechanism of a specific capsid binder resistance caused by mutations outside the binding pocket

Enteroviruses cause various acute and chronic diseases. The most promising therapeutics for these infections are capsid-binding molecules. These can act against a broad spectrum of enteroviruses, but emerging resistant virus variants threaten their efficacy. All known enterovirus variants with high-level resistance toward capsid-binding molecules have mutations of residues directly involved in the formation of the hydrophobic binding site. This is a first report of substitutions outside the binding pocket causing this type of drug resistance: I1207K and I1207R of the viral capsid protein 1 of coxsackievirus B3. Both substitutions completely abolish the antiviral activity of pleconaril (a capsid-binding molecule) but do not affect viral replication rates in vitro. Molecular dynamics simulations indicate that the resistance mechanism is mediated by a conformational rearrangement of R1095, which is a neighboring residue of 1207 located at the heel of the binding pocket. These insights provide a basis for the design of resistance-breaking inhibitors.

Computational and synthetic approaches for developing Lavendustin B derivatives as allosteric inhibitors of HIV-1 integrase

Through structure-based virtual screening and subsequent activity assays of selected natural products, Lavendustin B was previously identified as an inhibitor of HIV-1 integrase (IN) interaction with its cognate cellular cofactor, lens epithelium-derived growth factor (LEDGF/p75). In order to improve the inhibitory potency we have employed in silico-based approaches. Particularly, a series of new analogues was designed and docked into the LEDGF/p75 binding pocket of HIV-1 IN. To identify promising leads we used the Molecular Mechanics energies combined with the Generalized Born and Surface Area continuum solvation (MM-GBSA) method, molecular dynamics simulations and analysis of hydrogen bond occupancies. On the basis of these studies, six analogues of Lavendustine B, containing the benzylamino-hydroxybenzoic scaffold, were selected for synthesis and structure activity-relationship (SAR) studies. Our results demonstrated a good correlation between computational and experimental data, and all six analogues displayed an improved potency for inhibiting IN binding to LEDGF/p75 in vitro to respect to the parent compound Lavendustin B. Additionally, these analogs show to inhibit weakly LEDGF/p75-independent IN catalytic activity suggesting a multimodal allosteric mechanism of action. Nevertheless, for the synthesized compounds similar profiles for HIV-1 inhibition and cytoxicity were highlighted. Taken together, our studies elucidated the mode of action of Lavendustin B analogs and provided a path for their further development as a new promising class of HIV-1 integrase inhibitors.

Resveratrol binds and activates RKIP protein in colorectal cancer

Raf-1 kinase inhibitory protein (RKIP) acts as a tumor cell metastasis suppressor and prognostic indicator for survival in various cancers. Its use is predicted to improve therapy for various malignancies, including colorectal cancer (CRC). RKIP, frequently denoted as phosphatidylethanolamine-binding protein 1, is expressed in all normal mammalian tissues. RKIP functions as an inhibitor of the Raf-1, PI-3K, and MAP kinase (MAPK) pathways. In this study, we found that resveratrol induced the expression of RKIP at protein levels. To elucidate the structural basis of the interaction between resveratrol and RKIP, we performed computational studies that explore the binding affinity and ligand efficacy of resveratrol against RKIP. This study reveals the prognostic significance of RKIP metastasis suppressor activity against CRC and its structural arrangements during drug-target interactions.

9-Aminoacridine-based agents impair the bovine viral diarrhea virus (BVDV) replication targeting the RNA-dependent RNA polymerase (RdRp)

Bovine viral diarrhea virus (BVDV) infection is still a plague that causes important livestock pandemics. Despite the availability of vaccines against BVDV, and the implementation of massive eradication or control programs, this virus still constitutes a serious agronomic burden. Therefore, the alternative approach to combat Pestivirus infections, based on the development of antiviral agents that specifically inhibit the replication of these viruses, is of preeminent actuality and importance. Capitalizing from a long-standing experience in antiviral drug design and development, in this work we present and characterize a series of small molecules based on the 9-aminoacridine scaffold that exhibit potent anti-BVDV activity coupled with low cytotoxicity. The relevant viral protein target - the RNA-dependent RNA polymerase - the binding mode, and the mechanism of action of these new antivirals have been determined by a combination of in vitro (i.e., enzymatic inhibition, isothermal titration calorimetry and site-directed mutagenesis assays) and computational experiments. The overall results obtained confirm that these acridine-based derivatives are promising compounds in the treatment of BVDV infections and, based on the reported structure-activity relationship, can be selected as a starting point for the design of a new generation of improved, safe and selective anti-BVDV agents.

Discovery of urease inhibitory effect of sulfamate derivatives: Biological and computational studies

The discovery of life-changing medicines continues to be the driving force for the rapid exploration and expansion of chemical space, enabling access to innovative small molecules of medicinal importance. These small molecules remain the backbone for modern drug discovery. In this context, the treatment of ureolytic bacterial infections inspires the identification of potent and effective inhibitors of urease, a promising and highly needed target for H. pylori eradication. The present study explores the evaluation of sulfamate derivatives for the inhibition of urease enzyme. The tested compounds showed remarkable inhibitory effect and high level of potency. Compound 1q emerged as the lead inhibitor with an IC₅₀ value of 0.062 ± 0.001 µM, ∼360-fold more potent than thiourea (IC₅₀ = 22.31 ± 0.031 µM). The assessment of various contributing factors towards the inhibition profile allowed for the establishment of diverse structure-activity relationships. Kinetics studies revealed the competitive mode of inhibition of compound 1q while molecular modeling analysis identified various crucial binding interactions with ARG609, ARG439, HIS519, HIS492, HIS593, ALA440, and ALA636 in the active pocket of the enzyme. Finally, the calculated pharmacokinetic properties suggest a promising profile of our potent sulfamate-based urease inhibitors.

Screening of phytoconstituents of Andrographis paniculata against various targets of Japanese encephalitis virus: An in-silico and in-vitro target-based approach

Japanese encephalitis (JE) is one of the viral diseases affecting millions of peoples across the globe specifically developing countries. There is no specific treatment available, however, vaccines are available for its prevention. Unfortunately, available vaccines are not effective against all clinical isolates and are also associated with neurological complications in some individuals. We have screened the selected phytoconstituents of Andrographis paniculata against various targets of Japanese encephalitis virus (JEV) using Schrodinger suite 2019-3. Among all selected phytoconstituents, andrographolide has shown a good binding affinity towards NS3 protease as compared to NS3 helicase and NS5 Rdrp (RNA dependent RNA polymerase) of JEV. The molecular dynamics (MD) results have also shown good stability of andrographolide in the active site of NS3 protease. The absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis has also indicated a good pharmacokinetic and safety profile of andrographolide. Finally, the in-vitro target-based assay have confirmed the inhibitory potential of andrographolide against the NS3 protease of JEV. In conclusion, andrographolide could have the potential to develop as an antiviral agent against JEV through inhibition of protease, however, further investigations are required.

Sequestrating anionic and cationic dyes from wastewater using spray dried biopolymeric magnetic composite: Experimental and theoretical studies

Spray dried cross-linked chitosan/cobalt ferrite composite was synthesized and applied as an adsorbent for the removal of acid orange II and methylene blue. The composite was structurally, thermally, morphologically and magnetically characterized. The result obtained shows that the magnetic composite was in form of microspheres, while cobalt ferrite was encapsulated in the cross-linked chitosan with saturation magnetization of 10.79 emu g^-1. Adsorption studies revealed that acid orange II adsorbed more favorably on the composite than methylene blue. The adsorption process is spontaneous and exothermic. Liu isotherm model was found to be applicable for the adsorption process. Computational studies showed that the formation of hydrogen bond between acid orange II and the magnetic composite (at both acidic and alkaline pH) contributed to its better adsorption than methylene blue. Adsorption capacity of acid orange II at pH 3 and methylene blue at pH 12 are 542 and 173 mg g^-1 respectively at 303 K base on Liu isotherm model.

α-Aminophosphonates 4-XC6H4-NH-CH(4-BrC6H4)-P(O)(OiPr)2 (X = H, Br, MeO): Crystal structures, Hirshfeld surface analysis, computational studies and in silico molecular docking with the SARS-CoV-2 proteins

We report structural and computational studies of three α-aminophosphonates 4-XC6H4-NH-CH(4-BrC6H4)-P(O)(OiPr)2, namely diisopropyl((4-bromophenyl)(phenylamino)methyl)phosphonate (X = H, 1), diisopropyl((4-bromophenyl)((4-bromophenyl)amino)methyl)phosphonate (X = Br, 2) and diisopropyl((4-bromophenyl)((4-methoxyphenyl)amino)methyl)phosphonate (X = MeO, 3). The structures of 1-3 were fully confirmed by means of the 31P{1H} and 1H NMR spectroscopy. Crystal structures of 2 and 3 are isostructural and each contain two independent molecules in the asymmetric unit cell. Energy frameworks have been calculated to analyze the overall crystal packing of 1-3. The DFT calculations were performed to verify the structures of 1-3 as well as their electronic and optical properties. Molecular docking was applied to examine the influence of both the (S)- and (R)-enantiomers of 1-3 on a series of the SARS-CoV-2 proteins.