Letters in Drug Design & Discovery - Volume 21, Issue 2, 2024

Background: Although evaluating in vitro biological activity is an important part of the drug discovery process, few publications discuss the ideal inhibitory activity in these tests.Objective: To analyze the in vitro biological activity data from antiviral drugs to establish parameters that could increase success in developing new antiviral drug candidates.Methods: Information from in vitro tests for each antiviral medicine was obtained from the Thomson Reuters Integrity platform for antiviral drugs approved by FDA between 1963 and 2020 (35 years). The inhibitory activity data was collected from three references using the same determination method, and the values were reported as means.Results: 82 antiviral drugs were found to treat 11 different viruses. Most of these drugs were developed to treat HIV infections (33 of 82), followed by anti-HCV medicines (20 of 82). The anti-HIV phenotypic activities of most HIV-approved drugs had an IC50 < 50 nM; for the anti-HCV it was verified as IC50 < 0.2 μM. Combining the data for all drugs analyzed, the antiviral phenotypic activity in most cases exhibited an IC50 < 0.2 μM.Conclusion: The limited availability of antiviral drugs and in vitro activity data imposed limitations on this study. However, it could be inferred that an antiviral drug candidate would have more success in drug development when the IC50 was in the range of low micromolar. Ultimately, in vitro activity must be considered in combination with other factors in drug development processes.

Natural products have a broad diversity of multidimensional chemical formations, which play an important role, and indicate the crucial nature as a golden source for gaining herbal drug discovery. Thymoquinone performs various functions and impacts anticancer, anti-inflammatory, antioxidant, and anti-diabetic. It shows the significant influence on the treatment of different cancer types, such as bone cancer, bladder cancer, lung cancer, breast cancer, prostate cancer, and colon cancer. Sulforaphane has anticancer and antimicrobial properties and anticarcinogenic constituents. Phloretin is a dihydrochalcone flavonoid that indicates a potent antioxidant activity in peroxynitrite scavenging and restraint of lipid peroxidation. The most important health benefits of phloretin are anti-inflammatory and antioxidant activity and its impacts on cancer cells. Its antioxidant activity occurs through a reducer of lipid peroxidation, the scavenger of ROS, and its anti-inflammatory impacts happen through a declined level of cytokines, adhesion molecules, chemokines, suppression of NF-Κβ transcription, and decreased expression of COX- 2 and iNOS. Phloretin impacts cancer cells through cytotoxic and apoptotic activity and activation of immune cells against the tumor. Epigallocatechin-3-gallate is the most abundant tea polyphenol, followed by other polyphenols, namely, catechin, epicatechin, epigallocatechin, and epicatechin-3-gallate. This review manuscript mentions some important medical health advantages and pharmaceutical effects of thymoquinone, sulforaphane, phloretin, and epigallocatechin.

Background: A new series of ten composites with sulphur based carboxylic acid and benzylamine were synthesized by Ugi 4-components reaction (Ugi-4CR) and screened for antituberculosis activity against the Mycobacterium tuberculosis H37Rv strain.Objective: Target compounds were isolated, purified, identified, and characterized by MS, FT-IR, ¹HNMR, APT, and ¹³C-NMR then the antituberculosis activity was examined by Microplate Alamar Blue Assay (MABA) method.Methods: This study was based on the articulation of carboxamide linkage bearing S-linkage in the core unit by reacting four different units, i.e., 2-(pyrimidin-2-ylthio)acetic acid, aromatic aldehyde, benzylamine and tertiary butyl isocyanide at RT in an atom economy route of synthesis. The desired product (5a- 5j) was synthesized via one-pot and Metal-free conditions.Results: Compounds (5a-5j) synthesized in good yields and compared to MIC values of Isoniazid 0.05 (μg/mL), Rifampicin 0.1 (μm/mL), and Ethambutol 1.56 (μg/mL) as a positive control.Conclusion: Synthesized compounds give excellent yield. Among the ten derivatives, compound 5f has comparable antituberculosis activity.

Introduction: Macrophage Migration Inhibitory Factor (MIF), a cytokine that signals for inflammatory response, has been implicated in multiple inflammatory disorders, including RA. Inhibition of MIF activity by anti-MIF inhibitors can lead to improved prognosis and increased quality of life. Development of a medically viable MIF inhibitor has been pursued without success, and no inhibitor that binds to MIF active site has been approved as a drug. Current treatments of Rheumatoid Arthritis (RA), an inflammatory disorder driven by an autoimmune response, target pain management and control of progression, but the risk of toxicity and increased side effects lead to limited success.Methods: Our goal was to search for drug-like lead compounds that bind more potently to MIF active sites than current inhibitors. We selected ten classes of chemical compounds that have previously shown in vitro MIF inhibitory activity and screened ∼47,000 compounds belonging to these classes through virtual docking, alongside ∼900,000 compounds from ZINC and TCM (Traditional Chinese Medicine) databases. The ligands with the higher energy of binding than current inhibitors were analyzed for ADMET profiles and drug-likeness properties.Results: In total, 75 ligands showed binding energies higher than the threshold of -7.5 kcal/mol, and 5 lead compounds were identified with suitable pharmacokinetic profiles and drug-like characteristics. Among them, molecular dynamics simulation showed a stable ligand-protein complex for 3-[3-fluoro-4- (trifluoromethyl)phenyl] propanoic acid.Conclusion: With the identification of this lead compound, new opportunities can be sought in the pursuit of a novel treatment for Rheumatoid Arthritis.

Objective: Focal adhesion kinase (FAK) is a cytosolic tyrosine kinase that controls integrin and growth factor signaling pathways. FAK is a promising therapeutic target for cellular adhesion-related disorders, such as cancer.Methods: In this study, in silico techniques like quantitative structure-activity relationship (QSAR), Molecular Docking, and Dynamic Simulation were used to study the interactions between small molecules and FAK.Results: The constructed QSAR model showed good statistical parameters (Q²=0.8040 and R²=0.8499), indicating that it is stable and reliable. Based on this model, several new compounds were screened from small molecule databases and their inhibitory activities were validated by molecular docking and molecular dynamics simulation. Pharmacokinetic parameters were checked using in silico ADME testing.Conclusion: Results show that the protein-ligand complexes are stable during the simulation and are considered potential inhibitors of Focal Adhesion Kinase.

Background: Chronic inflammation is usually combated with non-steroidal anti-inflammatory drugs (NSAIDs). However, long-term use of NSAIDs causes side effects comprising gastric ulceration, abdominal discomfort, lack of anti-thrombolytic activity, and myocardial infarction. Emerging reports indicate alteration of arachidonic acid metabolism, via cyclooxygenase and lipoxygenase pathways, being investigated as potential anti-inflammatory agents. There is a dynamic balance shift toward lipoxygenase on cyclooxygenase inhibition, therefore there is a need to identify naïve dual COX-2/5-LOX inhibitory agents with better therapeutic and minimal side effects.Objective: The current research focused on identifying a prospective natural candidate molecule (1,3- diphenyl-2-propene-1-one derivative) as a dual COX-2/5-LOX inhibitor by using structure-based database screening, molecular modelling, and in-silico ADMET analysis.Methods: Virtual screening using the ZINC database, molecular docking of potential compounds, and ADME analysis of hit compounds were performed.Results: A virtual library of 116 chalcone-based molecules was screened out. The molecules were docked for COX-2 (PDB ID-3LN1) and 5-LOX (PDB ID-3V99) enzymatic active pockets and resulted in compounds C96, C8, C83, C45, C20 better than zileuton. The potent compounds and zileuton showed good binding affinity in the range of -8.0 to -8.7 Kcal/mol in the COX-2 and -7.0 to -8.7Kcal/mol in the 5-LOX active site respectively. These compounds were further subjected to ADME analysis giving two plausible lead compounds C45 and C64 following ideal pharmacokinetic properties.Conclusion: The research work provides abundant opportunities to explore computational and medicinal research areas which will facilitate the development of novel dual COX-2/5-LOX inhibitors in future experimental studies.

Background: The increased emergence of multidrug-resistant bacterial strains is a continuous life-threatening global problem. The best approach to prevent the reproduction and invasion of the pathogenic bacteria is to inhibit the replication stage. The untapped molecular machinery involved in the replication is ParE subunit of topoisomerase IV. In this study, compounds active against the ParE were selected.Objective: This study aimed to analyze the electronic parameters, chemical stability, kinetic stability, and binding modes of the compounds.Methods: Density functional theory (DFT) and molecular electrostatic potential (MESP) calculations were computed using Jaguar with a basis set of 6-31G**++ (B3LYP) in the gas phase. MD simulation was performed for the 100 ns using Desmond available in Maestro to determine the stability and obtain an insight into the molecular mechanism of E. coli ParE docked complexes.Results: From the DFT calculations, the energy gap ΔE -7.58 and -7.75 eV between the HOMO and LUMO of both the compounds P1 (4-(2-(2-(2-chloroacetamido)phenoxy)acetamido)-3-nitrobenzoic acid) and P2 (4-(2-(benzo[d]thiazol-2-ylthio)acetamido)-3-nitrobenzoic acid) explained the chemical and kinetic stability of the system. MD results demonstrated the minimum fluctuations and conformational stability of the protein structures.Conclusion: The P1 and P2 compounds were chemically and kinetically stable. Furthermore, MD results demonstrated the stability and inhibitory action of the ligands dependent on hydrophobic, ionic and water bridges than that of hydrogen-bonding interactions.

Background: Highly pathogenic bacteria colonize and maintain themselves with the aid of an enzyme called urease. Consequently, inhibiting urease enzymes can be a promising method for preventing ureolytic bacterial infections.Objective: This study aimed at synthesizing and screening a novel series of benzimidazole derivatives..Methods: Nine novel benzimidazole derivatives 10α-rdquo; were synthesized and isolated. Their structures were elucidated by ¹H-NMR and IR spectroscopic techniques besides HRMS. The urease inhibition activity of these compounds was evaluated using the standard urease enzyme inhibition kit. An MTT assay was performed on the NIH-3T3 cell line to investigate the cytotoxicity profile.Results: All benzimidazoles 10α-rdquo; exhibited higher urease inhibition activity (3.06128;“4.40 μM) than the reference standards thiourea and hydroxyurea (IC50: 22 and 100 μM, respectively). 10rdquo;-1 and 10α-1 exhibited the best activity with the IC50 values of 3.06 and 3.13 μM, respectively. Investigation of the cytotoxicity profile of the target compound showed that all 10α-rdquo; have IC50 values higher than 50 μM on the tested cell line.Conclusion: The results showed that synthesized benzimidazole derivatives could be highly effective as urease inhibitors.

Aim: This study aimed to evaluate the potential of different hydrophilic polymers to increase Arteether's water solubility.Background: Arteether is classified as a class II biopharmaceutical in the Biopharmaceutical Classification System (BCS), with low water solubility (17 g/mL) and dissolution rate, resulting in poor bioavailability.Objective: The goal of this research is to improve the water solubility of Arteether (ART) by using a solid dispersion and hydrotropic approach with a variety of carriers, such as PEG-6000 PVP K-30, Poloxamer- 188, Poloxamer-407, HPMC E 15LV, HPMC K-100M, sucrose, and mannitol, sodium benzoate, sodium citrate, Urea, nicotinamide, and beta-cyclodextrin.Methods: Melting and evaporation methods were used to make the solid dispersion. Instrumental examinations, including XRD, DSC, FTIR, and SEM, confirmed any physical changes caused by the interaction of ART and carriers.Results: The most significant increase in water solubility of Arteether was discovered with CD: PEG600:Pol -407, and the highest enhancement in solubility was 67 times. While 37.34 times and 49 times increase in solubility was observed at 1:4.3:3.7 weight ratio of AE: PEG-6000:Poloxamer-407 40 percent mix of nicotinamide, respectively. The in vitro results show that ART's dissolution rate in the solid dispersion system was dramatically reduced compared to pure drug. This might be because of the drug's enhanced wettability, dispersion ability, and transition from crystalline to amorphous form. Compared to the ART itself, the permeability of Arteether from solid dispersion was increased up to 7 times. However, the permeability of solid cyclodextrin dispersion was extremely low, just 4.42 times. This may be due to the drug encapsulation in the cyclodextrin cavity.Conclusion: This research successfully developed and optimized various polymer and solubility enhancement approaches for Arteether, resulting in increased water solubility, which may improve Arteether's oral bioavailability. The findings of this study might be utilized to develop an oral dosage of Arteether with enhanced bioavailability.

Background: The present work is an effort to develop novel propofol (PPF) and remifentanil (RFT) co-loaded nanoemulsion (NME) for the treatment of anesthetic effects.Methods: The PPF/RFT NME was prepared via the high-pressure homogenization method. Its physicochemical properties were assessed to ensure good quality and suitability for i.v. administration. We also studied the in vivo pharmacokinetics and pharmacodynamics of PPF/RFT NME in dogs with an optimized formulation.Results: This study showed that the mean particle size of PPF/RFT NME was 124.2 nm and the zeta potential was 136;'20.6 mV. In the stability test, the NME maintained a good round shape and did not demonstrate any significant changes in physicochemical characteristics. In terms of the in vitro release, the early burst release of the NME preparations containing PPF or RFT was ideal in clinical practice, where a loading dose or a rapid onset of the drug was required. Based on histopathological observations, no histological change occurred to the rat organs after the administration of PPF/RFT NME. Regarding pharmacodynamics, compared with the combination group at the same dose, PPF/RFT NME could make animals enter the anesthetic state faster and the anesthetic effects last longer. In addition, vital signs of PPF/RFT NME could be maintained in a good state while better effects were delivered.Conclusion: This study used PPF and RFT to prepare a compound NME. This could reduce the anesthesiologist's administration time and make the anesthesia process more efficient.

Background: Existing medications for treating cancer are reported to exhibit severe side effects, therefore, there is an urgent need to address these unprecedented health risks. With the advancements in ethnobotanical studies and research on phytochemicals, information on several medicinal plants is being revisited nowadays. Terminalia arjuna is a widely used medicinal plant in ayurvedic and Unani medicine for curing several diseases. Although the bioactives from this plant are reported to possess anticarcinogenic, antiproliferative and antioxidant activities, information on the potentials of its specific phytoconstituents on the inhibition of receptor molecules associated with lung cancer is scarce.Objectives: The primary goal of this study is to virtually screen the phytochemicals of Terminalia arjuna as potential drug candidate molecules for lung cancer. Considering all major reported receptor molecules that inevitably take part in lung cancer, it highlights the phytochemicals as novel multitargeted inhibitors of proteins responsible for lung cancer.Methods: A thorough literature review was done to select twenty-seven receptor molecules associated with lung cancer cases. The molecular docking study using PyRx predicts protein-ligand interactions and identifies potential drug targets. Evaluating the ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties of the phytochemicals present in Terminalia arjuna, this study takes into account thirty-four bioactive compounds as the chosen ligands in molecular docking. The binding affinity, inhibition constant (Ki), and the interacting residues of these phytochemicals with the receptors are compared with the docking results of twelve selected standard anticancer drugs. The study finally categorizes the phytochemicals that can potentially act as multitargeted inhibitors of proteins associated with lung cancer.Results: The results from PyRx highlighted the phytoconstituents having a higher binding affinity with inhibition constant comparable to the standard drugs. Among the standard anticancer drugs, alectinib, pralsetinib, and ibrutinib are marked as potent inhibitors of several lung cancer receptors. The phytochemicals of Terminalia arjuna proved to be the potential candidates against ALK2, ALK5, DDR2, BRAF, KRAS, Tankyrase, vasopressin V2, VEGFR1 and VEGFR2 mediated lung cancer but the effectiveness (in comparison to the standard drugs) is limited against Bcl-2, IL22R1, NCAM, RET, MET and ROS1 receptors.Conclusion: The findings indicate that phytochemicals namely luteolin, friedelin, oleanolic acid, and 14,16-dianhydrogitoxigenin bind strongly to multiple receptors under consideration with high affinity and hence could be investigated as effective alternatives for treating lung cancer with minimal side effects.

Background: Non-viral gene vectors have attracted much attention in the last few decades because of their potential activity and fewer side effects. Headgroup chemistry is a key aspect of lipid design.Methods: In this study, a group of sulfonium lipids were designed and constructed by combining tetrahydrothiophene or tetrahydrothiopyran with an ethoxy linker and carbon aliphatic chains and were evaluated in terms of their ability as potential gene vectors. The sulfonium lipids were synthesized and characterized by ¹H NMR, ¹³C NMR, and Mass. Condensates of sulfonium lipids (SL) and DNA were examined by gel electrophoresis and particle size and zeta potential were measured. Sulfonium compounds were tested on HepG2 cells for cytotoxicity. SL/DNA condensates were studied in cellular uptake and distribution using fluorescent microscopy.Results: 12 sulfonium lipids were obtained. Gel electrophoresis experiments showed that sulfonium cation can effectively interact with phosphorous in DNA. Compounds containing longer lipid chains can effectively retard DNA at an S/P ratio higher than 10/1 and can condense DNA into nano size particles with particle size in the range of 150 nm ∼ 300 nm and zeta potential in the range of +20∼+40. Sulfonium compounds were calculated against HepG2 cells in the range of 0.035 μg/mL to 1.64 μg/mL. The intracellular uptake experiments revealed that SL/DNA nanoparticle was taken into the cell at low efficiency.Conclusion: Sulfonium head group can interact with the phosphates of DNA. The structural environment of sulfonium ions influences the DNA bonding effect. The designed cyclic sulfonium ion was buried in the middle of the structure and thus hindered interaction with DNA. This type of molecule is worthy of further modification to increase DNA capacity and reduce cell cytotoxicity.

Background: Neuroendocrine tumors (NETs) can occur in most human epithelial organs, however, there are few studies on digestive system NETs.Aims: The study aims to analyze Pax5 expression in digestive tract NETs and discuss its diagnostic significance.Methods: This study included 64 cases of NETs diagnosed from 2019 to 2020. Expressions of paired box 5 (Pax5), CD56, synaptophysin (Syn), and chromogranin (CgA) were detected using the immunohistochemical assay. Clinicopathological parameters, including tumor location, histological classification, depth of infiltration, tumor diameter, lymph node metastasis, vascular tumor thrombus, and nerve invasion, were determined in Pax5 positive and negative patients. Spearman correlation analysis was performed to analyze the correlation between Pax5 and CD56, Syn, and CgA.Results: The positive rate of Pax5 expression in patients with NETs was 46.9% (30/64). There were more patients 137;¥60 years illustrating positive expression of Pax5 compared to those patients <60 years (χ²=8.438, P=0.004). There were significant differences in histological classification between Pax5 positive expression patients and Pax5 negative expression patients (χ²=17.639, P=0.011). Significant Pax5 positive expression patients demonstrated tumor size 137;¥3 cm, compared to Pax5 negative expression patients (χ²=6.764, P=0.009). Therefore, positive Pax5 expression was related to age, histological classification, and tumor size of NETs patients. Pax5 expression in digestive system NETs was not correlated with CD56 (χ²=0.233, r=0.024, P=0.853), Syn (χ²=0.635, r=0.047, P=0.715), CgA (χ²=2.346, r=0.170, P=0.179).Conclusion: Positive expression of Pax5 was related to age, tumor location, and tumor size of NETs patients. Pax5 can be used in combination with common immune markers (CD56/Syn/CgA) and can improve the diagnostic accuracy of digestive system NETs.

Background: The fast development of an effective vaccine is the major demand for protection against the SARS-COV-2 virus outbreak. With the vast volume of data and the requirement for automatic abstract property learning, machine learning (ML) as a branch of artificial intelligence (AI) has a significant contribution in areas of vaccine discovery. The rise of ML has greatly accelerated the often lengthy vaccine approval process. ML models for COVID-19 vaccine development focus on the prediction of potential epitopes by using a variety of techniques, such as artificial neural networks, gradient boosting decision trees and deep neural networks.In this regard, immuno-informatics tools are time-saving and cost-effective methods to hasten the design and establishment of a proficient multi-peptide candidate vaccine. The utilization of multi-epitope-based vaccines has been demonstrated to be a promising immunization approach against viruses due to the induction of long-term protective immunity.Methods: In the present study, a comprehensive computational and machine learning based approach was conducted to design a multi-epitope-based potential candidate vaccine composed of cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) epitopes of conserved regions of Spike and Nucleocapsid proteins. The potential viral peptides as the candidate vaccine were screened regarding convenient features like hydrophilicity, flexibility, antigenicity, and charging properties. In the next step, the vaccine efficacy needs to be improved by an immune adjuvant. For this purpose, the C-terminal domain of the heat shock protein gp96 (CT-GP96) was applied as a potent adjuvant for enhancing immunity. The five assembled constructs with different peptide orders were generated and fused with the assistance of suitable linkers. All five assembled candidate vaccine constructs were modeled and their 3D structures were assessed in terms of strong immune responses stimulation and their structural stability and immune processing for response induction. Finally, the best refined model was docked to toll-like receptor 4 (TLR4). Furthermore, Molecular Dynamics (MD) simulation of the vaccine-receptor complex was done to assess the stability and related physical movements of the vaccine-TLR4 docking complex. The final candidate vaccine was computationally cloned in E. coli expression host to guarantee its high level of production.Results: Following a comprehensive immune-informatics and machine learning-based approach, the best conserved CTL and HTL immune stimulant epitopes were selected and assembled in different orders to build five different constructs. The final validated candidate vaccine construct was selected according to its efficacy, stability, and exposure ability, molecular docking analysis with TLR4. The molecular simulations by iMODS software also confirmed the stability of the binding interface. Additionally, the computational cloning of the final assembled candidate vaccine with pET28a plasmid showed the possibility of high level production of the vaccine construct post transformation in an E. coli host.Conclusion: The computational analysis indicated that this construct can be proposed as a potent prophylactic and therapeutic candidate multi-epitope vaccine againstSARS-COV-2 once its effectiveness is verified by experimental and animal studies.

Background: Human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) have resulted in a global health threat. Meanwhile, due to the emergence of drugresistant HIV-1 strains, the discovery of potent compounds for antiretroviral therapy success is highly desirable.Objective: This study aimed to develop anti-HIV-1 candidates which can be effectively applied for the treatment of HIV infection.Methods: Based upon our previous results, a series of E isomers of C15-imines of matrine (3a-l) were semi-synthesized from a natural quinolizidine alkaloid matrine. Their anti-HIV-1 activities were evaluated against HIV-1133;¢B replication in acutely infected C8166 cells in vitro.Results: Derivatives 3c, 3h and 3j showed good anti-HIV-1 activities with EC50 and therapeutic index (TI) values of 0.0089/0.012/0.0091 mM, and 23.71/32.49/27.43, respectively.Conclusion: The substituents and their corresponding positions on the phenyl ring of C15-imine derivatives of matrine were vital for anti-HIV-1 activities. Compounds 3c, 3h and 3j can be used as leads for further structural modification as HIV-1 inhibitors.