Letters in Drug Design & Discovery - Volume 20, Issue 6, 2023

Background: Cancer incidence and mortality have been increasing, and cancer is still the leading cause of death all over the world. Therefore, expanding the arsenal of anticancer drugs with high efficiency and low toxicity is still one of the most challenging tasks. As a branch of antitumor drug design and discovery, dual-targeting drug candidates draw extensive attention. Objective: In this work, we try to construct a multitarget drug candidate and evaluate its antitumor effects. Methods: Hsp90 and histone deacetylase were selected as two targets to design a dual targeting inhibitor w11. Enzyme inhibition work, cell viability assay, and docking simulation were carried out to evaluate the activity of the compound. Results: w11 could inhibit the activity of Hsp90α and HDAC6 with the IC50of 50.1 nM and 8.1 nM, respectively. In cell viability assay, five human tumor cell lines Eca-109, FaDu, HN6, MCF-7 and MDAMB- 231 were used, results showed that w11 could potently inhibit the proliferation of three human lines with IC50values in the nM range. Molecular docking experiments proved the rationality of structure design. Conclusion: Compound w11 was a potent Hsp90 and HDAC dual inhibitor for anticancer research.

Background: Among Nitrogen-containing heterocyclic compounds, pyridazine derivatives serve as a necessary scaffold as they possess various pharmacological activities. Thus, in recent times, the design of novel synthetic schemes and the selection of a new target for the action of pyridazine derivatives have attracted the attention of researchers. Objective: This study has focused on synthesizing and evaluating the muscle relaxant activity of pyridazine analogs by in-silico screening and rotarod test. Methods: In the present work, pyridazine derivatives were synthesized from substituted pyridine and maleic anhydride yielding intermediates (1a-5a), which on reaction with hydrazine, yielded final pyridazine derivatives (1b-5b). They were then screened for muscle relaxant action by an in-silico docking study against muscarinic acetylcholine receptors with protein data bank ID: 5CXV with the use of Autodock 4.2 and Biovia discovery studio tools. Compounds were further tested for muscle relaxant activity by the rotarod test. Results: Synthesis of the designed compounds was carried out successfully. Obtained result showed that the final compounds (1b-5b) showed 1-3 interactions with acetylcholine muscarinic receptor with -7.2 to -7.9 Kcal/mole affinities. The findings were compared to the typical drug diazepam, which has one interaction with the target and binding energy of -7.7 Kcal/mole. Moreover, the result of the rotarod test showed that substitution by electron-withdrawing groups causes more muscle relaxant activity when compared with the electron releasing groups. Conclusion: The results of the experimental study showed that pyridazine derivatives could serve as a promising template for the further design and development of muscle relaxant agents.

Background: Cancer is one of the most devastating diseases, affecting the lives of millions of people around the world. Introduction: A series of acenaphtho[1,2-e][1,2,4]triazine containing different thiomethyl-1,2,3-triazole derivatives were designed based on a fragment-based and molecular hybridization approach as anti-cancer agents. Methods: Designed compounds were synthesized using cycloaddition condensation followed by click reaction. Cytotoxicity of prepared compounds was evaluated by MTT reduction assay against four different cancer cell lines. Results: The biological evaluation indicated that derivative 6d with para-fluorobenzyl moiety was the most active cytotoxic agent with IC50values of 70.1, 12.8, 41.5, and 16.0 μM against K562, MOLT-4, HT-29, and MCF-7 cells, respectively. Cell cycle analysis showed that acenaphtho triazine derivatives could induce G0/G1 phase arrest in MCF-7 breast cancer cells. Conclusion: Synthesized derivatives can be ideal candidates for further exploration as anti-cancer agents.

Background: In recent years, Chinese herbal medicine has been gradually emerging as a suitable treatment option for breast cancer. However, the mechanism underlying its effects remains to be elucidated. Objective: The drug targets and Flos Daturae targets were intersected to obtain 86 component-disease intersection genes. Methods: The String database and Cytoscape3.8.0 were employed, and finally, AKT1, MYC, EGFR, MAPK14 PTGS2, and VEGFA were obtained as the six core genes. Results: According to the Gene Expression Profiling Interactive Analysis (GEPIA), six core gene correlation analysis figures were constructed. The GO enrichment analysis and the KEGG pathway enrichment analysis were conducted using the R package. Finally, molecular docking between the core genes and the main active components was performed for verification. Conclusion: The results indicated that Flos Daturae has multiple components and multiple targets that regulate the body functions, through which it plays a role in the treatment of breast cancer. In addition, it was inferred that polygenic regulation is better than the single-gene approach in breast cancer treatment.

Background: Epilepsy is a seizure-related disease with different symptoms and types, depending on the origin and propagation region of the brain. There are several marketed anti-seizure medications (ASMs) available for choice of treatment by clinicians but there is a huge paucity of ideal first-line ASMs. Objective: The present study was undertaken to identify and get an insight into the major target (hub) proteins, which can be comprehensively used as a platform for designing first-line ASMs. Methods: Large-scale text mining was done to generate a data warehouse of available ASMs and their MOAs, followed by the identification of specific isoforms of target proteins for designing next-generation ASMs, using network biology and other in-silico approaches. Results: The study resulted in the identification of 3 major classes of target proteins of major ASMs and their specific isoforms, namely – GABA receptors (GABRA1, GABRB1, and GABARAP); VGSC (α- subunitSCN2A (Nav1.2)) and VGCC (α-subunitCACNA1G (Cav3.1)). The identified proteins were also observed to be concurrent with the target sites of majorly sold ASMs currently. Conclusion: The predicted hub protein families and their specific isoforms can be further validated and comprehensively used to design next-generation novel first-line ASM(s).

Background: The high mortality rate of cancer is endangering human health, and the research and development of new anticancer drugs have the attention of scientists worldwide. Sulfonamides have become the focus of anticancer drug research. 1,2,3-triazole compounds can inhibit the formation of a variety of tumor cells. Based on the excellent antitumor activity exhibited by the 1,2,3-triazole compound skeleton, the sulfonamide moiety in the sulfonamide structure can be introduced into the triazole compound skeleton to obtain highly active anticancer drugs. Methods: The Topomer CoMFA method was used to study the three-dimensional quantitative structureactivity relationship of 58 new 1,2,3-triazole compounds with sulfa groups, and a 3D-QSAR model was obtained. Results: The cross-validation coefficient q²is 0.545, the non-cross-correlation coefficient r²is 0. 754, r²predis 0.930, the optimal number of principal components N is 4, and the standard estimation error SEE is 0.319. These results show that the model has good internal and external forecasting capabilities. By searching for the R group in the Topomer search module and combining it with the more active groups in the existing molecules, 6 new compounds with theoretically higher anti-HL-60 (leukemia cell line) activity are obtained. Conclusion: The prediction result of the Topomer CoMFA model is good, and the statistical verification is effective. The prediction results of ADMET show that the 6 new compounds meet the drug requirements and are expected to become potential anti-HL-60 inhibitors, providing guidance for the synthesis of anti-tumor drugs.

Background: COVID-19 (coronavirus disease 2019) is still a major challenge worldwide. The disease is caused by binding the coronavirus to ACE2 receptors on lung cells, infecting the cells and triggering the onset of symptoms. The prevention of such a binding in which the virus is eventually unable to enter the cell could be a promising therapeutic approach. Methods: In this in silico study, 306 compounds of Lamiaceae family native in Iran (native Mints) were retrieved from several databases as 3D structures, and after that molecular docking and virtual screening, the compounds with inhibitory potential were selected in terms of free energy binding against the spike protein of the virus. The pharmacokinetic profile of selected compounds was evaluated, and by molecular dynamic simulation and MM/PBSA, four compounds were further assessed for binding affinities against the receptor-binding domain of the spike. Results: The results showed the Catechin gallate and Perovskone B from Stachys and Salvia genus generated a stronger binding affinity, and therefore could act as potential inhibitory compounds of RBD of the SARS-CoV-2 spike protein. Conclusion: This study revealed that some members of the Lamiaceae family could be employed to inhibit SARS-CoV-2 activity through interaction with spike protein and therefore could be used for further investigation in vitro and in vivo.

Introduction: This work was devoted to an in silico investigation conducted on twenty-eight Tacrine-hydroxamate derivatives as a potential treatment for Alzheimer’s disease using DFT and QSAR modeling techniques. Methods: The data set was randomly partitioned into a training set (22 compounds) and a test set (6 compounds). Then, fourteen models were built and were used to compute the predicted pIC50 of compounds belonging to the test set. Results: All built models were individually validated using both internal and external validation methods, including the Y-Randomization test and Golbraikh and Tropsha's model acceptance criteria. Then, one model was selected for its higher R², R²test, and Q²cvvalues (R² = 0.768, R²adj= 0.713, MSE = 0.304, R²test=0.973, Q²cv= 0.615). From these outcomes, the activity of the studied compounds toward the main protease of Cholinesterase (AChEs) seems to be influenced by 4 descriptors, i.e., the total dipole moment of the molecule (μ), number of rotatable bonds (RB), molecular topology radius (MTR) and molecular topology polar surface area (MTPSA). The effect of these descriptors on the activity was studied, in particular, the increase in the total dipole moment and the topological radius of the molecule and the reduction of the rotatable bond and topology polar surface area increase the activity. Conclusion: Some newly designed compounds with higher AChEs inhibitory activity have been designed based on the best-proposed QSAR model. In addition, ADMET pharmacokinetic properties were carried out for the proposed compounds, the toxicity results indicate that 7 molecules are nontoxic.

Background: Immunoglobulins (Igs) are produced in plasma cells in response to glycoproteinlike immunogens and they are also used as therapeutics in the pharmaceutical industry. It may be important to know the effects of therapeutic Igs on Ig levels during therapy to eliminate any misconceptions about the immunity of patients. Objective: This study aimed to investigate the effects of monoclonal antibody (mAb) derivative drugs and therapeutic antibody (intravenous Ig [IVIG] and hepatitis B immune globulin [HBIG]) treatments on blood IgG, IgA, IgM, IgE, complement component 3 (C3), and complement component 4 (C4) levels. Methods: N Protein Control SL / Low (Siemens, Marburg, Germany, Lot: 084654) was used as the control solution. Aliquots of IVIG, HBIG, rituximab, tocilizumab, and bevacizumab (20 μL) were added to 180 μL of the control solution, and the solutions were vortexed (5 s). The samples were studied using a Dade Behring BN II (Siemens, Marburg, Germany) nephelometer. All measurements were repeated three times by performing the same process in which distilled water (20 μL) was added to the control solution to determine the target value, and the average values were taken. The bias formula was used to calculate the amount by which the results deviated from the target value. Results: IVIG caused the greatest deviation (45.97%) to IgG levels. HBIG, rituximab, tocilizumab, and bevacizumab caused the IgG level to deviate by 0.81%, 9.68%, 27.42%, and 30.65%, respectively. In the IgA test, tocilizumab increased the reading by 8.66%, while the other therapeutics caused reductions in the reading, with the smallest and largest changes caused by HBIG (-0.93%) and bevacizumab (-4.98%). Tocilizumab increased the IgE level by 0.48%, and rituximab and bevacizumab reduced the IgE level by - 0.21% with -8.47%, respectively. Tocilizumab, IVIG, and HBIG caused 1.41%, 2.70%, and 4.32% deviations, respectively, in the C3 levels. Whereas bevacizumab (-1.08%) and rituximab (-5.41%) caused reductions in the C3 levels. Tocilizumab, HBIG, rituximab, IVIG, and bevacizumab caused deviations of 0.87%, -2.31%, -3.76%, -6.36%, -8.38%, respectively, in the C4 levels. Conclusion: Deviations in measured IgG levels after therapeutic Ig and mAb infusions may cause errors in clinical decisions. It is recommended that Ig levels be measured before infusion or when the therapeutic drug has been eliminated from the blood.

Background: The blood level of tacrolimus (TAC) used for post-transplant immunosuppression should be within the therapeutic index. Geriatric individuals may be at risk of organ rejection because, in this age group, routine drug use is usually disrupted, and the bioavailability of aging-related drugs is decreased. Objective: The aim of this study was to analyze the age-related variability of blood TAC levels in patients in Turkey. Methods: In this study, 697,616 patients who underwent TAC measurement in the laboratories of public, private, and university hospitals between 2018 and 2020 were identified from the Health-net database of the Ministry of Health. The results of patients aged ≥65 years were compared with those of patients aged <65 years. The differences between the sexes in the same age group were also examined. Data from the Turkish Ministry of Health National Electronic Database were used to design a multicenter retrospective cohort study. Results: The study included 697,616 patients. The mean TAC concentration was 7.2 ± 6.25 ng/mL for all the patients, 7.13 ± 6.7 ng/mL for the female patients, and 7.24 ± 5.96 ng/mL for the male patients. A statistically significant difference in TAC concentration was found between men and women in the general population. Groups aged ≥65 years were compared among themselves. A statistically significant decrease in TAC concentration was found only in the age group of 75–79 years (5.63 ± 4.09 ng/mL) of women compared with the men. In all other age groups, the TAC levels of the men were lower. Conclusion: The proportion of patients with TAC concentrations lower than the therapeutic index was higher in the groups aged ≥65 years. Thus, patients aged ≥65 years may be at risk of organ rejection, as optimum immunosuppression cannot be achieved. In these patients, more frequent drug monitoring and providing training to ensure the compliance of the patient and the patient's relatives in the use of TAC may be recommended.

Background: The occurrence of Tuberculosis (TB) has significantly increased worldwide. The extensively drug-resistant tuberculosis (XDR-TB) and multi-drug resistant tuberculosis (MDR-TB) have made it more challenging to treat this mycobacterial infection caused by the Mycobacterium tuberculosis MTB-H37Rv strain. The present treatments for tuberculosis are of long duration and with side effects. Thus, it is necessary to discover new drugs with short-term chemotherapy, fewer health hazards, and cost effectiveness. Objective: The objective of the study was to divulge the antitubercular properties of Betti base scaffolds. Method: Betti bases were designed, synthesized 4a-4h, 6a-6h, and investigated for their in vitro antitubercular activity using Microplate Alamar Blue assay (MABA) against the MTB-H37Rv strain. Their binding affinity with amino acids was studied by performing molecular docking studies using InhA (PDB ID: 2NSD) present in the MTB-H37Rv strain. Cytotoxicity assay and neutrophil function test (NFT) were also performed. Results: The Betti bases (4a-4h, 6d) showed minimum inhibitory concentration (MIC) values ranging from 1.6 μg/mL to 6.25 μg/mL against the MTB-H37Rv strain. The compounds (4a-4h, 6a-6h) were investigated for their ADME properties and good pharmacokinetic profiles were observed. In molecular docking studies, a strong binding affinity between InhA and the compounds (4a-4h, 6a-6h) was observed, which provided theoretical insight into the inhibitory action of the synthesized compounds (4a-4h, 6a-6h) against InhA. NFT of the compounds (4a-4h, 6a-6h) showed no harmful effects on the functions of neutrophils. In vitro cytotoxicity assay against Vero cell lines revealed the non-cytotoxic behavior of the compounds. Conclusion: Betti bases can be considered to be a promising class of molecular entities that can lead to the development of new anti-tubercular leads.

Aims: This study aimed at bioprospecting underexplored extreme habitats (Thar desert, India) for novel bio- and chemo-diversity. Background: Bioactive metabolites from microorganisms, such as fungi from underexplored habitats, serve as basic skeletons of therapeutic agents, including antimicrobials, combating the effect of multidrug resistance of pathogens. Objectives: The main objectives of the current study are (i) characterization of isolate TD-082 and (ii) metabolite fingerprinting of butanol extract showing antimicrobial compounds. Methods: In search of novel antimicrobial drugs, a promising microcolonial fungus TD-082, obtained from the Thar Desert, India, was identified by ITS1–5.8S–ITS2 sequencing. Phenotypic characteristics were marked by microscopy. The fungus was investigated for antimicrobial activity against a panel of Gram-positive, Gram-negative bacteria and fungi. Butanol extract that showed the best antimicrobial activity was partially purified; fractions exhibiting antimicrobial activity were pooled and fingerprinted by GC-MS analysis. Results: Sequencing data indicated that the isolate belonged to Aureobasidium sp. It showed 96% similarity to Aureobasidium iranianum and Kabatiella bupleuri, and 95 % to A. thailandense and A. subglaciale. Microscopy results confirmed that it belongs to Aurebasidium sp. Metabolite fingerprinting showed tentatively ten novel compounds belonging to three major categories, hydrocarbons, fatty acids, and peptides. Conclusion: The study shows that understudied habitats, such as deserts, can provide skeletons for novel compounds from novel microorganisms. The study can be expanded to other niche habitats with higher chances of identifying more novel bioactive compounds.

Background: Vibrio cholera is a facultative pathogenic bacterium that causes cholera pandemics, primarily in nations with hot and humid climates and large bodies of water containing a large quantity of organic debris. Consumption of V. cholera contaminated water or food causes acute diarrheal illness, followed by severe dehydration and mortality. Cholera is a highly infectious illness, with over 4 million cases recorded globally each year, and over a hundred thousand deaths. Objective: The only known therapy for cholera infection is oral rehydration solution along with antibiotics. Excessive antibiotic use causes pathogens to acquire antimicrobial drug resistance, resulting in a loss of efficacy. Furthermore, antibiotics are accompanied by a plethora of unfavorable side effects, restricting their usage. Methods: A riboswitch is a non-homologous proteinaceous therapeutic target that plays a regulatory role in the crucial process of bacterial translation. As a result, the bacterial riboswitch was investigated as a surrogate target for developing a therapeutic medication against V. cholera. Results: In silico screening with 24407 ligands was performed against the bacterial riboswitch to identify potential lead candidates, followed by pharmacophore modeling and bioisosteric lead modifications to design potential leads having an antagonistic impact on the pathogenic bacterial riboswitch. Conclusion: The riboswitch-based innovative therapy was anticipated to be devoid of the issues connected with the development of antimicrobial drug resistance as well as the unwanted side effects associated with antibiotic usage.

Introduction: Modified polymeric materials are nowadays most commonly used for making modified-release pharmaceutical dosage forms. Methods: In this present research study, a grafted copolymer is synthesized by using acrylamide and okra gum with the help of the redox initiator method. The method was optimized using a 3-factor, 2-level central composite design (CCD). Optimization of the synthetic process was done by the application of QbD; the amount of acrylamide (1-10g), amount of initiator (50-150 mg), and microwave irradiation exposure time (1-5 min) were taken as critical process variables, and response factors were selected as percentage grafting (% grafting) and percentage yield (% yield). Results: The optimized formulation (F13) exhibited a maximum percentage of grafting of 82.2 and a percentage yield of 12.54 of acrylamide (5.5g), amount of initiator as 100 mg, and microwave irradiation exposure time as 3 min. Conclusion: The characterization of synthesized grafted copolymer product was performed by using differential scanning calorimetry (DSC), FT-IR spectroscopy, and scanning electron microscopy (SEM).

Background: Medicinal plant oils are used in the treatment of various human diseases due to their phytochemical components. Recently, enzyme inhibition studies have been increasing in cosmetics, the food industry, and especially pharmaceuticals. Objective: The main goal of this study is to focus on a specific interaction between the essential oil components of Mentha longifolia ssp. longifolia and carbonic anhydrase (CA) enzyme in vitro and in silico. Methods: The chemical composition of the essential oil was identified by gas chromatography coupled with mass spectrometry (GC-MS). The CA inhibitory activity of M. longifolia essential oil was investigated by using esterase activity for the first time in this study. Molecular docking was performed separately for two different CA isoforms (CA-II and CA-IX). Results: Among fourteen components identified, piperitone (27.14%), 2-acetylcyclopentanone (21.05%), p-menthan-3-one (13.90%), menthan (6.60%), and piperitone oxide (6.52%) were defined as the major compounds. The essential oil showed remarkable inhibitory activity against CA with an IC50value of 0.010 mg/mL. According to the molecular docking analysis, caryophyllene oxide (-6.5 kcal/mol for CAIX isoform, -6.8 kcal/mol for CA-II isoform) and trans-caryophyllene (-6.3 kcal/mol for CA-IX isoform, - 6.7 kcal/mol for CA-II isoform) molecules showed the best inhibitory activity in two different CA isoforms. In this study, it was determined that all molecules are bioavailable by ADMET analyses. Conclusion: The results of this study are valuable for the development of natural and new CA enzyme inhibitors without side effects in the treatment of diseases, such as glaucoma, obesity, and epilepsy.

Background: Cancer is a leading cause of death worldwide. EGFR is one of the important targets considered for current chemotherapeutic agents. The problem of drug resistance can be overcome by the use of hybrid molecules. A hybrid of 1,3,4-oxadiazole and chalcone has been proved to be an anti- EGFR inhibitor. Objective: The aim of the study was to carry out pharmacophore optimization of the hybrid nucleus of 1,3,4- oxadiazole and chalcone by using literature findings and in-silico approach. A series of 24 substituted hybrid molecules of 2-(5-phenyl-1,3,4-oxadiazol-2-ylthio)-N-(4-((Z)-3-phenylacryloyl)phenyl)acetamide derivatives were subjected to 2D and 3D QSAR studies. Methods: The survey of literature was carried out for selected hybrid nucleus using different available databases. The 2D QSAR was performed by using the MLR, PLS, and PCR methods, while 3D QSAR was performed using the KNN-MFA method. Results: A summary of literature findings was prepared. For 2D QSAR, statistically significant model was obtained for the MLR method with r²=0.9128, q²=0.8065. For the 3D QSAR model, I was found to be significant with q²=0.834. The pharmacophoric requirements for inhibition of EGFR were optimized by use of the evidence attained after the generation of descriptors from QSAR studies and literature findings. Conclusion: This optimized pharmacophore will be useful in further drug design process.