Medicinal Chemistry - Volume 18, Issue 9, 2022

Bioisosterism is a unique approach used by medicinal chemists for the reasonable modification of lead compounds into safer, more clinically effective, economical, and therapeutically attractive drugs. It is one of the most crucial lead modification tools, widely applied in the field of rational drug design to amplify the desired activity and eliminate undesirable properties, thus facilitating the optimization of pharmacokinetic profile and achievement of target selectivity. This review demonstrates the importance of bioisosterism in the process of drug discovery and development and highlights its relevance in the molecular evolution of many classes of drugs such as antibacterial sulfonamides, anticancer drugs, antivirals, antifungals, anthelmintics, local anesthetics, barbiturates, antidepressants, antihistamines, proton pump inhibitors and work carried out by our team of researchers. The role of bioisosterism as a strategy to achieve inhibition of enzymes such as thymidylate synthase, DNA polymerase, reverse transcriptase and several others has also been pointed out. There are no limits to the classes of drugs where bioisosterism has been successfully applied.

Aims: The current study aimed to synthesize novel pyrazolo[1,5-a]pyrimidines based on 5- aminopyrazoles 3, evaluate their antimicrobial activity, and study the minimum inhibitory concentration (MIC) for the most active compounds. In addition, molecular docking studies and RNA polymerase inhibitory activity were determined. Background: Starting with our previously reported 5-aminopyrazoles 3, a number of novel pyrazolo[1,5- a]pyrimidines were synthesized. Due to the similarity of pyrazolopyrimidine derivatives with the purine systems, pyrazolopyrimidines are important in many different biological applications, most notably as anti-tumor, antibacterial, and hepatitis C virus inhibitors. The pharmaceutical applications of the pyrazolopyrimidine derivatives were explained in several approved drugs like Indiplon, Zaloplan, and Ocinaplon. Objective: To prepare a novel antimicrobial agent, namely pyrazolo[1,5-a]pyrimidine, reveal their structures using different spectral data, the minimum inhibitory concentration (MIC) for the most active compounds was evaluated, and both the molecular docking and the RNA polymerase inhibitory activity were determined. Methods: A number of different pyrazolopyrimidines namely 2-(phenylamino)-6,11-dihydrobenzo[g]pyrazolo [1,5-a]quinazoline-3-carboxamides (5a-c), (E)-5,7-dimethyl-2-(phenylamino)-6-(phenyldiazenyl)pyrazolo-[1,5- a]pyrimidine-3-carboxamides (7a-c), 7-amino-2-(phenylamino) pyrazolo[1,5-a]pyrimidine-3-carboxamides (11af), 7-amino-2-(phenylamino)-5-(2-thienyl)pyrazolo[1,5-a]pyrimidine-3-carboxamides (14-f) and ethyl 7-amino-3- carbamoyl-2-(phenylamino)-5-(4-pyridyl)pyrazolo[1,5-a]pyrimidine-6-carboxylate derivatives (14g-i) were synthesized through the reaction of 5-aminopyrazoles 3 with a variety of chemical reagents. On the other hand, the evaluation of the antimicrobial activity for all the prepared compounds was screened through different strains as Gram-positive bacteria, such as staphylococcus aureus and Streptococcus mutans, and Gram-negative bacteria, such as Escherichia coli, Pseudomonas aeruginosa, and klebsiella. The antifungal activity was determined by Candids Albicans fungal strain, and the MIC of the most active compounds was measured. The molecular docking was recorded, and the RNA polymerase inhibitory activity was estimated for the high docking score compounds. Results: Compounds 5a, 5b, 5c, 7a, 7b, 7c, 11d, 14b, and 14h were the most active compounds against some of the bacterial and fungal tested strains. MIC was determined for the most active tested compounds. As an antimicrobial agent, compound 7b was the most potent, with a high docking score and RNA polymerase inhibitory activity (IC50= 0.213 μg/ml) compared to Rifampicin (IC50= 0.244 μg/ml). The reactivity of the latter compound was attributed to the presence of 4-Br-C6H4 moiety. The results demonstrated that docking studies on the most active compounds in the RNA polymerase active site were consistent with in vitro assays. Conclusion: The resultant novel bioactive pyrazolo[1,5-a]pyrimidine derivatives were synthesized based on 5- aminopyrazole derivatives 3. The current study evaluated the antimicrobial activity for all the prepared compounds, followed by the determination of the MIC for the most potent active compounds. The molecular docking study was performed, and it was appropriate with the in vitro activity. The RNA polymerase inhibitory activity was assessed for the most active antimicrobial compounds with a high docking score (7b, 7c, 14a, 14b, 14e, 14i). Compound 7b was the most potent compound inhibiting RNA polymerase enzyme compared to the reference drug Rifampicin. Other: The novel prepared heterocyclic systems are extremely important in a variety of domains, especially biological and pharmacological ones.

Background: Quinoline is a well-established nucleus displaying various biological activities. Quinolin-8-ol-containing compounds are reported for antimicrobial as well as antimalarial activity. Hydrazone- and pyrazole-containing compounds are also reported for antimicrobial activity. In this work, we have synthesized hydrazonomethyl-quinolin–8–ol and pyrazol–3–yl-quinolin–8–ol derivatives retaining quinolin-8-ol along with hydrazone/pyrazole pharmacophores. Objective: The objective of this work was to synthesise and evaluate in vitro hydrazonomethylquinolin– 8–ol and pyrazol–3–yl-quinolin–8–ol derivatives for antifungal, antibacterial and antimalarial activity. Methods: Designed and synthesized hydrazonomethyl-quinolin–8–ol and pyrazol–3–yl-quinolin–8– ol derivatives were evaluated for antifungal (against Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans), antibacterial (against methicillin resistant Staphylococcus aureus (MRSA), Escherichia Coli, Pseudomonas aeruginosa and Klebsillae pneumoniae) as well as antimalarial (against Plasmodium falciparum D6 and W2 strains) activity. Results: Hydrazonomethyl-quinolin–8–ol (15.1-15.28) and pyrazol–3–yl-quinolin–8–ol derivatives (16.1-16.21 and 20.1-20.18) were synthesized in good to moderate yield. One-pot synthesis of pyrazol– 3–yl-quinolin–8–ol derivatives (16.1-16.21 and 20.1-20.18) was achieved. Compounds 15.3, 15.6, 15.7, 15.9-15.14, 15.16-15.19, 15.22 and 15.24 were found more potent compared to reference standard fluconazole (IC50 = 3.20 μM) against C. albicans with IC50 value less than 3 μM. Compounds 15.1, 15.2, 15.21 and 15.23 showed almost similar activity to reference standard fluconazole against C. albicans. Compounds 15.1-15.3, 15.9-15.12, 15.14-15.17, and 15.21-15.23 also showed good activity against fluconazole-resistant strain A. fumigatus with IC50 value less than 3 μM. Compounds 15.2-15.4, 15.7, 15.9, 15.17, 15.20 showed good antimalarial activity against P. falciparum D6 as well as P. falciparum W2 with IC50 values of 1.84, 1.83, 1.56, 1.49, 1.45, 1.97, 1.68 μM and 1.86, 1.40, 1.19, 1.71, 1.16, 1.34, 1.61 μM, respectively. 5-Pyrazol–3–yl-quinolin–8–ol derivatives, such as 16.3, 16.5, 16.11, 16.13, 16.19, 16.20, also showed antimalarial activity against P. falciparum D6 and W2 strains with IC50 values of 2.23, 2.16, 2.99, 2.99, 2.73, 2.12 μM and 2.91, 3.60, 4.61, 2.71, 2.31, 2.66 μM, respectively. Conclusion: Most of the 5-hydrazonomethyl-quinolin–8–ol derivatives showed good antifungal activity against C. albicans, A. fumigatus and C. neoformans. Most of the 5-hydrazonomethylquinolin– 8–ol derivatives were found more potent than reference standard fluconazole. These derivatives may be considered as leads for further development of antifungal agents.

Background: HIV-1 subtype C protease is a strategic target for antiretroviral treatment. However, resistance to protease inhibitors appears after months of treatment. Chromones and 2- biscoumarin derivatives show potential for inhibition of the HIV- subtype C protease. Objective: Different heterocyclic structures from the ZINC database were docked against Human Immunodeficiency Virus-1 (HIV) subtype C protease crystal structure 2R5Q and 2R5P. The 5 best molecules were selected to be docked against 62 homology models based on HIV-protease sequences from infants failing antiretroviral protease treatment. This experimentation was performed with two molecular docking programs: Autodock and Autodock Vina. These molecules were modified by substituting protons with different moieties, and the derivatives were docked against the same targets. Ligand-protein interactions, physical/chemical proprieties of the molecules, and dynamics simulations were analyzed. Methods: Docking of all of the molecules was performed to find out the binding sites of HIV-1 subtype C proteases. An in-house script was made to substitute protons of molecules with different moieties. According to the Lipinski rule of five, physical and chemical properties were determined. Complexes of certain ligands-protease were compared to the protein alone in molecular dynamics simulations. Results: From the first docking results, the 5 best (lowest energy) ligands (dibenz[a,h]acridine, dibenz[a, i]acridine, NSC114903, dibenz[c,h]acridine, benzo[a]acridine) were selected. The binding energy of the modified ligands increased, including the poorest-performing molecules. A correlation between nature, the position, and the resulting binding energy was observed. According to the Lipinski rules, the physico-chemical characteristics of the five best-modified ligands are ideal for oral bioavailability. Molecular dynamics simulations show that some lead-protease complexes were stable. Conclusion: Dibenz[a,h]acridine, dibenz[a, i]acridine, NSC114903, dibenz[c,h]acridine, benzo[ a]acridine and their derivatives might be considered as promising HIV-1 subtype C protease inhibitors. This could be confirmed through synthesis and subsequent in vitro assays.

Background: Oxazolidinones display several biological effects, including anticancer activity. The purpose of this present work was to investigate a series of novel oxazolidinone derivatives with potential antineoplastic activity. Their mechanisms of death induction and effects in the cell cycle were also evaluated. A molecular docking study was accomplished through proteins of the Cyclin-Dependent Kinases family (CDK). The new compound LPSF/NBM-2 was appeared to promote cell cycle arrest at the G2/M phase and increase the percentage of apoptotic cells. Methods: Oxazolidinone derivatives were obtained through Knoevenagel condensation. The cytotoxic assay was evaluated through the MTT method. Moreover, flow cytometry was performed in order to investigate the effects of the new compounds on the cell cycle, induction of cell death, and apoptosis. A blind docking was performed through the SwissDock online server and the analysis of the results was performed using the UCSF Chimera and Biovia discovery studio software. Results: LPSF/NBM-1 and LPSF/NBM-2 displayed the most cytotoxic activity against HL-60 (IC50 = 54.83 μM) and MOLT-4 (IC50 = 51.61 μM) cell lines. LPSF/NBM-2 showed an increased percentage of cell population at the G2/M phase. Molecular-docking results of LPSF/NBM-1 and LPSF/NBM-2 suggested a binding affinity with the evaluated CDK proteins. Conclusion: LPSF/NBM-1 and LPSF/NBM-2 displayed cytotoxic profiles against Hl-60 and MOLT-4. LPSF/NBM-2 increased cell population percentage at the G2/M phase and promoted cell death compared to non-treated cells in the MOLT-4 cell line. Based on these findings, oxazolidinone derivatives could be highlighted as possible cytostatic agents against lymphoma cells. Molecular docking results suggested the action of LPSF/NBM-1 and LPSF/NBM-2 compounds on enzymes of cyclin-dependent kinases family, however, more studies are needed to establish this correlation.

Background: NMDA (N-methyl-D-aspartate) receptor is one of the ionotropic receptor subtypes of glutamate, the most abundant excitatory neurotransmitter in the human brain. Besides physiological roles in learning and memory, neuronal plasticity and somatosensory function NMDAR overstimulation are also implicated in a pathophysiological mechanism of ‘excitotoxicity.’ In this study, an allosteric site has been focused on to design inhibitors of the most abundant form of this receptor of utility in many acute (stroke, traumatic brain injury) and chronic neurodegenerative diseases such as Parkinson’s disease, Huntington’s, Alzheimer’s, and others. Methods: In order to target this specific site at the interdimer interface of the ligand-binding domain of GluN2A-containing NMDA-Rs, blood-brain barrier-permeable potentially therapeutic compounds, as opposed to only pharmacological tools currently available, were sought. Pharmacophorebased virtual screening, docking, computational ADME prediction techniques, and MD simulation studies were used. Results: Proceeding through the in-silico methodology, the study was successful at reaching 5 compounds from ChEMBL Database, which were predicted to be potential NMDA inhibitor drugs. Conclusion: The products of the study are compounds that have been validated through pharmacophore and score-based screening and MD simulation techniques to be allosterically inhibiting NMDA receptors and with favorable pharmacokinetic profiles. They are likely to be therapeutic agents ready for in-vitro and in-vivo testing.

Background: The incidence of cancer has been increasing worldwide. Unfortunately, the drugs used in cancer chemotherapy are toxic to both neoplasms and normal tissues, while many available medications have low potencies. Conjugated α,β-unsaturated ketones differ structurally from contemporary anticancer medications , some of which have noteworthy antineoplastic properties. Objectives: This study aimed to design and synthesize highly potent cytotoxins with far greater toxicity to neoplasms than to non-malignant cells. Methods: A series of N-acyl-3,5-bis(benzylidene)-4-piperidone hydrochlorides 4a-n were prepared and evaluated against Ca9-22, HSC-2, HSC-3, and HSC-4 squamous cell carcinomas as well as against HGF, HPLF, and HPC non-malignant cells. QSAR and western blot analyses were performed. Results: The majority of compounds display submicromolar CC50 values towards the neoplasms; the figures for some of the compounds are below 10^-7 M. In general, 4a-n have much lower CC50 values than those of melphalan, 5-fluorouracil, and methotrexate, while some compounds are equitoxic with doxorubicin. The compounds are far less toxic to the non-malignant cells, giving rise to substantial selectivity index (SI) figures. A QSAR study revealed that both potency and the SI data were controlled to a large extent by the electronic properties of the substituents in the arylidene aryl rings. Two representative compounds, 4f and 4g, caused apoptosis in HSC-2 cells. Conclusion: The compounds in series 4 are potent cytotoxins displaying tumor-selective toxicity. In particular, 4g with an average CC50 value of 0.04 μM towards four malignant cell lines and a selectivity index of 46.3 is clearly a lead molecule that should be further evaluated.