Searching for novel N1-substituted benzimidazol-2-ones as non-nucleoside HIV-1 RT inhibitors

Crystal structure, Hirshfeld surface analysis, and calculations of inter-molecular inter-action energies and energy frameworks of 1-[(1-hexyl-1H-1,2,3-triazol-4-yl)meth-yl]-3-(1-methyl-ethen-yl)-benzimidazol-2-one

The benzimidazole moiety in the title mol-ecule, C19H25N5O, is almost planar and oriented nearly perpendicular to the triazole ring. In the crystal, C-H⋯O hydrogen bonds link the mol-ecules into a network structure. There are no π-π inter-actions present but two weak C-H⋯π(ring) inter-actions are observed. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (62.0%), H⋯C/C⋯H (16.1%), H⋯N/N⋯H (13.7%) and H⋯O/O⋯H (7.5%) inter-actions. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated via the dispersion energy contributions in the title compound.

Deciphering the enigmas of non-nucleoside reverse transcriptase inhibitors (NNRTIs): A medicinal chemistry expedition towards combating HIV drug resistance

The pivotal involvement of reverse transcriptase activity in the pathogenesis of the progressive HIV virus has stimulated gradual advancements in drug discovery initiatives spanning three decades. Consequently, nonnucleoside reverse transcriptase inhibitors (NNRTIs) have emerged as a preeminent category of therapeutic agents for HIV management. Academic institutions and pharmaceutical companies have developed numerous NNRTIs, an essential component of antiretroviral therapy. Six NNRTIs have received Food and Drug Administration approval and are widely used in clinical practice, significantly improving the quality of HIV patients. However, the rapid emergence of drug resistance has limited the effectiveness of these medications, underscoring the necessity for perpetual research and development of novel therapeutic alternatives. To supplement the existing literatures on NNRTIs, a comprehensive review has been compiled to synthesize this extensive dataset into a comprehensible format for the medicinal chemistry community. In this review, a thorough investigation and meticulous analysis were conducted on the progressions achieved in NNRTIs within the past 8 years (2016-2023), and the experiences and insights gained in the development of inhibitors with varying chemical structures were also summarized. The provision of a crucial point of reference for the development of wide-ranging anti-HIV medications is anticipated.

Crystal structure, Hirshfeld surface analysis, calculations of inter-molecular inter-action energies and energy frameworks and the DFT-optimized mol-ecular structure of 1-[(1-butyl-1H-1,2,3-triazol-4-yl)meth-yl]-3-(prop-1-en-2-yl)-1H-benzimidazol-2-one

The benzimidazole entity of the title mol-ecule, C17H21N5O, is almost planar (r.m.s. deviation = 0.0262 Å). In the crystal, bifurcated C-H⋯O hydrogen bonds link individual mol-ecules into layers extending parallel to the ac plane. Two weak C-H⋯π(ring) inter-actions may also be effective in the stabilization of the crystal structure. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (57.9%), H⋯C/C⋯H (18.1%) and H⋯O/O⋯H (14.9%) inter-actions. Hydrogen bonding and van der Waals inter-actions are the most dominant forces in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization of the title compound is dominated via dispersion energy contributions. The mol-ecular structure optimized by density functional theory (DFT) at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure in the solid state.

Unlocking the Pharmacological Potential of Benzimidazole Derivatives: A Pathway to Drug Development

Heterocyclic molecules have fascinated a massive interest in medicinal chemistry. They are heterocyclic compounds that have gained significance due to their diverse variety of pharmacological activities. Benzimidazole is a heterocyclic compound consisting of benzene and imidazole rings. The ease of synthesis and the structural versatility of benzimidazole make it a promising scaffold for drug development. Many biological actions of benzimidazole derivatives have been well documented, including antibacterial, antiviral, anticancer, anti-inflammatory, antitubercular, and anthelmintic properties. The mechanism of action of benzimidazole derivatives varies with their chemical structure and target enzyme. This review has explored numerous methods for producing benzimidazole derivatives as well as a broad range of pharmacological activities. SAR investigations are also discussed in this review as they provide crucial details regarding the essential structural qualities that benzimidazole derivatives must have in order to be biologically active, which could aid in the rational design of new drug candidates. Benzimidazole scaffold is an exclusive structure in drug design and discovery. Many new pharmaceutical drugs containing benzimidazole are anticipated to be available within the next ten years as a result of the extensive therapeutic applications of benzimidazole and its derivatives. This review inspired many researchers to develop more biologically active compounds bearing benzimidazole, expanding the scope of finding a remedy for other diseases. From this study, we concluded that 2-substituted benzimidazole was considered more extensively by researchers.

Synthesis, structure and Hirshfeld surface analysis of 1,3-bis-[(1-octyl-1H-1,2,3-triazol-4-yl)meth-yl]-1H-benzo[d]imidazol-2(3H)-one

The title mol-ecule, C29H44N8O, adopts a conformation resembling a two-bladed fan with the octyl chains largely in fully extended conformations. In the crystal, C-H⋯O hydrogen bonds form chains of mol-ecules extending along the b-axis direction, which are linked by weak C-H⋯N hydrogen bonds and C-H⋯π inter-actions to generate a three-dimensional network. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (68.3%), H⋯N/N⋯H (15.7%) and H⋯C/C⋯H (10.4%) inter-actions.

Recent achievements in the synthesis of benzimidazole derivatives

Benzimidazoles are a class of heterocyclic compounds in which a benzene ring is fused to the 4 and 5 positions of an imidazole ring. Benzimidazole refers to the parent compound, while benzimidazoles are a class of heterocyclic compounds having similar ring structures, but different substituents. Benzimidazole derivatives possess a wide range of bioactivities including antimicrobial, anthelmintic, antiviral, anticancer, and antihypertensive activities. Many compounds possessing a benzimidazole skeleton have been employed as drugs in the market. The application of benzimidazoles in other fields has also been documented. The synthesis of benzimidazole derivatives has attracted much attention from chemists and numerous articles on the synthesis of this class of heterocyclic compound have been reported over the years. The condensation between 1,2-benzenediamine and aldehydes has received intensive interest, while many novel methods have been developed. In this article, we will give a comprehensive review of studies on the synthesis of benzimidazole, which date back to 2013. We have also tried to describe reaction mechanisms as much as we can. The work might be useful for chemists who work in the synthesis of heterocycles or drug chemistry.

Exploring antiviral potency of N-1 substituted pyrimidines against HIV-1 and other DNA/RNA viruses: Design, synthesis, characterization, ADMET analysis, docking, molecular dynamics and biological activity

A novel series of pyrimidine derivatives, bearing modified benzimidazoles at N-1 position, has been designed, synthesized and screened as NNRTIs against HIV and as broad-spectrum antiviral agents. The molecules were screened against different HIV targets using molecular docking experiment. The docking results indicated that the molecules interacted well with the residues Lys101, Tyr181, Tyr188, Trp229, Phe227 and Tyr318 present in NNIBP of HIV-RT protein, formed quite stable complexes and, thus, behaved as probable NNRTIs. Among these compounds, 2b and 4b showed anti-HIV activity with IC50 values as 6.65 µg/mL (SI = 15.50) and 15.82 µg/mL (SI = 14.26), respectively. Similarly, compound 1a showed inhibitory property against coxsackie virus B4 and compound 3b against different viruses. Molecular dynamics simulation results unequivocally demonstrated the higher stability of the complex HIV-RT:2b than the HIV-RT:nevirapine complex. The MM/PBSA-based binding free energy (-) 114.92 kJ/mol of HIV-RT:2b complex in comparison to that of HIV-RT:nevirapine complex (-) 88.33 kJ/mol, further demonstrated the higher binding strength of 2b and thus, established the potential of compound 2b as a lead molecule as an HIV-RT inhibitor.

A Comprehensive Account on Recent Progress in Pharmacological Activities of Benzimidazole Derivatives

Nowadays, nitrogenous heterocyclic molecules have attracted a great deal of interest among medicinal chemists. Among these potential heterocyclic drugs, benzimidazole scaffolds are considerably prevalent. Due to their isostructural pharmacophore of naturally occurring active biomolecules, benzimidazole derivatives have significant importance as chemotherapeutic agents in diverse clinical conditions. Researchers have synthesized plenty of benzimidazole derivatives in the last decades, amidst a large share of these compounds exerted excellent bioactivity against many ailments with outstanding bioavailability, safety, and stability profiles. In this comprehensive review, we have summarized the bioactivity of the benzimidazole derivatives reported in recent literature (2012-2021) with their available structure-activity relationship. Compounds bearing benzimidazole nucleus possess broad-spectrum pharmacological properties ranging from common antibacterial effects to the world's most virulent diseases. Several promising therapeutic candidates are undergoing human trials, and some of these are going to be approved for clinical use. However, notable challenges, such as drug resistance, costly and tedious synthetic methods, little structural information of receptors, lack of advanced software, and so on, are still viable to be overcome for further research.

Recent Advances Towards Treatment of HIV: Synthesis and SAR Studies

In the present study, authors want to encourage the research exertions through structureactivity relationship for the identification of effective molecules for the treatment of Human immunodeficiency virus because nowadays AIDS is considered as one of the main causes of death in human beings. A diversity of biological resources has been searched and developed for the treatment of HIV but unfortunately, until now, no medicine is found to be fully effective and safe for the cure of patients. Human immunodeficiency virus is a type of lentivirus which causes the infection of HIV and once it enters the human body, it stays for a longer period of time triggering immunodeficiency syndrome. For searching and developing new potent and effective anti-HIV molecules, medicinal chemists have engaged in countless targets with the structure-activity relationship (SAR) of molecules and on this basis, many antiretroviral therapies have been developed to cure HIV infection. Most of these new searched molecules have been found to be clinically active against various types of AIDS patient and auxiliary research in this area may lead to better treatment in the near future. This article encompasses and highlights the recent advancement of innumerable inhibitors laterally through synthetic, semi-synthetic and structure-activity relationship approaches.

Alkylated benzimidazoles: Design, synthesis, docking, DFT analysis, ADMET property, molecular dynamics and activity against HIV and YFV

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New benzimidazole analogs synthesized as antivirals against HIV-1 and yellow fever virus.

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Molecular dynamics simulation studies indicated a stable ligand-protein complex of compound 3a within NNIBP of HIV-RT.

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DFT analysis confirmed the stability of hydrogen bonding interaction between the TRP 229 residue of HIV-RT and compound 3a.

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Molecules were tested for their anti-HIV and broad spectrum antiviral properties against different DNA and RNA viruses.

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Antiviral properties and cytotoxicity determined using MTT assay.

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Compound 3a showed anti-HIV activity and compound 2b showed excellent inhibition property against yellow fever virus.

A series of alkylated benzimidazole derivatives was synthesized and screened for their anti-HIV, anti-YFV, and broad-spectrum antiviral properties. The physicochemical parameters and drug-like properties of the compounds were assessed first, and then docking studies and MD simulations on HIV-RT allosteric sites were conducted to find the possible mode of their action. DFT analysis was also performed to confirm the nature of the hydrogen bonding interaction of active compounds. The in silico studies indicated that the molecules behaved like possible NNRTIs. The nature – polar or non-polar and position of the substituent present at fifth, sixth, and N-1 positions of the benzimidazole moiety played an important role in determining the antiviral properties of the compounds. Among the various compounds, 2-(5,6-dibromo-2-chloro-1H-benzimidazol-1-yl)ethan-1-ol (3a) showed anti-HIV activity with an appreciably low IC₅₀ value as 0.386 × 10⁻⁵μM. Similarly, compound 2b, 3-(2-chloro-5-nitro-1H-benzimidazol-1-yl) propan-1-ol, showed excellent inhibitory property against the yellow fever virus (YFV) with EC₅₀ value as 0.7824 × 10⁻²μM.

Exploiting the 1-(4-fluorobenzyl)piperazine fragment for the development of novel tyrosinase inhibitors as anti-melanogenic agents: Design, synthesis, structural insights and biological profile

The development of Tyrosinase inhibitors (TYRIs) could represent an efficacious strategy for pharmacological intervention on skin pathologies related to aberrant production of melanin. Based on in silico studies we designed and tested a library of twenty-four compounds bearing the 4-(4-fluorobenzyl)piperazin-1-yl]-fragment. As result, we identified several compounds with excellent inhibit effects at low micromolar concentration against TYR from Agaricus bisporus (TyM). Among them, compound 25 (IC₅₀ = 0.96 μM) proved to be ∼20-fold more potent than the reference compound kojic acid (IC₅₀ = 17.76 μM) having wide applications in the cosmetics and pharmaceutical industries. The mode of interaction of active inhibitor 25 was deciphered by means of crystallography as well as molecular docking and these results were consistent with kinetic experiments. Moreover, the identified compound 25 exhibited no considerable cytotoxicity and showed anti-melanogenic effects on B16F10 melanoma cells. Therefore, a combination of computational and biochemical approaches could represent a rational guidelines for further structural modification of this class of compounds as future anti-melanogenic agents.

Discovery of benzimidazole-based Leishmania mexicana cysteine protease CPB2.8ΔCTE inhibitors as potential therapeutics for leishmaniasis

Chemotherapy is currently the only effective approach to treat all forms of leishmaniasis. However, its effectiveness is severely limited due to high toxicity, long treatment length, drug resistance, or inadequate mode of administration. As a consequence, there is a need to identify new molecular scaffolds and targets as potential therapeutics for the treatment of this disease. We report a small series of 1,2-substituted-1H-benzo[d]imidazole derivatives (9a-d) showing affinity in the submicromolar range (K_i  = 0.15-0.69 μM) toward Leishmania mexicanaCPB2.8ΔCTE, one of the more promising targets for antileishmanial drug design. The compounds confirmed activity in vitro against intracellular amastigotes of Leishmania infantum with the best result being obtained with derivative 9d (IC₅₀  = 6.8 μM), although with some degree of cytotoxicity (CC₅₀  = 8.0 μM on PMM and CC₅₀  = 32.0 μM on MCR-5). In silico molecular docking studies and ADME-Tox properties prediction were performed to validate the hypothesis of the interaction with the intended target and to assess the drug-likeness of these derivatives.

Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review

Currently, millions of people are living with human immunodeficiency virus type 1 (HIV-1), which causes acquired immunodeficiency syndrome. However, the spread of the HIV-1 resistance to antiviral agents is the major problem in the antiretroviral therapy and medical management of HIV-infected patients. HIV-1 reverse transcriptase (RT) is one of the key viral targets for HIV-1 inhibition. Therefore, the studies on the combatting the HIV resistance that occurs due to the structural changes in RT, are in great demand. This work aims to provide an overview of the state-of-the-art molecular docking approaches applied to the studies of the HIV-1 resistance, associated with RT structure changes. We have reviewed recent studies using molecular docking with mutant forms of RT. The work discusses the modifications of molecular docking, which have been developed to find the novel molecules active against resistance mutants of RT and/or recombinant strains of HIV-1. The perspectives of the existing algorithms of molecular docking to the studies on molecular mechanisms of resistance and selection of the correct binding poses for the reverse transcriptase inhibitors are discussed.

I2-Mediated transition-metal-free aromatic C–H amination for the synthesis of benzimidazol-2-ones and related heterocycles

A practical I₂-mediated aromatic C–H amination reaction was established for benzimidazol-2-one synthesis under transition-metal-free conditions. The present reaction can be performed directly from disubstituted amines and isocyanates without the purification of the urea intermediates in a scalable fashion.

Investigating the geometrical preferences of a flexible benzimidazolone-based linker in the synthesis of coordination polymers

A series of new group 2 coordination polymers, MgL ={MgL(H₂O)(DMF)_0.75}_∞, CaL = {CaL(DMF)₂}_∞, SrL = {SrL(H₂O)_0.5}_∞ and BaL = {BaL(H₂O)_0.5}_∞, were synthesized using a flexible benzimidazolone diacetic acid linker (H₂L) in which the two carboxylic acid binding sites are connected to a planar core via {-CH₂-} spacers that can freely rotate in solution. In a 'curiosity-led' diversion from group 2 metals, the first row transition metal salts Mn²⁺, Cu²⁺ and Zn²⁺ were also reacted with L to yield crystals of MnL = {MnL(DMF)(H₂O)_3.33}_∞, Cu₃L₂  = {Cu₃L₂(DMF)₂(CHO₂)₂}_∞ and ZnL = {ZnL(DMF)}_∞. Crystal structures were obtained for all seven materials. All structures form as two-dimensional sheets and contain six-coordinate centres, with the exception of ZnL, which displays tetrahedrally coordinated metal centres, and Cu₃L₂ , which contains square planar coordinated metal centres and Cu paddle-wheels. In each structure, the linker adopts one of two distinct conformations, with the carboxylate groups either cis or trans with respect to the planar core. All materials were also characterized by powder X-ray diffraction and thermogravimetric analysis.