Molecular modeling of indazole-3-carboxylic acid and its metal complexes (Zn, Ni, Co, Fe and Mn) as NO synthase inhibitors: DFT calculations, docking studies and molecular dynamics simulations

An efficient and simple approach for synthesizing indazole compounds using palladium-catalyzed Suzuki-Miyaura cross-coupling

A series of indazole derivatives (6a-6i and 7a-7i) has been synthesized using Suzuki Miyaura cross-coupling with a palladium catalyst from readily available starting materials. An efficient and reliable methodology was employed for the synthesis, and the compounds were thoroughly characterized using 1H NMR, 13C NMR, FT-IR, and HRMS analysis to confirm their structural integrity and purity. Density function theory (DFT) computation identified four compounds (6g, 6h, 7g, and 7h) with significant energy band gaps. Additionally, the molecular electrostatic potential study highlighted the distinct electrical characteristics of these indazole molecules. Subsequent molecular docking investigations were carried out using the AUTODOCK method with two separate protein data bank (PDB) structures (6FEW, 4WA9) involved in renal cancer pathways. The results showed that eight substances PDB: 6FEW (6g, 6h, 7g, and 7h) and PDB: 4WA9 (6a, 6c, and 7c, 7g) had the highest binding energies, indicating their potential as therapeutic agents for treating kidney cancer.

Synthesis molecular docking and DFT studies on novel indazole derivatives

The amide bond is an important functional group used in various fields of chemistry, including organic synthesis, drug discovery, polymers, and biology. Although normal amides are planar, and the amide has an N-C(O) bond, herein, the 26 indazole derivatives were reported via amide cross-coupling (8a-8z). Using IR, 1H NMR, 13C NMR, and mass spectrometry, all of the produced compounds were analysed. A DFT computational study was also conducted using GAUSSIAN 09-Gaussian View 6.1, which revealed that 8a, 8c, and 8s had the most substantial HOMO-LUMO energy gap. The effectiveness of indazole moieties with renal cancer-related protein (PDB: 6FEW) was assessed by docking the derivatives using Autodock 4. The analysis showed that derivatives 8v, 8w, and 8y had the highest binding energies.

In silico approach identified benzoylguanidines as SARS-CoV-2 main protease (Mpro) potential inhibitors

The coronavirus disease-2019 (COVID-19) pandemic, caused by the novel coronavirus severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), became the highest public health crisis nowadays. Although the use of approved vaccines for emergency immunization and the reuse of FDA-approved drugs remains at the forefront, the search for new, more selective, and potent drug candidates from synthetic compounds is also a viable alternative to combat this viral disease. In this context, the present study employed a computational virtual screening approach based on molecular docking and molecular dynamics (MD) simulation to identify possible inhibitors for SARS-CoV-2 Mpro (main protease), an important molecular target required for the maturation of the various polyproteins involved in viral replication. The virtual screening approach selected four potential inhibitors against SARS-CoV-2 Mpro. In addition, MD simulation studies revealed changes in the positions of the ligands during the simulations compared to the complex obtained in the molecular docking studies, showing the benzoylguanidines LMed-110 and LMed-136 have a higher affinity for the active site compared to the other structures that tended to leave the active site. Besides, there was a better understanding of the formation and stability of the existing H-bonds in the formed complexes and the energetic contributions to the stability of the target-ligand molecular complexes. Finally, the in silico prediction of the ADME profile suggested that LMed-136 has drug-like characteristics and good pharmacokinetic properties. Therefore, from the present study, it can be suggested that these structures can inhibit SARS-CoV-2 Mpro. Nevertheless, further studies are needed in vitro assays to investigate the antiviral properties of these structures against SARS-CoV-2.

Unique Metal-Ligand Interplay in Directing Discrete and Polymeric Derivatives of Isomeric Azole-Carboxylate. Varying Electronic Form, C-C Coupling, and Receptor Feature

This article dealt with the ruthenium and osmium derivatives of isomeric 1H-indazole-3-carboxylic acid/2H-indazole-3-carboxylic acid (H₂L1) and 1H-benzimidazole-2-carboxylic acid (H₂L2) along with the π-acidic bpy (bpy = 2,2'-bipyridine) and pap (pap = 2-phenylazopyridine) co-ligands. It thus extended structurally authenticated monomeric ([(bpy)₂Ru^II(HL1^-)]ClO₄ [1]ClO₄, (pap)₂Ru^II(L1^2-) 2, (bpy)₂Os^II(L1^2-) 3, (pap)₂Os^II(L1^2-) 4, (bpy)₂Ru^II(L2^2-) 5, (bpy)₂Os^II(L2^2-) 8, and (pap)₂Os^II(L2^2-) 9) and dimeric ([(bpy)₂Ru^II(μ-L2^2-)Ru^II(bpy)₂](ClO₄)₂ [6](ClO₄)₂) complexes. It also described modified L2'^2- (L2'^2- = 2,2'-bisbenzimidazolate)-bridged [(pap)₂Ru^II(μ-L2'^2-)Ru^II(pap)₂](ClO₄)₂ [7](ClO₄)₂, where L2'^2- was developed selectively with the {Ru(pap)₂} metal fragment via in situ intermolecular C-C coupling of the two units of decarboxylated benzimidazolate. Moreover, chemical oxidation (Os^II to Os^III) of (bpy)₂Os^II(L1^2-) 3 (E⁰ = 0.11 V versus SCE) and (bpy)₂Os^II(L2^2-) 8 (E⁰ = 0.12 V versus SCE) by AgClO₄ yielded unprecedented Os^III-Ag^I derived polymeric {[(bpy)₂Os^III-L1^2--Ag^I(CH₃CN)](ClO₄)₂}_n {[10](ClO₄)₂}_n and dimeric [(bpy)₂Os^III-L2^2--Ag^I(CH₃CN)](ClO₄)₂ [11](ClO₄)₂ complexes as a function of trans and cis orientations of the active N2 donor with special reference to the carboxylate O2 of L^2-, respectively. Microscopic (FE-SEM, TEM-EDX, and AFM) and DLS experiments suggested a homogeneously dispersed hollow spherical shaped morphology of {[10](ClO₄)₂}_n with an average particle size of 200-400 nm as well as its non-dissociative feature in the aprotic medium. Experimental (structure, spectroscopy, and electrochemistry) and theoretical (DFT/TD-DFT) explorations revealed a redox non-innocent feature of L^2- in the present coordination situations and the selective anion sensing (X = F^-, CN^-, and OAc^-) event of [1]ClO₄ involving a free NH group at the backface of HL1^-, which proceeded via the NH···X hydrogen bonding interaction.