Synthesis and In Silico Evaluation of New 2-Amino-Thiophene Derivatives and Their Isosteres as Promising Anti-Leishmania Agents

Synthesis and In Silico Evaluation of New 2-Amino-Thiophene Derivatives and Their Isosteres as Promising Anti-Leishmania Agents

• Author
• Rodrigo Santos Aquino de Araújo
• Co-authors
• Ricardo Eduardo Pereira Coutinho , Bruna Kalyne Araújo da Silva , Marcus Tullius Scotti , Francisco Jaime Bezerra Mendonça Junior
• Abstract

• INTRODUCTION: Leishmaniasis is one of the main neglected diseases and, as such, is mainly distributed in countries in Africa, Asia and Latin America, with Brazil being one of the most affected. This infection is caused by protozoa of the genus Leishmania sp. and transmitted by the bit of female phlebotomine invertebrates [1,2]. It is responsible for the infection of more than 12 million people worldwide, with an annual average of 52,645 cases for the cutaneous form and 2,488 cases for the visceral form on the American continent alone [3]. However, the therapeutic alternatives for the treatment of leishmaniasis have remained the same over the last few decades, based on the use of first-line drugs, such as pentavalent antimonials, and second-line drugs, such as amphotericin B, or even combinations thereof. These drugs have high toxicity and high treatment costs, as well as leading to the emergence of resistant strains, highlighting the need to develop new, more effective and safer drugs [4,5]. Heterocycle compounds are of great interest due their broad biological potential, including their anti-Leishmania actions, such as thiophenic derivatives, structurally made up of five-membered rings containing sulfur as a heteroatom. Recent publications by our research group have highlighted the pharmacophoric role of indolic 2-amino-thiophene nuclei as leishmanicidal agents, allowing them to be used as prototypes in the rational planning of other possibly promising derivatives [6,7]. Medicinal chemistry has tools to support the planning of new drugs, such as molecular modification, which refers to structural changes other than in their pharmacophoric groups, and bioisosterism, which refers to the replacement of atoms or molecular groups by others with similar physicochemical properties; in both cases, the aim is to obtain compounds with improved pharmacological and/or pharmacokinetic profiles [8,9]. Medicinal chemistry also relies computational tools that make it possible to predict, among other characteristics, some of their pharmacokinetic properties, enabling this increase in the design of new desired compounds [10]. AIMS: The aim of this work was to synthesize new series of 2-amino-thiophenic and 2-amino-selenophenic indolic derivatives based on a promising pharmacophoric prototype with known anti-Leishmania potential, as well as their theoretical in silico evaluation in terms of their ADMET pharmacokinetic profiles, in order to predict their druglikeness and drug-score profiles. METHODS: The 2-amino-5,6,7,8,9-pentahidro-5H-cyclohepta-[b]selenophene-3-carbonitrile (1), 2-amino-5,6,7,8,9,10-hexahidro-cycloocta[b]-selenophene-3-carbonitrile (2) and 2-amino-[(7-N-Boc-5,6,8-trihidro)-piperidine]-[b]-thiophene-3-carbonitrile (3) adducts were synthesized according to known Gewald reaction [11], using their respective cyclic ketones (cycloheptanone, cyclooctanone or 4-N-Boc-piperidone), malononitrile and their respective chalcogens (sulfur or selenium), in a basic medium of triethylamine and N,N-dimethylformamide or ethanol. Once obtained, they were used as starting reagents for condensation reactions with substituted indolic aldehydes, under acid catalysis and in ethanolic media [12]. Obtaining the final compounds as solid precipitates allowed them to be purified by simple filtration. The physicochemical Properties of the derivatives obtained (i.e. appearance, yield, melting range and retention factor) were determined and their structural characterization was carried out using infrared spectroscopy and 1H and 13C nuclear magnetic resonance techniques. To predict the pharmacokinetic profiles, the Osiris Property software was used to generate the druglikeness and drug-score parameters by comparing the structures of the derivatives with known drugs, by matching the presence of functional grouos and/or consistent physical properties in a database with around 5,300 different fragments [13,14]. In addition, the use of SwissADME software enabled the generation of the Bioavailability Radar graph, which brings together a set of properties favorable to the bioavailability of molecules, reinforcing their druglikeness profiles based on their lipophilicity, size, polarity, solubility, flexibility and saturation. This same software generated a BOILED-Egg graph, which predicts the passive gastrointestinal absorption and blood-brain barrier permeability of the compounds analyzed, as well as their classification as P-glycoprotein substrates or not [14]. RESULTS AND DISCUSSION: Gewald adducts 1, 2 and 3 were obtained in yields ranging from 24.3% to 36.1%. With the exception of compound 2 (obtained impurely as a viscous oil), they were obtained in solid form. Their use as starting reagents in the second condensation stage enabled three new series of derivatives to be obtained, two series of indolic 2-amino-selenophenic derivatives and one series of indolic 2-amino-thiophenic derivatives, named, according to their starting adducts, 1a-f, 2a-k and 3a-f. All the derivatives were obtained in their solid forms as amorphous crystals, in yields ranging from 42.1% to 73% for 1a-f, from 14.2% to 83.7% for the 2a-k serie, and from 40.3% to 69.4% for the 3a-f series. It is Worth noting that the greater variation in yield for the final derivatives of series 2 was due to the failure to successfully isolate adduct 2 and, therefore, its crude in the next stage, leading to an inevitable variation in the initial mass of this reagent. A closer look at the yields of series 1 and 3 shows that the yields were moderate to good, in agreement with equivalent thiophenic derivatives obtained by Félix et al. (2016) [6] and Félix et al. (2020) [7], which demonstrates that there is no significant difference in reactivity between the sulfur and selenium heterocycles. Their structures were confirmed after infrared (IR) and nuclear magnetic resonance (NMR) spectroscopic characterization. The IR spectra showed characteristic absorption regions for groups such as imine (regions near to 1,600 cm-1), nitrile (regions near to 2,200 cm-1) and N-H of indole (regions near to 3,200 cm-1). For 1H NMR, characteristic chemical shifts were observed for N-H (? near to 12.0 ppm), imine hydrogen (? near to 9.0 ppm) and characteristic shifts in the aromatic (? between 7.0 and 9.0 ppm) and methylenic (? between 1.5 and 4.0 ppm) hydrogen regions. For 13C NMR, characteristic chemical shifts were observed for iminic carbon (? close to 156.0 ppm), nitrile group (? close to 116.0 ppm), aromatic carbons (? between 110.0 and 140.0 ppm) and methylenic carbons (in most cases with ? between 20.0 and 40.0 ppm). Once the final derivatives had been obtained and structurally confirmed, they were subjected to in silico analysis of their pharmacokinetic, druglikeness and drug-score profiles. The druglikeness profile is evaluated by comparing similar physicochemical properties with known commercial structures and the derivatives analyzed, and should reflect positive values when similarity is found. However, the structures of the derivatives obtained showed values ranging from -10,03 to -38,2, indicating that they do not have similar properties to other known drugs. Similarly, the drug-score percentages ranged from 11% to 35%. Despite the unpromising in silico results, it is important to note that these may not be decisive for their actual biological activities. The in silico results for the Bioavailability Radar obtained through SwissADME show that all the derivatives have a good prediction of bioavailability in oral administration, fitting in with good parameters for size, flexibility, solubility, lipophilicity, saturation and polarity. In addition, most of the compounds in series 1 and 2 presented good in silico profiles for intestinal absorption and blood-brain barrier permeability, while the derivatives in serie 3 only exhibited intestinal absorption profiles. With regard to their evaluation as substrates for P-glycoprotein, an efflux macromolecule responsible for expelling drugs from the cell interior, just compounds 3b and 3c showed no potential to act as a substrate for it. CONCLUSION: In general, starting from a known 2-amino-thiophene indolic prototype, the planned synthetic modifications were carried out successfully, obtaining the desired derivatives in yields ranging from moderate to good. In the isosterism evaluation, no significant differences in reactivity were observed between the sulfur and selenium derivatives. Their druglikeness and drug-score profiles were also evaluated in silico and, although their results were not comparable with known drug structures, it is worth noting that these are not determinants of the pharmacological and/or pharmacokinetic success of a molecule. Their oral bioavailability evaluations showed that the compounds obtained fit within parameters values analyzed, and their absorption profiles indicated good chances of intestinal and/or blood-brain permeability. The prediction that the compounds could act as substrates for P-glycoprotein may not represent a positive result, although, again, they may prove to be different when in contact with a biological environment in subsequent in vitro tests.  Based on the promising anti-Leishmania activity of the prototype pharmacophore, future tests are planned to evaluate the influence of the structural modifications made. ACKNOWLEDGEMENT: To the National Council for Scientific  and Technological Development and the Foundation for Research Support of the State of Paraíba, under process nº 421812/2022-2, in accordance with the program to support the establishment of young doctors in Paraíba.
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• Keywords
• 2-Amino-thiophene, Bioisosterism, Medicinal Chemistry, In Silico Evaluation
• Modality
• Pôster
• Subject Area
• Drug Design and Discovery, Synthesis and Natural Products