In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs

Rational drug design implies usage of molecular modeling techniques such as pharmacophore modeling, molecular dynamics, virtual screening, and molecular docking to explain the activity of biomolecules, define molecular determinants for interaction with the drug target, and design more efficient drug candidates. Kinases play an essential role in cell function and therefore are extensively studied targets in drug design and discovery. Kinase inhibitors are clinically very important and widely used antineoplastic drugs. In this review, computational methods used in rational drug design of kinase inhibitors are discussed and compared, considering some representative case studies

Identification of potential dual histamine H3 receptor antagonist and serotonin reuptake inhibitors through ligand-based and structure-based approaches

The major depressive disorder (MDD), routinely treated with selective serotonin reuptake inhibitors (SSRIs), is the second leading cause of disability worldwide. However, the treatment of MDD is complicated by high prevalence of residual symptoms connected to increased risk of relapse. Some of the most common residual symptoms are cognitive dysfunction and fatigue. Histamine H3 receptor (H3R) antagonists are both, pro-cognitive and wake-promoting agents. In pre-clinical study it was suggested that dual histamine H3R antagonist and SSRI may have utility as a more efficient antidepressant therapy. The aim of this in silico study was identification of novel dual SSRI/H3R antagonist using ligand-based and structure-based drug design techniques. Starting from structures and activities of known dual ligands, two GRIND-based 3D-QSAR models have been developed, SERT model (R2 = 0.97; Q2 = 0.79; SDEP= 0.124) and H3R model (R2 = 0.86; Q2 = 0.75; SDEP= 0.184), and 3Dpharmacophores were constructed. Further, homology model of H3R was built and refined with molecular dynamics. The hypotheses of binding modes for dual ligands were generated with molecular docking on H3R model and X-ray structure of SERT. In the second part of this study, ligand-based and structure-based virtual screening models were generated and validated. Prospective screening of ZINC database was performed in order to extract novel chemotypes of dual ligands. Final selection of ligands was performed based on generated pharmacophore and docking models as well as predicted pharmacokinetic properties. Few novel compounds were emphasized as promising starting point for development of new classes of dual antidepressants

3D-QSAR study of pyrazolo[3,4-d]pyrimidines and 1,3,4-thiadiazoles as BCR-ABL1 inhibitors

The treatment of chronic myeloid leukemia (CML) was revolutionized by introducing Bcr-Abl1 inhibitors to the extent that today it could be considered as manageable chronic disease. Although, ATP-competitive Bcr-Abl1 inhibitors set the milestone for treatment of CML, resistance on therapy in significant number of patients still remains major challenge. 3D quantitative structure-activity relationship (3D-QSAR) model of selected Bcr-Abl1 inhibitors was built in order to gain insight into structural requirements for inhibitory activity. The 3D-QSAR model with best validation parameters was selected for further study and design of novel inhibitors.14th International Conference on Fundamental and Applied Aspects of Physical Chemistry, September 24–28, 2018, Belgrad

Molecular modeling of 5 [(amidobenzyl)oxy] nicotinamides as sirtuin 2 inhibitors using alignment - (in)dependent 3D-QSAR analysis and molecular docking

The group of 5 [(amidobenzyl)oxy] nicotinamides (SIRT2) inhibitors. Despite structural similarity, representatives of this group of inhibitors displayed versatile mechanisms of inhibition which hamper rational drug design. The aim of this research was to form a 3D-QSAR (3D-Quantitative Structure-Activity Relationship) model, define the pharmacophore of this subgroup of SIRT2 inhibitors, define the mode of protein-ligand interactions and design new compounds with improved predicted activity and pharmacokinetics. For the 3D-QSAR study, data set was generated using structures and -conformations of compounds were optimized, alignment-independent GRIND2 descriptors were calculated and 3D-QSAR PLS models were generated using 70% of data set. To investigate bioactive conformations of inhibitors, molecular docking was used. Molecular docking analysis identified two clusters of predicted bioactive conformations which is in alignment with experimental observations. The defined pharmacophoric features were used to design novel inhibitors with improved predicted potency and ADMET profiles.1st International Conference on Chemo and BioInformatics, Kragujevac, October 26-27, 2021 Serbi

Correlating Basal Gene Expression across Chemical Sensitivity Data to Screen for Novel Synergistic Interactors of HDAC Inhibitors in Pancreatic Carcinoma

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal malignancies. Development of the chemoresistance in the PDAC is one of the key contributors to the poor survival outcomes and the major reason for urgent development of novel pharmacological approaches in a treatment of PDAC. Systematically tailored combination therapy holds the promise for advancing the treatment of PDAC. However, the number of possible combinations of pharmacological agents is too large to be explored experimentally. In respect to the many epigenetic alterations in PDAC, epigenetic drugs including histone deacetylase inhibitors (HDACi) could be seen as the game changers especially in combined therapy settings. In this work, we explored a possibility of using drug-sensitivity data together with the basal gene expression of pancreatic cell lines to predict combinatorial options available for HDACi. Developed bioinformatics screening protocol for predictions of synergistic drug combinations in PDAC identified the sphingolipid signaling pathway with associated downstream effectors as a promising novel targets for future development of multi-target therapeutics or combined therapy with HDACi. Through the experimental validation, we have characterized novel synergism between HDACi and a Rho-associated protein kinase (ROCK) inhibitor RKI-1447, and between HDACi and a sphingosine 1-phosphate (S1P) receptor agonist fingolimod

Medicinska hemija inhibitora histon deacetilaza

Today, we are witnessing an explosion of scientific concepts in cancer chemotherapy. It has been considered for a long time that genetic instability in cancer should be treated with drugs that directly damage the DNA. Understanding the molecular basis of malignant diseases shed light on studying phenotypic plasticity. In the era of epigenetics, many efforts are being made to alter the aberrant homeostasis in cancer without modifying the DNA sequence. One such strategy is modulation of the lysine acetylome in human cancers. To remove the acetyl group from the histones, cells use the enzymes that are called histone deacetylases (HDACs). The disturbed equilibrium between acetylation and deacetylation on lysine residues of histones can be manipulated with histone deacetylase inhibitors (HDACi). Throughout the review, an effort will be made to present the mechanistic basis of targeting the HDAC isoforms, discovered selective HDAC inhibitors, and their therapeutical implications and expectations in modern drug discovery.Savremena hemoterapija kancera se bazira na velikom broju različitih naučnih pristupa. Dugo se smatralo da bi genetsku nestabilnost u kancerskim oboljenjima trebalo lečiti agensima koji direktno oštećuju DNK. Razumevanje molekularnih osnova malignih oboljenja rasvetlilo je značaj fenotipske plastičnosti. U eri epigenetike, učinjeni su mnogi napori da se izmeni aberantna homeostaza u kancerskom oboljenju bez modifikovanja sekvence DNK. Jedna od takvih strategija je modulacija lizinskog acetiloma u humanim kancerima. Da bi se acetil grupa uklonila sa histona, ćelije koriste enzime histon deacetilaze. Poremećena ravnoteža acetilacije i deacetilacije na lizinskim ostacima histona može biti regulisana inhibitorima histon deacetilaza. Kroz ovaj pregledni rad, biće prikazani mehanizmi inhibicije izoformi histon deacetilaza, različiti inhibitori histon deacetilaza, kao i njihove terapijske primene i očekivanja u modernom razvoju lekova

Targeting Histone Deacetylases: Opportunities for Cancer Treatment and Chemoprevention

The dysregulation of gene expression is a critical event involved in all steps of tumorigenesis. Aberrant histone and non-histone acetylation modifications of gene expression due to the abnormal activation of histone deacetylases (HDAC) have been reported in hematologic and solid types of cancer. In this sense, the cancer-associated epigenetic alterations are promising targets for anticancer therapy and chemoprevention. HDAC inhibitors (HDACi) induce histone hyperacetylation within target proteins, altering cell cycle and proliferation, cell differentiation, and the regulation of cell death programs. Over the last three decades, an increasing number of synthetic and naturally derived compounds, such as dietary-derived products, have been demonstrated to act as HDACi and have provided biological and molecular insights with regard to the role of HDAC in cancer. The first part of this review is focused on the biological roles of the Zinc-dependent HDAC family in malignant diseases. Accordingly, the small-molecules and natural products such as HDACi are described in terms of cancer therapy and chemoprevention. Furthermore, structural considerations are included to improve the HDACi selectivity and combinatory potential with other specific targeting agents in bifunctional inhibitors and proteolysis targeting chimeras. Additionally, clinical trials that combine HDACi with current therapies are discussed, which may open new avenues in terms of the feasibility of HDACi’s future clinical applications in precision cancer therapies

Synthesis, in silico, and in vitro studies of novel dopamine D2 and D3 receptor ligands

Dopamine is an important neurotransmitter in the human brain and its altered concentrations can lead to various neurological diseases. We studied the binding of novel compounds at the dopamine D2 (D2R) and D3 (D3R) receptor subtypes, which belong to the D2-like receptor family. The synthesis, in silico, and in vitro characterization of 10 dopamine receptor ligands were performed. Novel ligands were docked into the D2R and D3R crystal structures to examine the precise binding mode. A quantum mechanics/molecular mechanics study was performed to gain insights into the nature of the intermolecular interactions between the newly introduced pentafluorosulfanyl (SF5) moiety and D2R and D3R. A radioligand displacement assay determined that all of the ligands showed moderate-to-low nanomolar affinities at D2R and D3R, with a slight preference for D3R, which was confirmed in the in silico studies. N-{4-[4-(2-Methoxyphenyl)piperazin-1-yl]butyl}-4-(pentafluoro-λ6-sulfanyl)benzamide (7i) showed the highest D3R affinity and selectivity (pKi values of 7.14 [D2R] and 8.42 [D3R])

Molecular dynamics‐based virtual screening of sirtuin 2 inhibitors

Modulacija aktivnosti epigenetičkog brisača, NAD‐zavisne protein deacetilaze sirtuina 2 (SIRT2), poslednjih godina se pokazala kao obećavajuća strategija u lečenju Parkinsonove bolesti, depresije, određenih tipova kancera, ishemijsko‐reperfuzionih povreda itd. Nasuprot terapijskom potencijalu, još uvek nijedan predstavnik ove grupe farmakološki aktivnih supstanci nije našao svoje mesto na tržištu. Najčešći problemi sa dosada opisanim SIRT2 inhibitorima predstavljaju niska potentnost, loša selektivnost, kao i loše farmakokinetičke osobine što dalje opravdava razvoj novih predstavnika. Cilj ovog rada je bio ispitivanje konformacionih promena SIRT2 u prisustvu inhibitora i dalje poboljšanje dostupnih kristalografskih modela u cilju razvoja efikasnijeg protokola virtual screening‐a. Polazeći od 5 različitih kristalografskih struktura SIRT2‐inhibitor kompleksa, ukupno 1,5 μs simulacija molekulske dinamike u eksplicitnom solventu je izvedeno. 3D deskriptori zasnovani na GRID‐u i linearna diskriminantna analiza su korišćeni za virtual screening (VS) studiju. Konformaciona fleksibilnost SIRT2‐inhibitor kompleksa zabeležena tokom simulacija ukazuje na značajnu fleksibilnost aktivnog mesta i posledično na multiple vezivne modove inhibitora. Nakon procedure klasterovanja trajektorije, nekoliko relevantnih modela kompleksa je izdvojeno i uključeno u dalju VS studiju. VS modeli generisani pomoću tri relevantna kompleksa dobijena studijom molekulske dinamike su pokazali značajno bolje performanse u poređenju sa modelima dobijenim pomoću do danas opisanih kristalografskih struktura. Performanse generisanog VS protokola su značajno poboljšane i u odnosu na do danas publikovane protokole. Rezultati ove studije jasno ukazuju na značaj uračunavanja fleksibilnosti aktivnog mesta u racionalni dizajn SIRT2 inhibitora. Novi hemotipovi potenijalnih inhibitora SIRT2 su izdvojeni iz baza komercijalno dostupnih jedinjenja primenom generisanih VS modela. U ovoj studiji formirani su realističniji modeli aktivnog mesta sirtuina 2 kojima su značajno poboljšane performanse virtual screening‐a u odnosu na do danas publikovane studije. Rezultati ove studije, uključujući i opisane konformacione promene doprinose sveobuhvatnom razumevanju odnosa strukture i aktivnosti SIRT2 inhibitora i dodatno racionalizuju dizajn selektivnijih i potentnijih inhibitora.Modulation of activity of epigenetic eraser, NAD‐dependent protein deacetylase sirtuin 2 (SIRT2), recently emerged as promising therapeutic strategy for the treatment of many diseases, including Parkinson’s disease, depression, some types of cancers, necrotic injuries (ischemic stroke, myocardial infarction) etc. Contrary to therapeutic potential, none of SIRT2 inhibitors reported to date has been approved for the market. Some of the most common problems with current SIRT2 inhibitors include poor potency, selectivity and pharmacokinetic properties which justify further development of novel inhibitors. The Aim of this study was to explore conformational space of sirtuin2‐inhibitor complexes and further refinement of available crystallographic structures in order to develop more efficient virtual screening (VS) protocol. Starting from five different crystallographic structures of SIRT2 co‐crystalized with inhibitors, total of 1.5 μs of molecular dynamics (MD) simulations in explicit solvent has been performed. GRID‐based 3D descriptors and linear discriminant analysis were used for virtual screening. Significant conformational flexibility of SIRT2‐inhibitor complexes was observed during simulations indicating overall binding site flexibility and multiple binding modes of inhibitors. Several atomistic models of SIRT2‐inhibitor complexes were extracted and used for structure‐based VS study. VS models generated from three extracted SIRT2‐inhibitor complexes were significantly better compared to VS models generated from available crystallographic structures. Generated VS protocol was also better in performance compared to published virtual screening studies. These results clearly indicate importance of considering flexibility of binding site in rational design of SIRT2 inhibitors. Obtained models were used for screening of commercial databases of compounds. Several chemotypes of potential novel SIRT2 inhibitors have been identified. Refined atomistic models of SIRT2‐inhibitor complexes have been generated and significant improvement of virtual screening performance has been achieved. These results further rationalize design of SIRT2 inhibitors with improved selectivity and potency.VII Kongres farmaceuta Srbije sa međunarodnim učešćem Zajedno stvaramo budućnost farmacije, Beograd, 10-14. oktobar 201

Epigenetic drug discovery: fragment-based drug design of novel 1-benzhydryl-piperazine derivatives as selective histone deacetylase 6 inhibitors

Selective histone deacetylase 6 (HDAC6) inhibition with small molecules is regarded as a rational strategy to develop safer anti-cancer drugs compared to non-selective HDAC inhibitors1. To date, structural motifs that are important for HDAC inhibitory activity and selectivity are defined as: surface recognition group (CAP group), aliphatic or aromatic linker and zinc-binding group (ZBG). Herein, we describe a comprehensive protocol for the computational fragment search of novel surface-recognition (CAP) groups aimed to design selective Histone Deacetylase 6 (HDAC6) inhibitors (Figure 1)2. Identified heterocyclic CAP group, 1-benzhydryl piperazine was employed to synthesize novel HDAC inhibitors with small structural perturbations in the hydrocarbon linker. Enzymatic in vitro HDAC screening identified two selective HDAC6 inhibitors (6b, IC50 = 186 nM and 9b, IC50 = 31 nM), as well as two non-selective nanomolar HDAC inhibitors (7b and 8b). The influence of linker chemistry of synthesized inhibitors on HDAC6 potency was studied using structure-based molecular modelling. References 1. J. Amengual, J. Lue, H. Ma, R. Lichtenstein, B. Shah, S. Cremers, S. Jones, A. Sawas, The Oncologist, 2021, 26(3), 184 e366. 2. D. Ruzic, M. Petkovic, D. Agbaba, A. Ganesan, K. Nikolic, Mol. Inform., 2019, 38(5), 1800083. Acknowledgments The authors acknowledge a Ministry of Education, Science and Technological Development of the Republic of Serbia Faculty of Pharmacy project (451-03-68/2022- 14/200161).8th Conference of Young Chemists of Serbia 29th October 2022 University of Belgrade, Faculty of Chemistry Book of Abstracts M32 DRuzic Abstracts_8 CYCS BGD 202