Design of Linear and Cyclic Mutant Analogues of Dirucotide Peptide (MBP82–98) against Multiple Sclerosis: Conformational and Binding Studies to MHC Class II

Background: Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system. MS is a T cell-mediated disease characterized by the proliferation, infiltration, and attack of the myelin sheath by immune cells. Previous studies have shown that cyclization provides molecules with strict conformation that could modulate the immune system. Methods: In this study, we synthesized peptide analogues derived from the myelin basic protein (MBP)82⁻98 encephalitogenic sequence (dirucotide), the linear altered peptide ligand MBP82⁻98 (Ala91), and their cyclic counterparts. Results: The synthesized peptides were evaluated for their binding to human leukocyte antigen (HLA)-DR2 and HLA-DR4 alleles, with cyclic MBP82⁻98 being a strong binder with the HLA-DR2 allele and having lower affinity binding to the HLA-DR4 allele. In a further step, conformational analyses were performed using NMR spectroscopy in solution to describe the conformational space occupied by the functional amino acids of both linear and cyclic peptide analogues. This structural data, in combination with crystallographic data, were used to study the molecular basis of their interaction with HLA-DR2 and HLA-DR4 alleles. Conclusion: The cyclic and APL analogues of dirucotide are promising leads that should be further evaluated for their ability to alter T cell responses for therapeutic benefit against MS

Novel Hit Compounds as Putative Antifungals: The Case of Aspergillus fumigatus

The prevalence of invasive fungal infections has been dramatically increased as the size of the immunocompromised population worldwide has grown. Aspergillus fumigatus is characterized as one of the most widespread and ubiquitous fungal pathogens. Among antifungal drugs, azoles have been the most widely used category for the treatment of fungal infections. However, increasingly, azole-resistant strains constitute a major problem to be faced. Towards this direction, our study focused on the identification of compounds bearing novel structural motifs which may evolve as a new class of antifungals. To fulfil this scope, a combination of in silico techniques and in vitro assays were implemented. Specifically, a ligand-based pharmacophore model was created and served as a 3D search query to screen the ZINC chemical database. Additionally, molecular docking and molecular dynamics simulations were used to improve the reliability and accuracy of virtual screening results. In total, eight compounds, bearing completely different chemical scaffolds from the commercially available azoles, were proposed and their antifungal activity was evaluated using in vitro assays. Results indicated that all tested compounds exhibit antifungal activity, especially compounds 1, 2, and 4, which presented the most promising minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) values and, therefore, could be subjected to further hit to lead optimization

The size matters? A computational tool to design bivalent ligands

Bivalent ligands are increasingly important such as for targeting G protein-coupled receptor (GPCR) dimers or proteolysis targeting chimeras (PROTACs). They contain two pharmacophoric units that simultaneously bind in their corresponding binding sites, connected with a spacer chain. Here, we report a molecular modelling tool that links the pharmacophore units via the shortest pathway along the receptors van der Waals surface and then scores the solutions providing prioritization for the design of new bivalent ligands. Bivalent ligands of known dimers of GPCRs, PROTACs and a model bivalent antibody/antigen system were analysed. The tool could rapidly assess the preferred linker length for the different systems and recapitulated the best reported results. In the case of GPCR dimers the results suggest that in some cases these ligands might bind to a secondary binding site at the extracellular entrance (vestibule or allosteric site) instead of the orthosteric binding site

Design and synthesis of a novel non peptide CN-NFATc signaling inhibitor for tumor suppression in triple negative breast cancer

The Ca2+/calmodulin-mediated phosphatase activity of calcineurin (CN) integrates calcium-mediated signaling with gene expression programs involved in the control of essential cellular processes in health and disease, such as the immune response and the pathogenesis of cancer progression and metastasis. In addition, CN is the target of the immunosuppressive drugs cyclosporine A (CsA) and FK-506 which are the cornerstone of immunosuppressant therapy. Unfortunately, long-term administration of these drugs results in severe side effects. Herein, we describe the design, synthesis and evaluation of new synthetic compounds that are capable of inhibiting NFATc activity in a dose-dependent manner, without interfering on CN phosphatase activity. These compounds were designed using the structure-based pharmacophore model of a peptide-derived PxIxIT sequence binding to calcineurin A subunit. Moreover, these compounds inhibit NFATc-dependent cytokine gene expression, secretion and proliferation of human T CD4(+) cells. More importantly, compound 5a reduces tumor weight and shows a tendency to reduce tumor angiogenesis in an orthotopic immunocompetent mouse model of triple negative breast cancer, suggesting that 5a has tumor suppressor activity. These findings validate compound 5a as an agent with therapeutic activity against CN-NFATc and highlight its potential as a tool for drug development with therapeutic purposes

Molecular epidemiology of SARS-CoV-2: the dominant role of arginine in mutations and infectivity

Background, Aims, Methods, Results, Conclusions: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global challenge due to its ability to mutate into variants that spread more rapidly than the wild-type virus. The molecular biology of this virus has been extensively studied and computational methods applied are an example paradigm for novel antiviral drug therapies. The rapid evolution of SARS-CoV-2 in the human population is driven, in part, by mutations in the receptor-binding domain (RBD) of the spike (S-) protein, some of which enable tighter binding to angiotensin-converting enzyme (ACE2). More stable RBD-ACE2 association is coupled with accelerated hydrolysis by proteases, such as furin, trypsin, and the Transmembrane Serine Protease 2 (TMPRSS2) that augment infection rates, while inhibition of the 3-chymotrypsin-like protease (3CLpro) can prevent the viral replication. Additionally, non-RBD and non-interfacial mutations may assist the S-protein in adopting thermodynamically favorable conformations for stronger binding. This study aimed to report variant distribution of SARS-CoV-2 across European Union (EU)/European Economic Area (EEA) countries and relate mutations with the driving forces that trigger infections. Variants’ distribution data for SARS-CoV-2 across EU/EEA countries were mined from the European Centre for Disease Prevention and Control (ECDC) based on the sequence or genotyping data that are deposited in the Global Science Initiative for providing genomic data (GISAID) and The European Surveillance System (TESSy) databases. Docking studies performed with AutoDock VINA revealed stabilizing interactions of putative antiviral drugs, e.g., selected anionic imidazole biphenyl tetrazoles, with the ACE2 receptor in the RBD-ACE2 complex. The driving forces of key mutations for Alpha, Beta, Gamma, Delta, Epsilon, Kappa, Lambda, and Omicron variants, which stabilize the RBD-ACE2 complex, were investigated by computational approaches. Arginine is the critical amino acid in the polybasic furin cleavage sites S1/S2 (681-PRRARS-686) S2′ (814-KRS-816). Critical mutations into arginine residues that were found in the delta variant (L452R, P681R) and may be responsible for the increased transmissibility and morbidity are also present in two widely spreading omicron variants, named BA.4.6 and BQ.1, where mutation R346T in the S-protein potentially contributes to neutralization escape. Arginine binders, such as Angiotensin Receptor Blockers (ARBs), could be a class of novel drugs for treating COVID-19

Structure - biological activity relations of antihypertensive agents through molecular modeling techniques and nuclear magnetic resonance (NMR)

Arterial   blood   pressure   is   regulated   by   the   renin-­‐angiotensin   system   in   which   the  angiotensin   II   receptor   and   renin   play   a   significant   role.   During   this   research  procedure,  in  silico methods  were  utilized  in  order  to  examine  the  function  of  these  proteins   upon   ligand   binding.   Conformational   and   energetic   changes   of   the   drug  aliskiren   upon   it’s   binding   to   the   human   renin   were   studied,   as   well   as   structural  properties   of   the   complexes   between   angiotensin  II   and   it’s   antagonists,   bound   to  angiotensin   type  1   receptor   (AT1).  Experimental  structural  data  and  binding   results  were   utilized   in   conformational   search,   homology   modeling,   docking   calculations  and   molecular   dynamics   studies   in   order   to   gain   information   on   these   receptor-­‐ligand  complexes  so  to  be  used  in  ligand  and  receptor  based  drug  design.Η αρτηριακή πίεση   ρυθμίζεται   μέσω   του   συστήματος   ρενίνης-­‐αγγειοτασίνης στο  οποίο   εμπλέκονται   ο   υποδοχέας   της   αγγειοτασίνης   ΙΙ   και   η   ρενίνη.   Στην   παρούσα  ερευνητική   εργασία,   χρησιμοποιήθηκαν   in   silico τεχνικές   για   τη   μελέτη   της  λειτουργίας   των   συμπλόκων   αυτών   των   πρωτεϊνών   με   τους   βιοδραστικούς  προσδέτες   τους.   Μελετήθηκαν   οι   διαμορφωτικές   και   ενεργειακές   αλλαγές   στις  οποίες   υπόκειται   η   αλισκιρένη   κατά   την   πρόσδεση   στη   ρενίνη   και   τα   δομικά  χαρακτηριστικά   των   συμπλόκων   μεταξύ   της   αγγειοτασίνης   ΙΙ   και   ενός   μεγάλου  αριθμού   ανταγωνιστών   της   με   τον   υποδοχέα   της   (ΑΤ1).   Στους   υπολογισμούς  ενσωματώθηκαν   πειραματικά   δεδομένα   σχετικά   με   τη   διαμόρφωση   ή   την   ισχύ  πρόσδεσης  αυτών  των  μορίων  προκειμένου  να  δημιουργηθούν  αξιόπιστα  μοντέλα  που   να   προσομοιάζουν   την   βιολογική   δράση   αυτών   των   συμπλόκων   και   να  χρησιμοποιηθούν  για  σχεδιασμό  νέων  δραστικών  ενώσεων

Computational approaches in target identification and drug discovery

In the big data era, voluminous datasets are routinely acquired, stored and analyzed with the aim to inform biomedical discoveries and validate hypotheses. No doubt, data volume and diversity have dramatically increased by the advent of new technologies and open data initiatives. Big data are used across the whole drug discovery pipeline from target identification and mechanism of action to identification of novel leads and drug candidates. Such methods are depicted and discussed, with the aim to provide a general view of computational tools and databases available. We feel that big data leveraging needs to be cost-effective and focus on personalized medicine. For this, we propose the interplay of information technologies and (chemo)informatic tools on the basis of their synergy

Family B G Protein-coupled Receptors and their Ligands: From Structure to Function

Background: Family B G protein-coupled receptors (GPCRs) play an important role in many physiological and pathophysiological processes. They are plasma-membrane proteins containing an extracellular N-domain, an intracellular C-tail, seven transmembrane domains (TMs), three extracellular (ELs) and three intracellular (ILs) loops. Objective: This review aims to summarize the current structural and functional information for family B GPCRs and their ligands, as well as, their physiological and pathophysiological role. Methods: Α thorough search of bibliographic databases for peer-reviewed research literature was undertaken. Moreover, molecular models of family B GPCRs were constructed and a structural alignment of their amino acid sequences was performed to demonstrate common structural characteristics. Results: In this review the family B GPCRs and their complexes with the receptor activity modifying proteins (RAMPs) were classified into five groups and the important physiological and pathophysiological role of these receptors was summarized. In addition, conserved residues of the Ndomain and the TMs of these receptors were numbered, thus making feasible the comparison of receptor structures and demonstrating common structural characteristics that are functionally important for all family B receptors. Molecular models created in this study were used to discuss the molecular mechanisms underlying ligand binding to family B GPCRs and receptor activation. Conclusion: The findings of this review provide information about the structural-functional determinants of family B GPCRs and their ligands, thus boosting the design of novel drugs with better potencies and bioavailabilities, which might enrich the therapeutic armory for the treatment of a wide spectrum of family B GPCRs-related disorders