The significance of halogen bonding in ligand-receptor interactions : the lesson learned from molecular dynamic simulations of the D4D_{4} receptor

Recently, a computational approach combining a structure–activity relationship library containing pairs of halogenated ligands and their corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was developed and used to search for amino acids frequently targeted by halogen bonding, also known as XB hot spots. However, the analysis of ligand–receptor complexes with halogen bonds obtained by molecular docking provides a limited ability to study the role and significance of halogen bonding in biological systems. Thus, a set of molecular dynamics simulations for the dopamine D4 receptor, recently crystallized with the antipsychotic drug nemonapride (5WIU), and the five XSAR sets were performed to verify the identified hot spots for halogen bonding, in other words, primary (V5x40), and secondary (S5x43, S5x461 and H6x55). The simulations confirmed the key role of halogen bonding with V5x40 and H6x55 and supported S5x43 and S5x461. The results showed that steric restrictions and the topology of the molecular core have a crucial impact on the stabilization of the ligand–receptor complex by halogen bonding

Use of Structure-And Ligand-Based Drug Design Tools for the Discovery of Small Molecule Inhibitors of Cysteine Proteases for the Treatment of Malaria and Sars Infection

A wide array of molecular modeling tools were utilized to design and develop inhibitors against cysteine protease of P. Falciparum Malaria and Severe Acute Respiratory Syndrome (SARS). A number of potent inhibitors were developed against cysteine protease and hemoglobinase of P. falciparum , referred as Falcipains (FPs), by the structure-based virtual screening of the focused libraries enriched in soft-electrophiles containing compounds. Twenty one diverse, non-peptidic, low micromolar hits were identified. A combined data mining and combinatorial library synthesis approach was performed to discover analogs of virtual screening hits and establish the structure-activity relationships (SAR). However, the resulting SAR of the identified hits was unusually steep in some cases and could not be explained by a traditional analysis of the interactions (electrostatics, van der Waals or H-bond). To gain insights, a statistical thermodynamic analysis of explicit solvent in the ligand binding domain of FP-2 and FP-3 was performed that explained some of the complex trends in the SAR. Furthermore, the moderate potency of a subset of FP-2 hits was elucidated using quantum mechanics calculations that shoreduced reactivity of the electrophilic center of these hits. In addition, solvent thermodynamics and reactivity analysis also helped to elucidate the complex trends in SAR of peptidomimetic inhibitors of FP-2 and FP-3 synthesized in our laboratory. Multi nanosecond explicit solvent molecular dynamics simulations were carried out using the docking poses of the known inhibitors in the binding site of SARS-3CLpro, a cysteine protease important for replication of SARS virus, to study the overall stability of the binding site interactions as well as identify important changes in the interaction profile that were not apparent from the docking study. Analysis of the simulation studies led to the identification of certain protein-ligand interaction patterns which would be useful in further structure based design efforts against cysteine protease (3CLpro) of SARS

Probing Apoptotic Caspase Allostery and Exosite Interactions for Alternative Regulation

Programmed cell death, or apoptosis is a critical homeostatic pathway that monitors the balance of cell life and death. Apoptosis is regulated by a class of enzymes known as the cysteine aspartic proteases, or the caspases. The 12 human caspases that play important roles in the progression and regulation of apoptosis and inflammation. Caspases are tightly regulated by numerous factors including enzymatic activation, post-translational modifications, metal ligand binding, and protein modulation. Aberrant caspase activation and regulation has been implicated in the progression of numerous diseases such as proliferative diseases and neurodegeneration. The deeply entwined nature of caspases and apoptosis makes them interesting targets for therapeutic intervention of apoptotic diseases. However, the highly conserved fold and overlapping active site specificities makes the development of specific caspase modulators difficult. Therefore, it is critical to understand the mechanistic details of each caspases function, dynamics and specificity to further differentiate these homologous enzymes and uncover new scaffolds for select targeting of these enzymes. In this work, we aim to identify distal residues that comprise protein exosites which mediate the recruitment of proteins for enzymatic hydrolysis. First we developed an evolved specificity caspase that may be utilized for the identification of specific substrate that utilize exosite for caspase recognition and recruitment. Next we probed the details of caspase regulation by zinc validating the emerging signaling atom as an essential regulator of the caspases. Next we identified a putative exosite of caspase-6 located within the N-terminal domain that is essential for protein substrate recruitment and also modulates the dynamics of unique 130’s helix to strand interconversion of the enzyme. Lastly, we identified an active site adjacent inhibitor of caspase-6 that takes advantage of a unique evolutionarily conserved cysteine of caspase-6. Modulation of this distal cysteine serves as an anchor for the most selective, potent and cell permeable inhibitor of caspase-6 to date. The identification of exosites provides new scaffolds for development of specific inhibitors that take advantage of the unique characteristics of this family of enzymes. Interestingly, uncovering the details of protein exosites also provides the unique opportunity block substrate hydrolysis by targeting either the enzyme exosite or the substrate exosite, thereby expanding the chemical space for effective modulation and therapeutic intervention

Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure-Activity Relationship Insights and Evolution Perspectives

The viral main protease is one of the most attractive targets among all key enzymes involved in the SARS-CoV-2 life cycle. Covalent inhibition of the cysteine145 of SARS-CoV-2 MPRO with selective antiviral drugs will arrest the replication process of the virus without affecting human catalytic pathways. In this Perspective, we analyzed the in silico, in vitro, and in vivo data of the most representative examples of covalent SARS-CoV-2 MPRO inhibitors reported in the literature to date. In particular, the studied molecules were classified into eight different categories according to their reactive electrophilic warheads, highlighting the differences between their reversible/irreversible mechanism of inhibition. Furthermore, the analyses of the most recurrent pharmacophoric moieties and stereochemistry of chiral carbons were reported. The analyses of noncovalent and covalent in silico protocols, provided in this Perspective, would be useful for the scientific community to discover new and more efficient covalent SARS-CoV-2 MPRO inhibitors

IN SILICO METHODS FOR DRUG DESIGN AND DISCOVERY

Computer-aided drug design (CADD) methodologies are playing an ever-increasing role in drug discovery that are critical in the cost-effective identification of promising drug candidates. These computational methods are relevant in limiting the use of animal models in pharmacological research, for aiding the rational design of novel and safe drug candidates, and for repositioning marketed drugs, supporting medicinal chemists and pharmacologists during the drug discovery trajectory.Within this field of research, we launched a Research Topic in Frontiers in Chemistry in March 2019 entitled “In silico Methods for Drug Design and Discovery,” which involved two sections of the journal: Medicinal and Pharmaceutical Chemistry and Theoretical and Computational Chemistry. For the reasons mentioned, this Research Topic attracted the attention of scientists and received a large number of submitted manuscripts. Among them 27 Original Research articles, five Review articles, and two Perspective articles have been published within the Research Topic. The Original Research articles cover most of the topics in CADD, reporting advanced in silico methods in drug discovery, while the Review articles offer a point of view of some computer-driven techniques applied to drug research. Finally, the Perspective articles provide a vision of specific computational approaches with an outlook in the modern era of CADD

The Halogen Bond

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design

Towards the Chemical Control of Membrane Protein Function

Thesis advisor: Jianmin GaoThe oligomerization of membrane proteins has been shown to play a critical role in a myriad of cellular processes, some of which include signal propagation, cell-to-cell communication, and a cell's ability to interact with its surroundings. Diseases that are associated with disruption of protein-protein interactions in the membrane include cystic fibrosis, certain cancers, and bone growth disorders. Although significant progress has been made in our mechanistic understanding of protein-protein interactions in membranes, it remains difficult to predict the oligomerization state of transmembrane domains and explain the physiological consequences of a point mutation within a membrane embedded protein. The development of novel classes of chemical tools will allow us to better understand the energetics of transmembrane domain association at the molecular level. Herein, we demonstrate that fluorinated aromatic amino acids offer intriguing potential as chemical mediators of transmembrane protein association. We have systematically examined the effects of fluorination on the physical properties of aromatic systems in the context of a soluble protein model system. Our results illustrate the ability of fluorinated aromatic amino acids to simultaneously stabilize protein structure and facilitate highly specific protein self-assembly. An improved understanding of the fundamental energetics of aromatic interactions should allow for their more efficient incorporation into designed inhibitors of transmembrane protein association. In addition to chemical tools, the development of simple methods for directly monitoring transmembrane domain association in vitro and in vivo is necessary to advance our understanding of these interactions. Towards this goal, we have established FlAsH-tetracysteine display as an effective approach to quantifying the association propensities of transmembrane α-helices (TMHs) in vitro. Our assay is compatible with two of the most commonly utilized model membrane systems, detergent micelles and vesicles. The high spatial resolution of FlAsH binding (˂ 10 Å) allows for the differentiation of parallel and antiparallel oligomerization events. Importantly, preliminary studies suggest the assay's ability to detect inhibition from exogenous TMHs. Encouraged by our understanding of aromatic interactions and the success of our assay, we are beginning to incorporate fluorinated aromatics in the model TMHs and monitoring their ability to associate. The ultimate goal is to modulate the association of endogenous TMHs such as ErbB2. Research in this direction is ongoing.Thesis (PhD) — Boston College, 2013.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: Chemistry