Pritika Ramharack

Zika virus NS5 protein potential inhibitors: an enhanced in silico approach in drug discovery

The re-emerging Zika virus (ZIKV) is an arthropod-borne virus that has been described to have explosive potential as a worldwide pandemic. The initial transmission of the virus was through a mosquito vector, however, evolving modes of transmission has allowed the spread of the disease over continents. The virus has already been linked to irreversible chronic central nervous system conditions. The concerns of the scientific and clinical community are the consequences of Zika viral mutations, thus suggesting the urgent need for viral inhibitors. There have been large strides in vaccine development against the virus but there are still no FDA approved drugs available. Rapid rational drug design and discovery research is fundamental in the production of potent inhibitors against the virus that will not just mask the virus, but destroy it completely. In silico drug design allows for this prompt screening of potential leads, thus decreasing the consumption of precious time and resources. This study demonstrates an optimized and proven screening technique in the discovery of two potential small molecule inhibitors of ZIKV Methyltransferase and RNA dependent RNA polymerase. This in silico ‘per-residue energy decomposition pharmacophore’ virtual screening approach will be critical in aiding scientists in the discovery of not only effective inhibitors of Zika viral targets, but also a wide range of anti-viral agents.

Zika virus drug targets: a missing link in drug design and discovery – a route map to fill the gap

Zika virus is an emerging virus that has been defined by the World Health Organization as a serious global biological-threat. Zika virus is an arbovirus from the flavivirus genus that is linked to microcephaly after prenatal transmission from the infected mother and most recently Guillain–Barre Syndrome. The need for innovative research methods is urgent due to the ambiguity surrounding Zika virus. The lack of experimental data regarding potential drug targets, strategies for design and drug resistance has prompted us to provide a comprehensive framework with structured theoretical and technical guidelines on potential drug targets, modeling and design of inhibitors against the virus, thus assisting and encouraging scientists from different research domains to fill the gap in this research area. We have also presented a 3D homology model of the ideal Zika viral target, the non-structural protein 5, identified the active binding sites of each domain of the protein and found potential compounds that may act as inhibitors. This report will be immensely beneficial toward the design of Zika virus drug inhibitors.

Delving into Zika virus structural dynamics – a closer look at NS3 helicase loop flexibility and its role in drug discovery

The Zika virus has emerged as a pathogen of major health concern. The rapid spread of the virus has led to uproar in the medical domain as scientists frantically race to develop effective vaccines and small molecules to inhibit the virus. In the past year, there has been a flood of Zika knowledge published including its characteristics, transmission routes and its role in disease conditions such as microcephaly and Gullian–Barŕe syndrome. Targeted therapy against specific viral maturation proteins is necessary in halting the replication of the virus in the human host, thus decreasing host–host transmission. This prompted us to investigate the structural properties of the Zika NS3 helicase when bound to ATP-competitive inhibitor, NITD008. In this study, comparative molecular dynamic simulations were employed for APO and bound protein to demonstrate the molecular mechanism of the helicase. Results clearly revealed that NITD008-binding caused significant residue fluctuations at the P-loop compared to the rigid nature of the APO conformation. The NITD008-helicase complex also revealed residues 339–348 to transition from a 310-helix to a stable α-helix. These protein fluctuations were verified by investigation of dynamic cross correlation and principal component analysis. The fundamental dynamic analysis presented in this report is crucial in understanding Zika NS3 helicase function, thereby giving insights toward an inhibition mechanism. The information reported on the binding mode at the ATPase active site may also assist in designing effective inhibitors against this detrimental viral target.

Brain grants permission of access to Zika virus but denies entry to drugs: a molecular modeling perspective to infiltrate the boundary

The magnetism of the Zika virus to neuronal cells proves to be one of the major concerns in the development of effective inhibitors. Although the blood–brain barrier limits the entry of most drugs, tailored small molecule inhibitors and drug delivery systems are currently being designed to overcome this obstacle. We have identified the core challenge to be addressed – blood–brain barrier permeability – and provided insight into strategies that can be used to improve drug delivery to the brain. We have compiled drugs that have previously been proposed as potential Zika virus inhibitors and classified chemical features of those drugs, which influence blood–brain barrier permeability. Thereafter, we created a route map to design drugs with improved blood–brain barrier permeability. An alternative approach using drug delivery systems to transport membrane-impermeable Zika virus inhibitors to the brain is also proposed, along with descriptions of known drug carriers. This review provides information for further research toward inhibitors of Zika virus.

Egress and invasion machinery of malaria: an in-depth look into the structural and functional features of the flap dynamics of plasmepsin IX and X

Plasmepsins, a family of aspartic proteases expressed by Plasmodium falciparum parasite, have been identified as key mediators in the onset of lethal malaria. Precedence has been placed on this family of enzymes due their essential role in the virulence of the parasite, thus highlighting their importance as novel drug targets. A previously published study by our group proposed a set of parameters used to define the flap motion of aspartic proteases. These parameters were used in the study of Plm I–V and focused on the flap flexibility as well as structural dynamics. Recent studies have highlighted the essential role played by Plm IX and X in egress and invasion of the malarial parasite. This study aims to close the gap on the latter family, investigating the flap dynamics of Plms IX and X. Molecular dynamics simulations demonstrated an “open and close” mechanism at the region of the catalytic site. Further computation of the dihedral angles at the catalytic region revealed tractability at both the flap tip and flexible loop. This structural versatility enhances the interaction of variant ligand sizes, in comparison to other Plm family members. The results obtained from this study signify the essential role of structural flap dynamics and its resultant effect on the binding landscapes of Plm IX and X. We believe that this unique structural mechanism may be integrated in the design and development of effective anti-malarial drugs.

Using bioinformatics tools for the discovery of Dengue RNA-dependent RNA polymerase inhibitors

Background Dengue fever has rapidly manifested into a serious global health concern. The emergence of various viral serotypes has prompted the urgent need for innovative drug design techniques. Of the viral non-structural enzymes, the NS5 RNA-dependent RNA polymerase has been established as a promising target due to its lack of an enzymatic counterpart in mammalian cells and its conserved structure amongst all serotypes. The onus is now on scientists to probe further into understanding this enzyme and its mechanism of action. The field of bioinformatics has evolved greatly over recent decades, with updated drug design tools now being publically available. Methods In this study, bioinformatics tools were used to provide a comprehensive sequence and structural analysis of the two most prominent serotypes of Dengue RNA-dependent RNA polymerase. A list of popular flavivirus inhibitors were also chosen to dock to the active site of the enzyme. The best docked compound was then used as a template to generate a pharmacophore model that may assist in the design of target-specific Dengue virus inhibitors. Results Comparative sequence alignment exhibited similarity between all three domains of serotype 2 and 3.Sequence analysis revealed highly conserved regions at residues Meth530, Thr543 Asp597, Glu616, Arg659 and Pro671. Mapping of the active site demonstrated two highly conserved residues: Ser710 and Arg729. Of the active site interacting residues, Ser796 was common amongst all ten docked compounds, indicating its importance in the drug design process. Of the ten docked flavivirus inhibitors, NITD-203 showed the best binding affinity to the active site. Further pharmacophore modeling of NITD-203 depicted significant pharmacophoric elements that are necessary for stable binding to the active site. Discussion This study utilized publically available bioinformatics tools to provide a comprehensive framework on Dengue RNA-dependent RNA polymerase. Based on docking studies, a pharmacophore model was also designed to unveil the crucial pharmacophoric elements that are required when constructing an efficacious DENV inhibitor. We believe that this study will be a cornerstone in paving the road toward the design of target-specific inhibitors against DENV RdRp.

Synergistic Interplay of The Co-administration of Rifampin And Newly Developed Anti-TB Drug: Could It Be a Promising New Line of TB Therapy?

BACKGROUND Rifampin resistance has dampened the existing efforts being made to control the global crisis of Tuberculosis and antimicrobial resistance in general. Previous studies that attempted to provide insights into the structural mechanism of Rifampin resistance did not utilize the X-ray crystal structure of Mycobacterium tuberculosis RNA polymerase due to its unavailability. METHODS/RESULTS We provide an atomistic mechanism of Rifampin resistance in a single active site mutating Mycobacterium tuberculosis RNA polymerase, using a recently resolved crystal structure. We also unravel the structural interplay of this mutation upon co-binding of Rifampin with a novel inhibitor, D-AAP1. Mutation distorted the overall conformational landscape of Mycobacterium tuberculosis RNA polymerase, reduced binding affinity of Rifampin and shifted the overall residue interaction network of the enzyme upon binding of only Rifampin. Interestingly, co-binding with DAAP1, though impacted by the mutation, exhibited improved Rifampin binding interactions amidst a distorted residue interaction network. CONCLUSION Findings offer vital conformational dynamics and structural mechanisms of mutant enzyme-single ligand and mutant enzyme-dual ligand interactions which could potentially shift the current therapeutic protocol of Tuberculosis infections.

Road Map for the Structure-Based Design of Selective Covalent HCV NS3/4A Protease Inhibitors

Over the last 2 decades, covalent inhibitors have gained much popularity and is living up to its reputation as a powerful tool in drug discovery. Covalent inhibitors possess many significant advantages including increased biochemical efficiency, prolonged duration and the ability to target shallow, solvent exposed substrate-binding domains. However, rapidly mounting concerns over the potential toxicity, highly reactive nature and general lack of selectivity have negatively impacted covalent inhibitor development. Recently, a great deal of emphasis by the pharmaceutical industry has been placed toward the development of novel approaches to alleviate the major challenges experienced through covalent inhibition. This has unexpectedly led to the emergence of “selective” covalent inhibitors. The purpose of this review is not only to provide an overview from literature but to introduce a technical guidance as to how to initiate a systematic “road map” for the design of selective covalent inhibitors which we believe may assist in the design and development of optimized potential selective covalent HCV NS3/4A viral protease inhibitors.