F24 PHRM415 Lecture 1_Nonantiretroviral drugs_ 2024 final.pdf

PHRM 415: Pathophysiology, Drug Action, and Therapeutics – 5 1  Antiviral Agents 1- Non-Antiretroviral drugs Lecture -1 Prof. Adnan Kadi; Prof. Ebtehal Al Abdullah 2 Objectives: ▪ Under...

PHRM 415: Pathophysiology, Drug Action, and Therapeutics – 5 1  Antiviral Agents 1- Non-Antiretroviral drugs Lecture -1 Prof. Adnan Kadi; Prof. Ebtehal Al Abdullah 2 Objectives: ▪ Understand the different antiviral agents’ chemical classes covered in this course. ▪ Predict the biological activity, if any, of a chemical structure on the therapeutic targets covered in this course. ▪ Relate the structural features of a compound to its physiochemical properties, which may have a major effect on its biological response, or on the design of modern therapeutic agents. ▪ Understand the metabolic fate, if any, of agents covered in the class. 3 Introduction Viruses are the smallest infecting organisms, 20-300nm in diameter. Not considered a “true life form”. However, show life attributes such as Replication & Adoption to external stimuli. Viruses are either DNA or RNA viruses. DNA Viruses: Most contain double stranded DNA (e.g. Papillomavirus, adenovirus, and herpesvirus). Some contain a single stranded DNA, e.g. Parvoviruses. 4 Cont RNA Viruses: Non-retroviruses: ✴ mRNA (sense, +) viruses, e.g. picornaviruses (HBV), coronaviruses, flaviviruses (HCV)…etc ✴ Antisense (-) RNA viruses, e.g. orthomyxoviruses (influenza), paramyxoviruses, rhabdoviruses…etc Retroviruses: single-stranded RNA exists as a dimer of sense (+) and antisense (-) RNA strands, e.g. HIV. Require a reverse transcriptase (RNA —> DNA) 5 Viral chemotherapy General approaches ▪ Antiviral drugs are targeted to some process in the virus that is not present in the host cell. ▪ A variety of factors make the design of effective antiviral agents difficult including their ability to undergo antigenic changes. ▪ Antiviral agents’ design followed diverse pathways: ✓ agents that disrupt viruses attachment to host cell, penetration, or uncoating ✓ agents that inhibit virus-associated enzymes ( DNA-polymerase ) ✓ agents that inhibit viral transcription ✓ agents that inhibit viral translation ✓ agents that interfere with viral regulatory proteins ✓ agents that inhibit the release of viruses from cell surface membranes 6 Non-retroviral viruses Non-retroviral viruses are believed to have originated in fossils. Examples include influenza, coronavirus, West Nile virus, and Zika virus. Introduction to humans is believed to result from accidental integration mediated by various mechanisms that are encoded either by the viral genome or by the host genome, such as DNA repair processes or resident retrotransposons. 7  Non-retroviral viruses Drug classes: Neurominidase inhibtors, Oseltamivir, zanamivir , adamantanes:, amantadine, rimantadine, acyclovir, valacyclovir endonuclease inhibitor, baloxavir, Interferons 8  Structure and mechanism of neuraminidase ▪ In order for the virus to reach the epithelial host cells of the upper respiratory tract, the virus has to negotiate a layer of protective mucus and it is thought that the viral protein NA is instrumental in achieving this. ▪ The mucosal secretions are rich in glycoproteins and glycolipids which bear a terminal sugar substituent called sialic acid (also called N -acetylneuraminic acid ). ▪ NA (also called sialidase ) is an enzyme which cleaves sialic acid from these glycoproteins and glycolipids thus degrading the mucus layer and allowing the virus to reach the surface of epithelial cells. 9 ▪ NA is involved in catalytically cleaving glycosidic bonds between terminal sialic acid residue and adjacent sugars on glycoprotein HA. ▪ The cleavage of sialic acid bonds facilitates the spread of the viruses. So by inhibiting this cleavage form will interfere with the spread of infection ▪ Since neuraminidase (NA) has crucial roles in the infectious process it is a promising target for potential antiviral agents. ▪ Due to the ease with which mutations occur, there is a wide diversity of amino acids (29 amino acids) making up the various types and subtypes of the enzyme. As the active site remains constant ( 18 amino acids), any inhibitor designed to fit it has a good chance of inhibiting all strains of the flu virus. ▪ Moreover, it has been observed that the active site is quite different in structure from the active sites of comparable bacterial or mammalian enzymes, so there is a strong possibility that inhibitors can be designed that are selective antiviral drugs. ▪ 10 ▪ Indeed, researchers set out to design a mechanism-based transition-state inhibitor. ▪ The enzyme has been crystallized with sialic acid (the product of the enzyme- catalysed reaction) bound to the active site and the structure determined by X-ray crystallography. ▪ A molecular model of the complex was created which resembled the observed crystal structure as closely as possible. From this it was calculated that sialic acid was bound to the active site through a network of hydrogen bonds and ionic interactions 11 ▪ The most important interactions involve the carboxylate ion of sialic acid, which is involved in ionic interactions ▪ and hydrogen bonds with three arginine residues, particularly with Arg-371. ▪ In order to achieve these interactions, the sialic acid has to be distorted from a stable chair conformation (where the carboxylate ion is in the axial position) to a less stable pseudo-boat conformation where the carboxylate ion is 12 equatorial. 13  There are three other important binding regions or pockets within the active site. 1. The glycerol side chain of sialic acid at C6 fills one of these pockets, interacting with glutamate residues and a water molecule by hydrogen bonding 2. The hydroxyl group at C-4 is situated in another binding pocket, interacting with a glutamate residue. 3. Finally, the acetamido substituent at C5 fits into a hydrophobic pocket which is important for Hydrogen bonding interaction between sialic acid and active site of molecular recognition. neuraminidase 14 Neuraminidase inhibitors Transition-state inhibitors: Development of zanamivir (Relenza) 15  Studying the transition state of NA with sialic acid showed: ▪ It has a planar trigonal center at C-2 and so sialic acid analogues containing a double bond between positions C-2 and C-3 were synthesized to achieve that same trigonal geometry at C-2. This resulted in the discovery of the inhibitor 2-deoxy-2,3-dehydro- N - acetylneuraminic acid ( Neu5Ac2en ) ▪ Unfortunately, this compound also inhibited Bacterial and mammalian sialidases and could not be used therapeutically. Moreover, it was inactive in vivo. 16 ▪ Molecular modelling studies lead to the synthesis of 4-Amino-Neu5Ac2en in which it contains the amine group instead of hydroxyl group and was found to be more potent than Neu5Ac2en. ▪ Moreover, it was active in animal studies and showed selectivity against the viral enzyme, implying that the region of the active site which normally binds the 4-hydroxyl group of the substrate is different in the viral enzyme from comparable bacterial or mammalian enzymes. 17 Molecular modelling studies had suggested that the larger guanidinium group would be capable of even greater hydrogen bonding interactions, as well as favourable van der Waals interactions. 18 The most important result from these studies was A crystal structure of the inhibitor bound to the enzyme confirmed the binding pattern predicted by the molecular modeling The substitution of the 4-OH with NH2 or larger guanidine group should increase binding of the inhibitor to NA. The 4-NH2 derivative was found to bind to glu119 in the receptor through a salt bridge, whereas the 4-guanidine derivative was able to form both a salt bridge and a charge-charge interaction with glu227 Binding interaction of aminium and guanidium This leading to increase binding so lead to effective moieties at C-4 with active site of neuraminidase competitive inhibition of enzyme. 19  The result was the development of the 4-guanidine analog zanamivir zanamivir was, indeed, found to be a more potent inhibitor having a 100-fold increase in activity. the polar nature of the molecule means it has poor oral bioavailability Laninamivir is a closely related structure which was approved in Japan during 2010. 20 Carbocyclic analogues: development of oseltamivir ▪ The dihydropyran oxygen of Neu5Ac2en and related inhibitors have no important role to play in binding these structures to the active site of NA. ▪ Therefore, it should be possible to replace it with a methylene isostere to form carbocyclic analogues such as structure I. ▪ This would have the advantage of removing a polar oxygen atom which would increase hydrophobicity and potentially increase oral bioavailability. 21 Carbocyclic analogues: development of oseltamivir ▪ Moreover, it would be possible to synthesize cyclohexene analogues, such as structure II, which more closely match the stereochemistry of the reaction’s transition state than previous inhibitors (compare the reaction intermediate. ▪ A series of alkoxy analogues of structure III was now synthesized in order to maximize hydrophobic interactions in the region of the active site. ▪ This lead to synthesis oseltamivir (Tamiflu) 22  Oseltamivir (Tamiflu®) SAR: The maximum binding occurred when C-6 was substituted with 3-pentyloxy side chain Esterification with ethanol give orally active compound This would have the advantage of removing a polar oxygen atom which would increase hydrophobicity and potentially increase oral bioavailability. 23  Oseltamivir Metabolism: Readily absorbed from GI It is prodrug that metabolized in liver Ester hydrolysis to active carboxylic acid Two oxidative metabolites ( ω- carboxylic acid is the major) 24  Peramivir Using structure-based design, It contains a cyclopentane ring structure that replaces the sialic acid core and dose not contain a glycerol side chain was designed to take advantage of both hydrophobic pockets in the active site. It was prepared as a racemic mixture. Still In phase III 25  Agents Inhibiting Virus Attachement, Penetration, and Early Viral Replication Ion Channel Disrupters: Amantadine and Rimantadine Amantadine and rimantadine are related adamantanes with similar mechanisms of action and can inhibit viral infection in two ways. At low concentration (50 μg/ml), the basic nature of the compounds becomes important and they buffer the pH of endosomes to prevent the acidic environment needed for HA (haemagglutinin) to fuse the viral membrane with that of the endosome. These mechanisms inhibit penetration and uncoating of the virus. 26 Agents Inhibiting Virus Attachement, Penetration, and Early Viral Replication Ion Channel Disrupters: Amantadine and Rimantadine Rimantadine: α-methyl-1-adamantanemethylamine HCl Rimantadine is more effective with fewer CNS side effects Unfortunately, neither agent is effective against influenza B as this virus does not contain the matrix (M2) protein. 27  Inhibitors of viral DNA polymerase: Acyclovir Agents Interfering with Viral Nucleic Acid Replication Acyclovir has a nucleoside-like structure and contains the same nucleic acid base as deoxyguanosine. However, it lacks the complete sugar ring. In virally infected cells, it is phosphorylated in three stages to form a triphosphate which is the active agent, and so acyclovir is a prodrug. Comparison of aciclovir triphosphate and deoxyguanosine triphosphate. 28  The first phosphorylation reaction catalyzed by the viral enzyme thymidine kinase. Once formed, the monophosphate is converted to the active triphosphate by cellular enzymes. Acyclovir triphosphate, which competitively inhibits viral DNA polymerase, incorporates into terminates the growing viral DNA chain, and inactivates the viral DNA polymerase 29  WHY? However, what is to stop aciclovir triphosphate inhibiting DNA polymerase in normal, uninfected cells? The explanation : The first phosphorylation reaction catalyzed by the viral enzyme thymidine kinase. is 100 times more effective at converting aciclovir to its monophosphate than host cell thymidine kinase. Therefore, in normal, uninfected cells, aciclovir is a poor substrate for cellular thymidine kinase and remains as the prodrug. 30 Prodrugs and analogues of acyclovir. Valacyclovir The oral bioavailability of aciclovir is quite low (15–30%). To overcome this, various prodrugs were developed to increase water solubility. Valacyclovir is amino acid ester prodrug of acyclovir. is an l-valyl ester prodrug absorbed from the gut far more effectively than aciclovir. Because of its polarity and ionization no more able to cross the cell membranes of the gut wall by passive diffusion Moreover, poorer absorption is observed if d-valine is used for the prodrug instead of l-valine, suggesting that a specific binding interaction is involved in the absorption process. Once valaciclovir is absorbed, it is hydrolysed to aciclovir in the liver and gut wall. 31 Prodrugs and analogues of acyclovir. Desciclovir Desciclovir ( 6-deoxy aciclovir) is a prodrug of aciclovir which lacks the carbonyl group at position 6 of the purine ring and is more water soluble. Once in the blood supply, metabolism by cellular xanthine oxidase oxidizes the 6-position to give aciclovir. 32 Prodrugs and analogues of acyclovir. Ganciclovir is an analogue of aciclovir and bears an extra hydroxymethylene group; valganciclovir acts as a prodrug for this compound. 33  Famciclovir Diacetyl 6-deoxy ester of penciclovir. Penciclovir and its prodrug famciclovir are analogues of ganciclovir. In famciclovir, the two alcohol groups of penciclovir are masked as esters making the structure less polar, resulting in better absorption. Once absorbed, the acetyl groups are hydrolysed by esterases and the purine ring is oxidized by aldehyde oxidase in the liver to generate penciclovir. Phosphorylation reactions then take place in virally infected cells, as described previously. 34 Metabolism Aciclovir is metabolized to 9- carboxymethoxy methyl guanine, which is inactive 35  Endonuclease inhibitors: Baloxavir marboxil (Xofluza®) Endonuclease inhibitors are a type of antiviral drugs that inhibit a viral enzyme called Endonuclease. The cap-dependent endonuclease is an enzyme essential for the initiation of viral replication in the influenza virus1. By inhibiting cap-dependent endonuclease, viral replication is prevented, which reduces the viral load and influenza infection1 36 Cont. Baloxavir marboxil (BXM) is a prodrug (what is the metabolic pathway of BXM?). Active agent is baloxavir acid (BXA), released rapidly in BXM vivo. BXM’s hydrolysis is catalyzed by arylacetamide deacetylases in the blood, liver, and lumen of the small intestine. BXA 37 Interferons: Interferons Small natural proteins, discovered in 1957. Produced by host cells as a response to ‘foreign invaders’. They inhibit protein synthesis and other aspects of viral replication in infected cells. Essentially shut the cell down —> intracellular immune response. Interferons are seen as a possible approach to treating flu, hepatitis, herpes, and colds. Interferons are named by source: α-interferons from lymphocytes. β-interferons from fibroblasts. γ-interferons from T-cells. α-Interferon (also called alferon or IFN-alpha) is the most widely used of the three types. 38 References ▪ An Introduction to Medicinal Chemistry, Fifth Edition- Graham L. Patrick. Chapter 20. ▪ Foye's Principles of Medicinal Chemistry. Seventh edition- W. Foye, T. L. Lemke, David A. Williams. Chapter 38. 39