Design, synthesis & structural investigations of template-assisted peptides and synthesis of novel peptide derivatives as potential central nervous system Active agents

Abstract

Preamble: Template assisted peptide folding is an important phenomenon that allows nature to carry many important biological functions. It is a process in which molecules adopt a well-defined low energy minimum conformation through non-covalent interactions like van der Wall forces, π- π interactions, hydrogen bonding and so on. Of the several non-covalent interactions present, hydrogen bonding finds several applications due to its strength, directionality and specificity. Synthetic peptide analogues are also widely recognized as important lead compounds for the generation of novel CNS active agents. NMDA receptor has drawn particular interest as it covers a wide range of CNS disorders. Non-proteinogenic amino acids designed and synthesized by chemists are largely used to mimic the secondary structure of peptides. Contents: This thesis is divided into three chapters. The first chapter deals with the design of dimedone-based rigid synthetic scaffold for organizing symmetrical peptide chains attached on a single carbon. It describes the synthesis and conformational investigations of single stranded and double stranded peptide chains attached to dimedone as an organic scaffold. The second chapter deals with the design, synthesis and characterization of novel unnatural amino acid incorporated close structural mimics of potent antidepressant drug rapastinel. The last chapter chronicles the design, synthesis and characterization of novel azepine and norquetiapine derived hybrid drug analogues as potential central nervous system active agents. Chapter 1: Design, synthesis and conformational investigations of novel single stranded and double stranded peptide chains attached to dimedone as an organic scaffold. This chapter describes the synthesis and its structural investigations of symmetrical peptide chains attached to scaffold containing dimedone. There are a large number of template molecules that are found in the literature which stimulates and stabilizes secondary and tertiary structures of the peptides covalently attached to them. The main hurdle in handling secondary structures of small peptides is their inherently flexible nature, thus posing a serious problem in controlling the molecular orientation, a prerequisite for creating ordered supramolecular assemblies. Dimedone-sulfur intermediate A as a template consisting of two carbonyls as hydrogen bond acceptor is a simple synthetic molecule that plays a major role in the synthesis of various supramolecular architectures (Fig. 1.1).

Figure 1.1: Synthetic route for the template-assisted synthesis of double-stranded peptides from dimedone-sulfur intermediate A. Tripeptide Boc-Lue-Aib-Val-OMe 3a, tetrapeptide Boc-Ala-Lue-Aib-Val-OMe 4a, heptapeptide Boc-Gly-Lue-Aib-Val-Ala-Lue-Aib-Val-OMe 5a, octapeptide Boc-Gly-Lue-Aib-Val-Ala-Lue-Aib-Val-OMe 6, pentadecapeptide Boc-Gly-Lue-Aib-Val-Ala-Lue-Aib-Val-Lue-Aib-Val-Ala-Lue-Aib-Val-OMe 7 and hexadecapeptide Boc-Gly-Lue-Aib-Val-Ala-Lue-Aib-Val-Gly-Lue-Aib-Val-Ala-Lue-Aib-Val-OMe 8 were synthesized using EDC.HCl as a coupling agent in solution phase which was then Boc-deprotected using TFA and treated with dimedone-sulfur intermediate 10a and 10b to furnish corresponding symmetrical double-stranded peptide derivatives in good yields as shown in Fig. 1.2a.

Figure 1.2a: Synthesis of dimedone-assisted symmetrical double-stranded peptides. Dimedone based template-assisted single-stranded peptides were also prepared by treating dimedone-sulfur intermediate 9 with various peptides as shown in Fig. 1.2b.

Figure 1.2b: Synthesis of dimedone-assisted single-stranded peptides.

Figure 1.3a: PyMOL rendered crystal structures of dimedone-assisted single stranded octapeptide 9c (left), Boc-octapeptide 6 (middle), dimedone-attached symmetrical double stranded peptide 13a (right). When two symmetrical peptide chains are attached to the scaffold containing dimedone, peptide chains get oriented in such a way that it forms a strong C-12 and C-15 intramolecular bifurcated hydrogen bonding with the dimedone's carbonyl all together adopting a different conformation in the solid state as shown for 13a (Fig. 1.3a). This is also evident in short peptides in the solid state as shown for 11b in Fig. 1.3b.

11b Figure 1.3b: PyMOL rendered crystal structure of dimedone-assisted double-stranded peptide 11b. We have also investigated the conformational preferences of higher oligopeptides by solution-state NMR spectroscopy and MD simulation studies. Extensive NMR investigations revealed the existence of 13-helix conformation for the higher oligopeptides 7, 8, 9d and 9e.

Figure 1.4 : (A) Minimum energy structures obtained from the ROEs derived distances for compounds 9d and 9e. Top view of 9d (a) side view of 9d (b) top view of 9e (c) and side view of 9e (d); (B) characteristic nOe's of Compound 9d. Chapter 2: Design and synthesis of novel unnatural amino acid incorporated structural mimics of potent antidepressant drug Rapastinel. Part A: Novel silaproline (Sip)-incorporated close structural mimics of potent antidepressant peptide drug rapastinel. Silaproline (Sip) is a proline (Pro) analogue in which the γ-methylene carbon is substituted by dimethyl silyl group. Sip induces and exhibits comparable conformational properties as the natural amino acid Pro. This part describes the synthesis of a new class of rapastinel drug analogues carrying silaproline (Sip) - a well-known surrogate for proline, using standard peptide coupling strategy in the solution-phase.

Figure 2.1: Structure of proline and silaproline (left). Molecular structures of peptide analogues 7, 11, 16 containing silaproline as proline surrogate(right). Silaproline was incorporated into rapastinel peptide sequence, considering its utility to enhance the pharmacokinetic profiles of proline-containing peptides such as lipophilicity, hydrophobicity, cell permeability and conformational stability. All novel peptides were well characterized by spectroscopic tools. Part B: Novel Aib, Fenclonine and L-threo-3-phenylserine incorporated close structural mimics of potent antidepressant peptide drug rapastinel.

Rapastinel analogues containing Aib, p-chlorophenylalanine and L-threo-3-phenylserine were synthesized using standard peptide coupling strategy in the solution-phase as shown in Fig. 2.2. All novel peptides were well characterized by spectroscopic tools.

Figure 2.2: Molecular structures of potent antidepressant drug rapastinel analogues synthesized.

Chapter 3: Design and synthesis of novel 10,11-dihydro-5H-dibenz[b,f]azepine and Norquetiapine derived hybrid drug molecules as potential CNS active agents.

Tricyclic antidepressants (TCAs) and Tetracyclic antidepressants (TeCAs) are a class of medications that are used primarily as antidepressants. Novel 10,11-dihydro-5H-dibenz[b,f]azepine and Norquetiapine derived hybrid drug analogues containing molecules such as Gabapentin, Fenclonine, L-threo phenyl serine and Boc-Glu(OtBu)OH were synthesized using standard peptide coupling strategy in the solution-phase as shown in Fig. 3.1. All novel hybrid molecules were well characterized by spectroscopic tools.

Figure 3.1: Molecular structures of potent azepine and norquetiapine containing analogues synthesized.

Figure 3.2: Molecular structures of potent antidepressant drug azepine and norquetiapine containing rapastinel analogues synthesized.

Azepine and Norquetapine incorporated rapastinel analogues were also synthesized using standard peptide coupling strategy in the solution-phase as shown in Fig. 3.2. All novel molecules were well characterized by spectroscopic tools. These molecules were synthesized considering its utility to enhance the pharmacokinetic profiles such as lipophilicity, hydrophobicity, cell permeability and conformational stability.