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https://t.me/med1917
Kannan Sadasivam, Venkata Surya Kumar Choutipalli
✶
,
and Lalitha Gummidi
✶
14 Computer-aided design of peptidomimetic
therapeutics
Abstract: Over the past two decades, the pharmaceutical industry has transitioned from
small molecule detection to biologic-based therapies. Amino acid-based medications, in-
cluding proteins, peptides, and peptidomimetics, offer effective treatments for drug re-
sistance and molecular deficiencies. Computational tools play a crucial role in designing
and developing these therapies. Traditional therapeutic product development is time-
consuming and costly. By adopting contemporary methodologies like computer-aided de-
sign, the cost, examination phase, and failure rate of drug discovery can be reduced.
Computational techniques enable the discovery of diverse biotherapeutics, expanding
the possibilities in amino acid-based therapy design. Amino acid-based therapies are
well-suited for targeting pathogens and malfunctioning organs. They offer selectivity
and fewer adverse effects compared to small molecules. Recent interest in developing
amino acid-based treatments, such as proteins, peptides, and peptidomimetics, has
grown among pharmaceutical researchers. These macromolecules can effectively iden-
tify specific targets within densely packed cells, providing promising avenues for thera-
peutic development. This study focuses on the computational aspects involved in amino
acid-based medicine design. The main motive of this chapter is the better understanding
of peptidomimetics and the crucial role of computational tools in the design and devel-
opment of such highly pharmaceutically valued compounds.
Keywords: Protein-based drugs, in silico designing, peptide, peptidomimetics
14.1 Introduction
Peptidomimetics are the synthetic compounds engineered to replicate the functional
structure of individual peptides or particular peptide segments found within proteins
[1]. Over time, peptidomimetic design has played a crucial role in the field of drug
✶
Corresponding author: Venkata Surya Kumar Choutipalli, Department of Chemistry
and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA,
email: surya_choutipalli@baylor.edu
✶
Corresponding author: Lalitha Gummidi, Department of Chemistry, Indiana University Bloomington,
800 E Kirkwood Ave, Bloomington, IN 47405, USA, email: lgummidi@iu.edu
Kannan Sadasivam, Department of Physics, Government Arts College for Men, Krishnagiri, 635 001,
Tamil Nadu, India
https://doi.org/10.1515/9783111207117-014
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discovery. However, it remains a formidable task, influenced by the specific target
and its binding characteristics with ligands. The intricacy is particularly evident when
developing peptidomimetics for inhibiting protein–protein interactions (PPIs) involv-
ing expansive protein interfaces [2, 3]. In such instances, the challenge lies in the fact
that a single small molecule must effectively disrupt numerous specific interactions
formed by complementary protein surfaces, accounting for the gained free energy
during the process. As a result, innovative approaches are essential to overcome these
hurdles, and a comprehensive understanding of PPIs is vital for the successful devel-
opment of peptidomimetic drugs.
For the past few years, theoretical approaches for investigating the structural and
dynamic aspects of macromolecules have been on a constant rise [4–8]. This growth
can be attributed to the continuous enhancement of methodologies, algorithms, and the
availability of high-performance computing facilities. The significance of theoretical
methodologies has been steadily increasing in various scientific domains and has now
become paramount in the realm of drug design. The impact of computational techni-
ques on drug discovery is evident, with numerous examples showcasing their vital role
in identifying new molecules effective against different diseases [9, 10]. In the modern
era, computer-aided drug design has proven successful not only in developing small
molecules but also in tackling the more intricate task of designing larger compounds
such as peptides or peptide-like molecules (peptoids or peptidomimetics) [11, 12]. These
larger compounds retain the physicochemical attributes of bioactive proteins or poly-
peptide chains. One noteworthy feature of peptides is their conformational plasticity,
enabling them to interact with larger and more accessible surfaces compared to the
confined binding pockets targeted by small molecules. Consequently, peptides and pep-
tidomimetics have emerged as highly promising candidates for addressing PPIs [13, 14].
Thus, understanding peptidomimetics in-depth is of utmost importance for the
advancement of pharmaceutical sciences. This chapter delves into the historical con-
text and evolution of peptidomimetics, shedding light on the significant contributions
of computational research in this field. Moreover, comprehensive discussions on the
future prospects of peptidomimetics are presented, providing valuable insights into
the potential directions and innovations that lie ahead. As we explore the fascinating
world of peptidomimetics, we come to realize the profound impact it can have on the
development of novel and effective pharmaceutical interventions.
14.2 Historical insights and current development
trends on therapeutic peptides
Peptides are a special family of pharmacological substances that are both biochemi-
cally and therapeutically distinct from both proteins and small molecules. Peptides
offer a chance for thera peutic intervention that closely resembles natural pathways
352 Kannan Sadasivam, Venkata Surya Kumar Choutipalli, and Lalitha Gummidi
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because they are intrinsic signaling molecules for numerous physiological activities.
In fact, a number of peptide medications are basically “replacement therapies” that
restore or supplement peptide hormones when endogenous levels are insufficient or
nonexistent. This is demonstrated by the separation of insulin and its initial therapeu-
tic application in diabetics who were unable to manufacture enough of the hormone
in the 1920s [15]. With the purification of adrenocorticotrophic hormone (ACTH) from
cattle pituitary glands to treat a range of endocrine problems in patients, the practice
of isolating peptides from entire animal tissue progressed [16]. In the first part of the
twentieth century, peptides extracted from natural sources, such as insulin and
ACTH, produced life-saving medications. Synthetic oxytocin and vasopressin also
gained clinical usage in the 1950s, when sequence elucidation and chemical synthesis
of peptides became practical. Isolation of natural products from unusual sources has
become a common technique for discovering novel potential treatments as venoms of
arthropods and cephalopods have come to be recognized as treasure troves of bioac-
tive peptides. Following the identification and molecular characterization of many sig-
nificant endogenous peptides, hormone receptors during the genomi c era, business
and academia started looking for new peptidic ligands for these receptors.
Oral bioavailability is another barrier to the development of peptidic drugs be-
cause peptide hormones’ high polarity and molecular weight severely restrict intesti-
nal permeability and digestive enzymes made to degrade amide bonds of consumed
proteins are also effective at degrading the same bonds in peptide hormones. Peptides
were a less desirable option for diseases requiring prolonged, outpatient therapy
since oral administration is frequently seen as attractive for promoting patient com-
pliance. In addition, the availability of high-throughput screening (HTS) technology
and large combinatorial chemistry libraries tipped the pendulum in favor of small
compounds that target peptide receptors. The difficulty lies in finding a small mole-
cule that mimics a peptide ligand’s receptor binding and selective modulation because
small molecules are typically easier to make and more suited for oral delivery than
peptides. The assumption that leads compounds may be found, optimized, and turned
into medications was backed by the quantity and variety of scaffolds present in con-
temporary screening libraries. By revealing crucial chemical interactions at receptor
active regions that might be tapped by any class of ligand, structural biology adds an-
other arrow to the quiver [17, 18].
A deeper understanding of the potential of peptide therapies has lately come to
light. Through the modification of amino acids or amino acid backbones, the addition
of nonnatural ami no acids, and the conjugation of moieties that extend half-l ife or
improve solubility, novel synthetic strategies enable the modulation of pharmacoki-
netic properties and target specificity; novel formulation strategies minimize injection
frequency while enhancing stability and other physical properties. Figure 14.1 elicits
the challenges involved in the multiscale pharmacokinetics. Assessing the pharmaco-
kinetic effects of a drug requires a cautious examination of the pertinent physiological
scales related to drug absorption, distribution, metabolism, excretion, and toxicity.
14 Computer-aided design of peptidomimetic therapeutics 353
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