Computer-aided approaches in drug design: the exigent way forward: dynamic perspectives into the mechanistic activities of small molecule inhibitors toward antiviral, antitubercular and anticancer therapeutic interventions.
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Date
2021
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Abstract
The crucial role of CADD in the drug design process is now indisputable and has proven over the
years that it can accelerate the discovery potential drug candidates while reducing the associated
cost. Using knowledge and information about biological target or knowledge about a ligand with
proven bioactivity, CADD, and its techniques can influence various drug discovery pipeline stages.
The ability CADD approaches to elucidate drug-target interactions at the atomistic level allows
for investigations of the mechanism of drugs' actions, revealing atomistic insights that influence
drug design and improvement. CADD approaches also seek to augment traditional in vitro and in
vivo experimental techniques and not replace them since CADD approaches can also allow
modeling complex biological processes that hitherto seemed impossible to explore using
experimental methods.
According to the World Health Organization (WHO), featuring prominently in the top ten causes
of death are cancer, lower respiratory tract infection, tuberculosis (TB), and viral infections such
as HIV/AIDS. Collectively, these diseases are of global health concerns, considering a large
number of associated deaths yearly. Over the years, several therapeutic interventions have been
employed to treat, manage, or cure these diseases, including chemotherapy, surgery, and
radiotherapy. Of these options, small molecule inhibitors have constituted an integral component
in chemotherapy, thereby undoubtedly playing an essential role in patient management.
Although significant success has been achieved using existing therapeutic approaches, the
emergence of drug resistance and the challenges of associated adverse side effects has prompted
the need for the drug design processes against these diseases to remain innovative, including
combining existing drugs and establishing improved therapeutic options that could overcome
resistance while maintaining minimal side effects to patients. Therefore, an exploration of drug
target interactions towards unraveling mechanisms of actions as performed in the reports in this
thesis are relevant since the molecular mechanism provided could form the basis for the design
and identification of new therapeutic agents, improvement of the therapeutic activity of existing
drugs, and also aid in the development of novel therapeutic strategies against these diseases of
global health concern.
Therefore the studies in this thesis employed CADD approaches to investigates molecular
mechanisms of actions of novel therapeutic strategies directed towards some crucial therapeutics
implicated in viral infections, tuberculosis, and cancer. Therapeutic targets studied included;
SARS-CoV-2 RNA dependent RNA polymerase (SARS-CoV-2 RdRp), Human Rhinovirus B14
(HRV-B14) and human N-myristoyltransferases in viral infections, Dihydrofolate reductase
(DHFR) and Flavin-dependent thymidylate synthase (FDTS) in TB, human variants of TCRCD1d,
and Protein Tyrosine Phosphatase Receptor Zeta (PTPRZ) in cancer.
The studies in this thesis is divided into three domains and begins with a thorough review of the
concept of druggability and drug-likeness since the crux of the subsequent reports revolved around
therapeutic targets and their inhibitions by small molecule inhibitors. This review highlights the
principles of druggability and drug-likeness while detailing the recent advancements in drug
discovery. The review concludes by presenting the different computational, highlighting their
reliability for predictive analysis.
In the first domain of the research, we sought to unravel the inhibitory mechanism of some small
molecule inhibitors against some therapeutic targets in viral infections by explicitly focusing on
the therapeutic targets; SARS-CoV-2 RdRp, HRV-B14, and N-myristoyltransferase.
Therapeutic targeting of SARS-CoV-2 RdRp has been extensively explored as a viable approach
in the treatment of COVID-19. By examining the binding mechanism of Remdesivir, which
hitherto was unclear, this study sought to unravel the structural and conformational implications
on SARS-CoV-2 RdRp and subsequently identify crucial pharmacophoric moieties of Remdesivir
required for its inhibitory potency. Computational analysis showed that the modulatory activity of
Remdesivir is characterized by an extensive array of high-affinity and consistent molecular
interactions with specific active site residues that anchor Remdemsivir within the binding pocket
for efficient binding. Results also showed that Remdesivir binding induces minimal individual
amino acid perturbations, subtly interferes with deviations of C-α atoms, and restricts the
systematic transition of SARS-CoV-2 RdRp from the “buried” hydrophobic region to the “surface exposed”
hydrophilic region. Based on observed high-affinity interactions with SARS-CoV-2
RdRp, a pharmacophore model was generated, which showcased the crucial functional moieties
of Remdesivir. The pharmacophore was subsequently employed for virtual screening to identify
potential inhibitors of SARS-CoV-2 RdRp. The structural insights and the optimized
pharmacophoric model provided would augment the design of improved analogs of Remdesivir
that could expand treatment options for COVID-19.
The next study sought to explore the therapeutic targeting of human rhinoviruses (HRV) amidst
challenges associated with the existence of a wide variety of HRV serotypes. By employing
advanced computational techniques, the molecular mechanism of inhibition of a novel
benzothiophene derivative that reportedly binds HRV-B14 was investigated. An analysis of the
residue-residue interaction profile revealed of HRV upon the benzothiophene derivative binding
revealed a distortion of the hitherto compacted and extensively networked HRV structure. This
was evidenced by the fewer inter-residue hydrogen bonds, reduced van der Waals interactions, and
increased residue flexibility. However, a decrease in the north-south wall's flexibility around the
canyon region also suggested that the benzothiophene derivative's binding impedes the “breathing
motion” of HRV-B14; hence its inhibition.
The next study in the first domain of the research investigated the structural and molecular
mechanisms of action associated with the dual inhibitory activity of IMP-1088. This novel
compound reportedly inhibits human N-myristoyltransferase subtypes 1 and 2 towards common
cold therapy. This is because it has emerged that the pharmacological inhibition of Nmyristoyltransferase
is an efficient non-cytotoxic strategy to completely thwart the replication
process of rhinovirus toward common cold treatment. Using augmentative computational and
nanosecond-based analyses, findings of the study revealed that the steady and consistent
interactions of IMP-1088 with specific residues; Tyr296, Phe190, Tyr420, Leu453, Gln496,
Val181, Leu474, Glu182, and Asn246, shared within the binding pockets of both HNMT subtypes,
in addition to peculiar structural changes account for its dual inhibitory potency. Findings thus
unveiled atomistic and structural perspectives that could form the basis for designing novel dualacting
inhibitors of N-myristoyltransferase towards common cold therapy.
In the second domain of the research, the mechanism of action of some small molecule inhibitors
against DHFR, FDTS, and Mtb ATP synthase in treating tuberculosis is extensively investigated
and reportedly subsequently.
To begin with, the dual therapeutic targeting of crucial enzymes in the folate biosynthetic pathway
was explored towards developing novel treatment methods for TB. Therefore, the study
investigated the molecular mechanisms and structural dynamics associated with dual inhibitory
activity of PAS-M against both DHFR and FDTS, which hitherto was unclear. MD simulations
revealed that PAS-M binding towards DHFR and FDTS is characterized by a recurrence of strong
conventional hydrogen bond interactions between a peculiar site residue the 2-aminov
decahydropteridin-4-ol group of PAS-M. Structural dynamics of the bound complexes of both
enzymes revealed that, upon binding, PAS-M is anchored at the entrance of hydrophobic pockets
by a strong hydrogen bond interaction while the rest of the structure gains access to deeper
hydrophobic residues to engage in favorable interactions. Further analysis of atomistic changes of
both enzymes showed increased C-α atom deviations and an increase C-α atoms radius of gyration
consistent with structural disorientations. These conformational changes possibly interfered with
the enzymes' biological functions and hence their inhibition as experimentally reported.
Additionally, in this domain, the therapeutic targeting of the ATP machinery of Mtb by
Bedaquiline (BDQ) was explored towards unravelling the structures and atomistic perspectives
that account for the ability of BDQ to selectively inhibits mycobacterial F1Fo-ATP synthase via its
rotor c-ring. BDQ is shown to form strong interaction with Glu65B and Asp32B and, consequently,
block these residues' role in proton binding and ion. BDQ binding was also revealed to impede the
rotatory motion of the rotor c-ring by inducing a compact conformation on the ring with its bulky
structure. Complementary binding of two molecules of BDQ to the rotor c-ring, proving that
increasing the number of BDQ molecule enhances inhibitory potency.
The last study in this research domain investigated the impact of triple mutations (L59V, E61D,
and I66M) on the binding of BDQ to Mtb F1F0 ATP-synthase. The study showed that the
mutations significantly impacted the binding affinity of BDQ, evidenced by a decrease in the
estimated binding free energy (ΔG). Likewise, the structural integrity and conformational
architecture of F1F0 ATP-synthase was distorted due to the mutation, which could have interfered
with the binding of BDQ.
The third domain of the research in this thesis investigated some small molecule inhibitors'
inhibitory mechanism against some therapeutic targets in cancer, specifically PTPRZ and hTCRvi
CD1d. Studies in the third domain of the research in the thesis began with the investigation of the
investigation of the inhibitory mechanism of NAZ2329, an allosteric inhibitor of PTPRZ, by
specifical investigating its binding effect on the atomic flexibility of the WPD-loop. Having been
established as crucial determinant of the catalytic activity of PTPRZ an implicated protein in
glioblastoma cells, its successfully therapeutic modulation could present a viable treatment option
in glioblastoma. Structural insights from an MD simulation revealed that NAZ2329 binding
induces an open conformation of the WPD-loop which subsequently prevents the participation of
the catalytic aspartate of PTPRZ from participating in catalysis hence inhibiting the activity of
PTPRZ. A pharmacophore was also created based of high energy contributing residues which
highlighted essential moieties of NAZ2329 and could be used in screening compound libraries for
potential inhibitors of PTPRZ.
A second study in this domain sought to explore how structural modification could improve a
therapeutic agent's potency from an atomistic perspective. This study was based on an earlier report
in which the incorporation of a hydrocinnamoyl ester on C6’’ and C4-OH truncation of the
sphingoid base of KRN7000 generated a novel compound AH10-7 high therapeutic potency and
selectivity in human TCR-CD1d and subsequently results in the activation of invariant natural
killer T cells (iNKT). The hydrocinnamoyl ester moiety was shown to engage in high-affinity
interactions, possibly accounting for the selectivity and higher potency of AH10-7. Molecular and
structural perspectives provided could aid in the design of novel α-GalCer derivatives for cancer
immunotherapeutics.
Chapter 3 provides theoretical insights into the various molecular modeling tools and techniques
employed to investigate the various conformational changes, structural conformations, and the
associated mechanism of inhibitions of the studied inhibitors towards viral, tuberculosis, and
cancer therapy.
Chapter 4 provided sufficient details on druggability and drug-likeness principles and their recent
advancements in the drug discovery field. The study also presents the different computational tools
and their reliability of predictive analysis in the drug discovery domain. It thus provides a
comprehensive guide for computational-oriented drug discovery research.
Chapter 5 provides an understanding of the binding mechanism of Remdesivir, providing structural
and conformational implications on SARS-CoV-2 RdRp upon its binding and identifying its
crucial pharmacophoric moieties.
Chapter 6 explains the mechanism of inhibition of a novel benzothiophene derivative, revealing
its distortion of the native extensively networked and compact residue profile.
Chapter 7 unravels molecular and structural bases behind this dual inhibitory potential of the novel
inhibitor IMP-1088 toward common cold therapy using augmentative computational and
cheminformatics methods. The study also highlights the pharmacological propensities of IMP-
1088.
Chapter 8 unravels the molecular mechanisms and structural dynamics of the dual inhibitory
activity of PAS-M towards DHFR and FDTS.
Chapter 9 reports the structural dynamics and atomistic perspectives that account for the reported
ability of BDQ to halt the ion shuttling ability of mycobacterial c-ring.
Chapter 10 presents the structural dynamics and conformational changes that occur on Mtb F1F0
ATP-synthase binding as a result of the triple mutations using molecular dynamics simulations,
free energy binding, and residue interaction network (RIN) analyses.
Chapter 11 explored the impact of NAZ2329, a recently identified allosteric inhibitor of Protein
Tyrosine Phosphatase Receptor Zeta (PTPRZ), on the atomic flexibility of the WPD-loop, an
essential loop in the inhibition of PTPRZ. The study also presents the drug-likeness of NAZ2329
using in silico techniques and its general inhibitory mechanism.
Chapter 12 provides atomistic insights into the structural dynamics and selective mechanisms of
AH10-7 for human TCR-CD1d towards activating iNKT cells.
The studies in this thesis collectively present a thorough and comprehensive in silico perspective
that characterizes the pharmacological inhibition of some known therapeutic targets in viral
infections, tuberculosis, and cancer. The augmentative integration of computational methods to
provide structural insights could help design highly selective inhibitors of these therapeutic targets.
Therefore, the findings presented are fundamental to the design and development of next generation
lead compounds with improved therapeutic activities and minimal toxicities.
Description
Doctoral Degree. University of KwaZulu-Natal, Durban.