| Frontiers
in Drug Design and Discovery
ISBN: 90-77527-03-6
Frontiers in Drug Design
& Discovery
Volume 3, 2007
Contents
Editorial: Structure-Based
Drug Design in the 21st
Century Pp. i-iii
G.W. Caldwell, Atta-ur-Rahman, M.R. Player and M.I. Choudhary
Alpha-Helix Mimetics: Progress Towards
Effective Modulation of Protein-Protein Complexes
Pp. 5-44
D.J. Parks and M.R. Player
[Abstract]
Structures of HIV Protease Guide Inhibitors Design
to Overcome Drug Resistance Pp. 45-62
I.T. Weber, A.Y. Kovalevsky and R.W. Harrison
[Abstract]
Structure and Function of G Protein-Coupled Receptors
Studied Using Sequence Analysis, Molecular Modeling and Receptor
Engineering: Adenosine Receptors Pp. 63-79
S. Costanzi, A.A. Ivanov, I.G. Tikhonova and K.A. Jacobson
[Abstract]
Virtual Docking: How Are We Doing And How Can We Improve?
Pp. 81-103
R.L. DesJarlais, M.D. Cummings and A.C. Gibbs
[Abstract]
Fragment-Based Lead Discovery by NMR Pp.
105-119
M. Schade
[Abstract]
Targeting Drug Resistant Mutations Using Novel Binding
Interactions – Lessons Learned from Abl-T315I and their
Implications in Drug Design Pp. 121-144
G. Noronha, J. Cao, C. Chow, E. Dneprovskaia, L. Hwang,
D. Lohse, C.C. Mak, A. McPherson, R.M. Fine, X. Kang, B. Klebansky,
M.S.S. Palanki, V.P. Pathak, J. Renick, R. Soll and B. Zeng
[Abstract]
Recent Advances in the Structure-Guided Design of
Protein Kinase Inhibitors Pp. 145-170
C. McInnes
[Abstract]
Fragment-Based Approaches to Lead Discovery
Pp. 171-202
D.F. Wyss and H.L. Eaton
[Abstract]
Recent Advances in Structure-Based Design of Nuclear
Hormone Receptors Pp. 203-224
R.L. Magolda, W.S. Somers and R.J. Unwalla
[Abstract]
Structure-Based Drug Development Against Malaria
Pp. 225-255
K. Buchholz, B.M. Mailu, R.H. Schirmer and K. Becker
[Abstract]
Virtual Screening of Compound Libraries Using In
silico Three Dimensional Pharmacophores to Aid the Discovery
and Design of Antimalarial and Antileishmanial Agents Pp.
257-292
A.K. Bhattacharjee
[Abstract]
DNA Helicases Implicated in Chromosomal Instability
Disorders as Targets for the Discovery of Novel Anti-Cancer
Agents Pp. 293-316
R. Gupta and R.M. Brosh, Jr.
[Abstract]
Scoring Functions for Virtual Screening Pp.
317-379
F. Spyrakis, G.E. Kellogg, A. Amadasi and P. Cozzini
[Abstract]
Reactivators of Tabun-Inhibited Acetylcholinesterase:
Structure Biological Activity Relationship Pp. 381-394
K. Kuca, D. Jun, K. Musilek and J. Bajgar
[Abstract]
Peptide Diversity in Drug Discovery Pp. 395-432
M.P. Brennan, D. Cox and A.J. Chubb
[Abstract]
Protection of Neurovascular Injury by Vasoprotective
Agents: A Novel Therapeutic Strategy for Ischemic Brain Edema
Pp. 433-454
F. Han, N. Shioda, Y. Shirasaki and K. Fukunaga
[Abstract]
Protein Flexibility and Mobility in Structure-Based
Drug Design Pp. 455-476
A. Ahmed, S. Kazemi and H. Gohlke
[Abstract]
Structure-Based Virtual Screening Pp. 477-502
T. Polgár and G.M. Keseru
[Abstract]
Computer-Aided Engineering of GPCRS and its Application
to Drug Discovery Pp. 503-523
A. Lavecchia
[Abstract]
Antibody-Drug Conjugates in Targeted Therapy for Cancer
Pp. 525-537
R. Tang, S. Cohen, O. Legrand and J.-P. Marie
[Abstract]
Structure-Activity Relationships in Peptides: From
Modelling to Rational Drug Design Pp. 539-558
E. Benedetti, C. Pedone and M. Saviano
[Abstract]
Rational Design Strategies for the Development of
Synthetic Quinoline and Acridine Based Antimalarials
Pp. 559-609
M.J. Dascombe, M.G.B. Drew, P.G. Evans and F.M.D. Ismail
[Abstract]
Contributors
Pp. 611-617
Subject Index Pp. 619
Abstracts
[Back to top]
Editorial: Structure-Based Drug Design
in the 21st
Century
G.W. Caldwell, Atta-ur-Rahman, M.R. Player and M.I. Choudhary
Bringing affordable, safe and therapeutically useful
drugs to patients globally is a primary goal for many governmental,
academic and pharmaceutical scientists worldwide. The Frontier
in Drug Design and Discovery series is dedicated to assembling
these eminent scientists and allowing them to present comprehensive
reviews with fresh new ideas on drug design and drug discovery.
The first volume (2005) brought together experts to review
and discuss the advantages and limitations of modern screening
techniques used in the drug discovery process to identify
potential drug candidates. The second volume (2006) discussed
new technological and conceptual approaches to accelerate
and to improve the predictability of the discoveries made
in the laboratory into clinical testing. In the third volume
of this series, reviews and discussions are presented applying
structure-based design to identify potent lead drug candidates
for a variety of diseases using techniques such as in-silico
virtual screening, peptidomimetics, fragment-based approaches,
protein crystallography, and NMR spectroscopy.
The importance of understanding the fundamentals of the energetics
of a drug molecule binding to a biomacromolecule target has
emerged over the years enabling scientists to think intelligently
about molecular modifications that will impact binding of
a designed drug. Understanding the energetic of a drug interacting
with a target has had a profound impact not only on drug design,
but also on the elucidation of molecular mechanism of disease.
An early structure of hemoglobin allowed the study of the
basis of sickle-cell anemia as well as the mechanism of drugs
that inhibited sickling. Initially, structure-based drug design
was based on structural determination of related proteins
where the protein of interest was yet unsolved. For example,
drug design for important targets such as angiotensin converting
enzyme and renin were aided by determination of related enzymes
such as thermolysin and fungal aspartyl proteases. However
today, higher throughput protein crystallography, NMR spectroscopy
and computational techniques are providing key insights on
a large variety of drug-protein complexes.
The drug design field has continued to evolve to encompass
de novo design of ligands based on protein structure,
transformation of peptide ligands into smaller, more druglike
compounds and structure-based design of inhibitors of heretofore
challenging classes such as protein-protein interfaces. In
addition, NMR has come into its own as a new means of structure-based
design. Technical advances in robotics, crystallization screens
and computational analysis has raised x-ray crystallography
to the level where it can support fragment-based design; where
co-structures of small fragments are solved and the fragments
are pieced together to yield tighter binding ligands.
We have selected authors that have contributed 22 chapters
to the review of a range of topics involving drug design.
D.J. Parks and colleagues have contributed a chapter outlining
how the uses of small molecules that mimic key secondary motifs,
such as α-helical
mimetics, have been successful in disrupting protein-protein
interactions. The chapter by I.T. Weber and colleagues gives
an interesting review on how intelligent data mining approaches,
along medicinal chemistry, kinetic and X-ray crystallographic
analysis, can be used to overcome HIV drug resistance. S.
Costanzi and colleagues introduces the reader to the use of
computational approaches to study various rhodopsin-based
homology models of the adenosine receptors. R.L DesJarlais,
M.D. Cummings and A.C Gibbs give an overview of how virtual
docking and scoring techniques can be used to select lead
screening candidates. D.F. Wyss and H.L. Eaton give a well-balanced
review of fragment-based approaches in drug discovery. G.
Noronha and colleagues describe a novel conceptual design
process to obtain potent inhibitors targeting the active form
of Src, a cellular tyrosine kinase that plays a role in cellular
proliferation and growth.
The chapter by C. McInnes
summarizes the progress made in the development of new structure
based approaches for the discovery of protein kinase inhibitor
drugs. M. Schade has prepared a chapter reviewing NMR techniques
for fragment-based drug discovery. R.L. Magolda and colleagues
have contributed a chapter highlighting the strategies and
challenges facing the design of specific ligands for nuclear
hormone receptors using X-ray crystallographic analysis and
molecular modeling methods. K. Buchholz and colleagues present
an interesting review on the major current structural-based
antimalarial approaches and an overview of inhibitors that
have been developed on the basis of these known parasite protein
structures. Along these same lines, A.K Bhattacharjee presents
a review on how in-silico methodologies have been
successfully applied to virtual screening of compound libraries,
to aid in the discovery and design of antimalarial and antileishmanial
agents. R. Gupta and R. M. Brosh Jr. have prepared a review
for the rational development of helicase inhibitors for improved
chemotherapeutic options for treating cancers.
P. Cozzini introduces the reader to the problems related to
docking/scoring techniques for in-silico screening.
K. Kuca and colleagues have contributed a chapter highlighting
acetylcholinesterase reactivators (i.e., oximes) that are
drug used to treat intoxications of organophosphorus pesticides.
The main structural requirements for this class of drugs are
discussed. A.J. Chubb and colleagues discuss the history and
advances in peptide synthesis as it relates to peptidomimetics
development. F. Han and colleagues present a novel therapeutic
strategy for ischemic brain edema. H. Gohlke and colleagues
give a well-balanced review of how to incorporate the influence
of protein flexibility and mobility into drug design approaches.
G.M. Keseru and T. Polgár have written an excellent
chapter describing structure-based virtual screening approaches
using various case studies. A. Lavecchia presents a review
on the current status of G protein-coupled receptor modeling
highlighting alternative computational approaches for rhodopsin-based
homology building. R. Tang and colleagues present an interesting
review on how monoclonal antibody-drug conjugates are used
to target cancers. In the review, antibody engineering, the
process of drug selection, and the development of linker to
optimize clinical trials are discussed. M. Saviano and colleagues
have contributed a chapter outlining the structural properties
of the main constrained non-coded amino acids to illustrate
the use of peptidomimetic approaches. M.J. Dascombe and colleagues
review the evolution and drug design of clinically effective
antimalarial drugs such as 4-aminoquinolines, 8-aminoquinolines
and 9-amino-acridines.
Gary W. Caldwell
Atta-ur-Rahman
Mark R. Player
M. Iqbal Choudhary
[Back to top]
Alpha-Helix Mimetics: Progress Towards
Effective Modulation of Protein-Protein Complexes
D.J. Parks and M.R. Player
Protein-protein interactions are one of the most common modes
of signaling, but can be one of the most challenging to disrupt.
This is primarily due to the relatively shallow and hydrophobic
nature of the interacting protein surfaces that may extend
over large areas. Even so, progress has been made on this
frontier using small molecules that mimic key secondary structural
motifs, called proteomimetics. In particular, α-helix
mimetics have been successful in disrupting protein-protein
interactions. This chapter will discuss the variety of approaches
taken to obtain α-helical
mimicry in low molecular weight, drug-like molecules. Targets
such as the BCl-2 family of proteins, HDM2-p53, various calmodulin-binding
proteins, and gp41 have a wealth of literature describing
α-helix
mimetics as protein-protein interaction disruptors having
therapeutic value in the areas of cancer, Alzheimer’s
disease, and AIDS. The approaches taken vary from stabilizing
the α-helical
structure of short peptides to a diversity of non-peptide,
small molecule scaffolds allowing for the correct spatial
orientation of substituents for interaction with the protein
target. This chapter will compare and contrast the various
scaffolds successfully shown to inhibit protein-protein interactions.
[Back to top]
Structures of HIV Protease Guide Inhibitors Design
to Overcome Drug Resistance
I.T. Weber, A.Y. Kovalevsky and R.W. Harrison
The HIV/AIDS infection continues to be a major epidemic worldwide
despite the initial promise of antiviral drugs. Current therapy
includes a combination of drugs that inhibit two of the virally-encoded
enzymes, the reverse transcriptase and the protease. The first
generation of HIV protease inhibitors that have been in clinical
use for treatment of AIDS since 1995 was developed with the
aid of structural analysis of protease-inhibitor complexes.
These drugs were successful in improving the life span of
HIV-infected people. Subsequently, the rapid emergence of
drug resistance has necessitated the design of new inhibitors
that target mutant proteases. This second generation of antiviral
protease inhibitors has been developed with the aid of data
from medicinal chemistry, kinetics, and X-ray crystallographic
analysis. Traditional computational methods such as molecular
mechanics and dynamics can be supplemented with intelligent
data mining approaches. One approach, based on similarities
to the protease interactions with substrates, is to incorporate
additional interactions with main chain atoms that cannot
easily be eliminated by mutations. Our structural and inhibition
data for darunavir have helped to understand its antiviral
activity and effectiveness on drug resistant HIV and demonstrate
the success of this approach.
[Back to top]
Structure and Function of G Protein-Coupled Receptors
Studied Using Sequence Analysis, Molecular Modeling and Receptor
Engineering: Adenosine Receptors
S. Costanzi, A.A. Ivanov, I.G. Tikhonova and K.A. Jacobson
Rhodopsin is the only member of the G protein-coupled receptors
(GPCRs) superfamily for which crystallographic data are available.
Thus, the study of the structure-function relationships of
most GPCRs relies on bioinformatics, rhodopsin-based homology
modeling, and docking experiments conducted in an iterative
manner utilizing site-directed mutagenesis and chemical modification
of the ligands. Adenosine receptors (ARs) are presented as
a case study to illustrate this indirect composite approach
relying on an intimate combination of computational and experimental
techniques. In the first section we discuss the phylogenesis
of the ARs from an evolutionary perspective. Furthermore,
we review sequence comparison studies from the perspective
of similarities with other GPCRs, chemogenomics, and coupling
to G proteins. In the second section, we review various rhodopsin-based
homology models of the ARs and docking studies of agonists
and antagonists. As reported for other GPCRs, several different
modes have been hypothesized for ligands binding to ARs. Here,
we critically review the proposed binding modes of agonists
and antagonists in light of the available mutagenesis data
and the structure-activity relationships of ligands. Lastly,
we review an experimentally-supported strategy for validating
theoretical binding hypotheses based on the complementary
reengineering of receptors and ligands (neoceptors and neoligands).
[Back to top]
Virtual Docking: How Are We Doing And How Can We Improve?
R.L. DesJarlais, M.D. Cummings and A.C. Gibbs
The virtual docking and scoring of a large number of molecules
in a protein active site has proven to be a useful method
for selecting molecules for screening. It has the potential
to be less biased than pharmacophore-based methods, since
the only assumption one must make is the region of the protein
surface to target. In this chapter, we will briefly outline
the steps in a generic docking procedure, and compare and
contrast how the more commonly used methods approach each
of these steps. Several groups have recently compared a variety
of popular docking methods using different test systems. These
studies are remarkable for the similarity of their conclusions
and as a group give a good picture of the state of the art.
We will then focus in on two aspects of the docking problem
that are receiving increased attention and have potential
to significantly improve docking results: ligand preparation
and protein flexibility. Ligand preparation is a fundamental
aspect of virtual screening that has not been systematically
investigated. Issues with ligand preparation include ionization
states, tautomerization, and stereochemistry. If these are
not treated accurately, one can miss a promising lead or overwhelm
the docking with molecules that are unlikely to be present
under physiologic conditions. Both false positives and false
negatives can result. Proteins are not rigid entities. It
is clear that docking to a rigid model of a protein, even
if it is an experimentally determined model, does not capture
the dynamic behavior of the protein in solution. Current approaches
such as docking to different models of the same protein or
allowing limited side chain flexibility are steps toward more
realistic modeling of the protein target.
[Back to top]
Fragment-Based Lead Discovery by NMR
M. Schade
NMR is a powerful tool for fragment-based lead discovery comprising
robust techniques for screening, core elaboration and fragment
linking as well as 3D protein-ligand structure determination.
Utilizing a direct binding assay that solely contains protein
and ligand, NMR detects loose fragment binders with unparalleled
sensitivity and robustness even in the millimolar affinity
range. Excellent research during the last ten years established
protein- and ligand-detected NMR screening assays for soluble
proteins below and above 50 kD, respectively. Site-specific
methods, such as spin-label perturbation and InterLigand-NOE
(ILOE) NMR screening allow one to selectively detect fragment
binding to allosteric or adjacent second sites. Target-immobilized
NMR screening (TINS) reduces protein consumption and potentially
enables screening of membrane proteins.
NMR supports fragment-to-lead optimization through chemical
shift perturbation SAR maps and fragment linking through ILOE
information at timely throughput of >= 20 compounds / day.
3D protein-ligand structures for structure-based design require
more time (> 1 month / compound) and thus are limited to
few representative ligands.
Further research is required to make such NMR techniques amenable
to proteins with poor expression yield, low solubility, sole
expression in mammalian systems and ultimately to membrane
proteins. Some of these bottlenecks are circumvented by integrating
NMR into HTS, computational docking and co-crystallization
platforms, which is an important future direction.
[Back to top]
Targeting Drug Resistant Mutations Using Novel Binding
Interactions – Lessons Learned from Abl-T315I and their
Implications in Drug Design
G. Noronha, J. Cao, C. Chow, E. Dneprovskaia, L. Hwang,
D. Lohse, C.C. Mak, A. McPherson, R.M. Fine, X. Kang, B. Klebansky,
M.S.S. Palanki, V.P. Pathak, J. Renick, R. Soll and B. Zeng
Tyrosine kinases regulate various biological processes including
cell proliferation, migration, differentiation and survival.
Src and Abl are cellular tyrosine kinases that play roles
in cellular function, including proliferation and growth.
Both are usually under tight regulatory control in normal
cells. Disruption in certain regulatory mechanisms results
in the activation of Src mediated pathways, which have been
implicated in cancers, stroke, myocardial infarction, and
bone disorders. The formation of the Philadelphia chromosome
results in the production of the fusion protein Bcr-Abl with
a constitutively active Abl kinase portion, causative for
chronic myelogenous leukemia (CML). Gleevec (Imatinib) targeting
the Abl ATP site is the current standard of care for treating
CML. Drug resistance to treatment with Gleevec in 50-90% of
cases arises due to mutations mostly clustered around the
Gleevec binding site. Since all known inhibitors of Src that
bind at the ATP site are also inhibitors of Abl, several Src
and Abl inhibitors are being intensely studied as they target
many of the Abl mutations seen in Gleevec resistance, potentially
due to differential binding modes. Sprycel, a highly potent
Src and Abl inhibitor was advanced and has now been approved
for the treatment of Gleevec resistant CML. None of these
inhibitors target the particularly challenging mutation of
the gatekeeper residue, the T315I mutation. The gatekeeper
residue sits at the entrance to the hydrophobic pocket –
a region proximal to the hinge and one that several classes
of ATP site binding inhibitors exploit since it serves to
enhance both potency and selectivity. We describe a novel
conceptual design used to obtain potent inhibitors targeting
the active form of Src. This powerful concept was further
applied to design inhibitors targeting the Abl-T315I mutant.
The approach targets an acid functional group on the αC-helix
located deep within this hydrophobic pocket and that is available
only after kinase activation. This designed interaction provides
a “magic bullet” in overcoming the steric clashes
arising from the Ile-315, and changes poor (ca. 10 µM)
inhibitors into those with low nM potency. Targeting the active
state of the kinase via this unique and relatively
unexplored portion of the active kinase, the Glu on the αC-helix,
has implications for targeting disease states with upregulated
or constitutively activated kinase pathways.
[Back to top]
Recent Advances in the Structure-Guided Design of
Protein Kinase Inhibitors
C. McInnes
The successful approval and launch of several small molecule
protein kinase inhibitor drugs has stimulated further interest
and research into therapeutics targeting kinases implicated
in disease pathways. The use of protein structural information
obtained from the kinase catalytic domain or substrate binding
site has and continues to play a major role in the discovery
and optimization of novel pharmacophores. A summary of progress
made recently in the development of new structure based approaches
for the discovery of kinase inhibitors is described. In addition,
a number of case studies are presented demonstrating successful
application of structure-guided design methods to the development
of selective inhibitors targeting the cyclin dependent kinases,
MAP kinases, and receptor tyrosine kinases. Inhibitors that
preferentially bind to inactive kinase conformations are also
covered as an area of recent exciting developments. In addition,
the development of a new generation of selective kinase inhibitor
drugs through targeting alternate binding sites distinct from
the ATP cleft is presented.
[Back to top]
Fragment-Based Approaches to Lead Discovery
D.F. Wyss and H.L. Eaton
Fragment-based lead discovery is a recent approach in which
much lower molecular weight compounds are screened relative
to those in high throughput screening campaigns. In theory,
fragment-based methods offer the possibility of identifying
novel leads with improved affinity, selectivity, and pharmaceutical
properties, and the rationale behind these fragment-based
strategies makes intuitive sense. However, fragment-based
hits are typically weak inhibitors/binders (IC50/Kd
~ μM-mM
range), and therefore need to be screened at higher concentrations
using very sensitive detection techniques. Although fragment
hits are simpler, less functionalized compounds with correspondingly
lower potencies, they typically possess high ‘ligand
efficiency’ and so are highly suitable for optimization
into clinical candidates with good drug-like properties. Nevertheless,
elaborating, linking or exploring weak-binding fragments into
high-affinity binders can be challenging and fragment-based
lead discovery can be difficult in practice. Both the discovery
of fragment hits and how to advance or link them are areas
of intense research. This paper discusses the concepts of
fragment-based lead discovery, the design of fragment-based
screening libraries, various screening techniques utilized
in this approach, and a choice of specific examples which
illustrate diverse approaches to fragment-based lead discovery.
[Back to top]
Recent Advances in Structure-Based Design of Nuclear
Hormone Receptors
R.L. Magolda, W.S. Somers and R.J. Unwalla
The family of nuclear hormone receptors continues to be a
rich source of drug discovery targets. In addition to traditional
structure-based design methods for receptor-ligand design,
the nuclear hormone receptor family presents an additional
challenge. The receptor-ligand complex can adopt a conformation
that attracts a family of co-activators and co repressor proteins
leading to very specific biological profiles. Several specific
receptor modulators have been discovered that exhibit novel
biological properties that have either entered the clinic
or are in the advanced stages of preclinical research. Some
examples will be presented to highlight how this exciting
area has emerged over the past decade while projecting some
future trends. The focus of this chapter will not be a comprehensive
summary of the many examples in the last decade since several
reviews are available [1]. Rather, this chapter will highlight
some of the strategies and challenges facing the design of
specific ligands using X-ray and molecular modeling methods.
[Back to top]
Structure-Based Drug Development Against Malaria
K. Buchholz, B.M. Mailu, R.H. Schirmer and K. Becker
The protozoon Plasmodium falciparum is the causative
agent of tropical malaria which causes up to three million
human deaths and up to 500 million episodes of clinical illness
throughout the world annually. Children in African countries
bear the largest part of this burden. Due to the rapid development
of resistance to clinically used drugs like chloroquine and
mefloquine and the increasing risk of resistance to artemisinins,
novel effective and affordable antimalarial agents are urgently
required. The progress made over the last years in the fields
of genomics, proteomics, and clinical medicine coupled with
improved facilities as well as technical progress in structural
biology and high throughput screening methods are essential
to support these drug development approaches. Furthermore
concerted programs supported by governments, industry and
academia contribute significantly to the progress in the field
of antimalarial chemotherapy. Among the most interesting antimalarial
target proteins currently studied are proteases, like plasmepsins,
falcipains and falcilysin, but also protein kinases, glycolytic
enzymes and enzymes involved in lipid metabolism and DNA replication.
In addition, redox active proteins like glutathione reductase,
thioredoxin reductase and glutathione S-transferase
have become increasingly interesting. In this article we summarize
the major current structure-based antimalarial drug development
approaches. We briefly review the presently available three-dimensional
structures of Plasmodium proteins together with their
potential as drug targets. In parallel, we give an overview
over inhibitors that have been developed on the basis of these
known parasite protein structures or related structures of
proteins from other organisms.
[Back to top]
Virtual Screening of Compound Libraries Using In
silico Three Dimensional Pharmacophores to Aid the Discovery
and Design of Antimalarial and Antileishmanial Agents
A.K. Bhattacharjee
New chemotherapies to treat malaria and leishmania are needed
to combat the growing resistance of available drugs and rapid
spread of the diseases in many parts of the world. In the
past, drug development efforts have primarily focused on identifying
compounds that inhibited the growth of these parasites in
culture. With the emergence of structure-based drug design
and in silco methodologies, drug development efforts
have shifted to targeting specific proteins in the parasites
that are unique yet critical for their growth and survival.
However, target proteins for potent antimalarial agents are
often unknown. The review discusses how in silico
methodologies have been successfully applied to virtual screening
of compound libraries to aid discovery and design of antimalarial
and antileishmanial agents in recent years. The main focus
will be on how by developing ligand-based and 3D shape-based
pharmacophores from known structure-activity studies, virtual
screening of compound libraries are performed to identify
potent lead candidates. In silico pharmacophores
are geometric distribution of chemical features, such as hydrogen
bond acceptor, hydrogen bond donor, aliphatic and aromatic
hydrophobic functions, ring aromatic, etc., in three-dimensional
space of a molecular structure which are considered responsible
for target specific biological activity. Pharmacophores are
generated from multiple conformations from a set of molecules
having experimental activity data. When the structure of a
protein is unknown, this methodology is a very efficient approach
to determine the active conformation of a set of molecules.
[Back to top]
DNA Helicases Implicated in Chromosomal Instability
Disorders as Targets for the Discovery of Novel Anti-Cancer
Agents
R. Gupta and R.M. Brosh, Jr.
Replication-dependent or independent DNA lesions induced by
DNA damaging agents or radiation have been a useful strategy
for cancer treatment. A growing number of novel anti-cancer
agents have been designed on the basis of their ability to
inhibit DNA repair processes or promote cellular senescence.
The functions of DNA helicases in the DNA damage response,
replication, or avoidance of cellular senescence suggest that
this class of enzymes may be a useful target for the development
of a new generation of chemotherapy drugs. Biochemical, cellular
and genetic characterization of helicases has proven to be
insightful for the delineation of their respective functions
and biological roles in pathways of DNA metabolism that confer
genomic stability. In this review, we will discuss the rationale
for development of helicase inhibitors that might improve
chemotherapeutic options for treating cancers. As a guide
for the discovery of novel anti-cancer agents, the human helicases
implicated in disorders associated with age-related disease,
cancer, and/or chromosomal instability will be considered
to elucidate potential mechanisms of chemotherapy drug action.
Interactions of these DNA helicases with the tumor suppressor
and genome stability factors p53, BRCA1, and BRCA2 suggest
potential anti-cancer strategies.
[Back to top]
Scoring Functions for Virtual Screening
F. Spyrakis, G.E. Kellogg, A. Amadasi and P. Cozzini
The docking and scoring paradigm can be considered as the
combination of two separate problems. The first aspect is
a geometric, or more broadly an informatics problem: how can
we place a solid object (ligand) within a “cavity”
of another solid (protein) or close to another molecule in
a well-defined Cartesian space? The second one is a more intriguing
chemical problem: how can we properly predict the free energy
of binding considering all the possible contributions involved
in biological interactions? There is a wide range of algorithms
and approaches used to produce docking poses and, consequently,
a wide range of associated scoring functions used to judge
the possible poses. In several cases the scoring functions
are deeply entwined with the search method and can not be
considered separately. In other cases, more than one scoring
function is provided in docking programs, each showing different
strengths and limitations. Consensus scoring approaches, combining
multiple methods into a single metric, have been created to
overcome the weaknesses characterizing the different docking
algorithms and the associated scoring functions. Correctly
predicting not just the binding mode, but also the binding
energy, is a primary exigency in all docking simulations and,
in particular, in virtual screening applications. Accurate
estimation of binding free energy would allow, not only good
discrimination between active and inactive molecules, but
also among closely related analogs, this latter case being
particularly important for drug design. In this chapter we
discuss problems related to docking/scoring techniques for
in silico screening and we review the most common
scoring methods.
[Back to top]
Reactivators of Tabun-Inhibited Acetylcholinesterase:
Structure Biological Activity Relationship
K. Kuca, D. Jun, K. Musilek and J. Bajgar
Acetylcholinesterase (AChE; EC 3.1.1.7) reactivators (called
oximes) are important group of drugs used as antidotes in
the treatment of intoxications with highly toxic organophosphorus
compounds such as pesticides (paraoxon, chlorpyrifos etc.)
and nerve agents (sarin, tabun etc.). After the sarin terroristic
attack in Tokyo subway, their development employed many scientists
from both - military and civilian sectors. Due to the rapid
synthesis and evaluation of the biological activity of many
new structurally different potential antidotes in our laboratories,
we would like to discuss relationship between the structure
of currently available AChE reactivators and their biological
activity.
There is a wide range of organophosphorus nerve agents and
pesticides and, therefore, our article was focused on reactivators
of tabun-inhibited AChE only. This agent was chosen for its
poor ability of currently commercially available oximes to
reactivate AChE inhibited by this nerve agent.
Presented results arised from our in vitro studies
comprising more than one hundred structurally different AChE
reactivators, which were published during last five years.
In this article, the main structural requirements (presence
of the quaternary nitrogens; choice, presence, and position
of the nucleophilic group; length, shape, and rigidity of
the connection chain) influencing reactivation potency of
currently available oximes is discussed.
[Back to top]
Peptide Diversity in Drug Discovery
M.P. Brennan, D. Cox and A.J. Chubb
Solid-phase peptide synthesis is the archetypal example of
combinatorial chemistry. Advances in amino acid synthesis
allow unprecedented structural diversity using automated synthesis.
In this chapter we briefly introduce the history and advances
in peptide synthesis and include strategies for peptidomimetic
development. We highlight examples of the use of peptides
in drug development, including pharmacophore extrapolation,
substrate/ligand mimicry, and post-genomics target protein
identification. We also describe methods for virtual combinatorial
peptide construction, using databases of commercially available,
non-natural amino acids, as well as strategies for high throughput
virtual screening and de novo design of inhibitors.
Finally, we offer suggestions for using peptide diversity
for lead compound identification and optimisation, as well
as a number of pitfalls in both peptide synthesis and virtual
screening that need to be avoided.
[Back to top]
Protection of Neurovascular Injury by Vasoprotective
Agents: A Novel Therapeutic Strategy for Ischemic Brain Edema
F. Han, N. Shioda, Y. Shirasaki and K. Fukunaga
The blood-brain barrier (BBB) in brain microvessels maintains
homeostasis of the brain microenvironment mostly through maintenance
of tight junctions between brain vascular endothelial cells,
thereby preventing passage of hydrophilic molecules or toxic
substances from the blood to the brain. Vascular damage following
embolic stoke leads to disruption of BBB, thereby eliciting
brain edema. Therefore, microvascular endothelial cell is
likely potential therapeutic target to rescue neurons from
brain edema. Vasoprotective agents such as free radical scavengers,
matrix metalloproteinase inhibitors and HMG-CoA reductase
inhibitors are potential candidates to inhibit BBB disruption.
In this review, we focus on mechanisms of decreased brain
infarction by these vasoprotective agents. In addition, nitric
oxide and peroxynitrite are known to elicit cerebral microvascular
injury resulting BBB disruption following cerebral ischemia.
Of note, inhibition of nitric oxide synthase (NOS) attenuates
BBB disruption following brain ischemia. We recently introduced
a novel vasoprotective drug, DY-9760e, which is a novel calmodulin-dependent
NOS inhibitor. We confirmed that DY-9760e, can protect microvascular
endothelial cells in rat embolic stoke model, thereby attenuating
BBB disruption. Taken together, we propose a therapeutic modality
that target cerebrovascular would represent powerful approaches
to prevent brain edema following cerebral ischemia.
[Back to top]
Protein Flexibility and Mobility in Structure-Based
Drug Design
A. Ahmed, S. Kazemi and H. Gohlke
Initially, structure-based drug design (SBDD) approaches relied
on the validity of the “lock and key” model, although
this assumption leads to clear limitations. Thus, there are
considerable efforts nowadays to incorporate the influence
of (changes of) protein flexibility and mobility into recent
drug design approaches. These efforts are grounded on the
“induced-fit” and “conformational selection”
models of ligand binding to proteins. Here we will summarize
computational approaches in SBDD that address these issues,
with a focus on methods that account for receptor plasticity.
In particular, we consider how protein plasticity can be incorporated
into docking strategies. Two requirements need to be met for
this: first, one needs to detect what can move and how; second,
this knowledge needs to be transformed into a docking algorithm.
With regard to the former, knowledge about moving protein
parts can be gained from experimental information as well
as established techniques such as molecular dynamics simulations,
graph theoretical and geometry-based approaches, or harmonic
analysis-based methods. With regard to the latter, a plethora
of approaches has been presented recently that range from
considering protein plasticity only implicitly to modeling
sidechain movements to also including backbone changes. A
hallmark of all these approaches is that they need to balance
accuracy and efficiency. Case studies of SBDD for which the
inclusion of protein plasticity was crucial to success are
noted along these lines. This provides a picture of scope
and limitations of the current approaches as well as guidelines
for further developments.
[Back to top]
Structure-Based Virtual Screening
T. Polgár and G.M. Keseru
Drug discovery and development is an expensive and time-consuming
process; taking from identification and validation of disease
target through lead discovery and optimisation to clinical
tests and regulatory approval. High-throughput in silico
screening techniques offer an enormous benefit to drug discovery
being both fast and practical for a seamless integration into
daily research routines.
Structural genomics and high-throughput X-ray crystallography
initiated a growth in the number of available X-ray structures
that enabled structure-based virtual screening approaches
to be dominant techniques in drug discovery. Ligand-supported
homology modelling provides improved 3D structures in quality
to further promote the application of structure-based methods.
Up to date many success stories and excellent reviews have
been published revealing the importance of docking preparation
and drawing attention to protein conformation, protonation
states or tautomerism. Evaluation and ranking of predicted
ligand conformations proves to be another crucial aspect of
structure-based virtual screening. As the incorporation of
the protein flexibility in docking calculations still reserves
some untapped possibilities further improvements are expected
in this field.
Here, we provide a full-length review of structure-based virtual
screening approaches supporting our views by various case
studies. The applicability and the performance of structure-based
virtual screening processes in industrial environment are
also demonstrated through some in-house studies. Hereby a
picturesque review of structure-based virtual screening from
the protocol development to its application focusing on the
critical aspects is given.
[Back to top]
Computer-Aided Engineering of GPCRS and its Application
to Drug Discovery
A. Lavecchia
G protein-coupled receptors (GPCRs) represent the largest
family of signal transduction membrane proteins and play a
critical role in many key physiological processes such as
neurotransmission, cellular metabolism, secretion, cell growth,
immune defence, and differentiation. Therefore, it is not
sur-prising that these receptors represent a realized and
ongoing opportunity for drug development. In this scenario,
structure-based drug design techniques turned out to be a
really attractive approach, leading to a breakthrough in the
discovery of novel therapeutic agents. Indeed, much of this
success has to be attributed to the pioneering elucidation
of the bovine rhodopsin crystal structure, which represents
a milestone in the understanding of GPCRs structures. Starting
from the experimentally found rhodopsin 3D coordinates, the
tandem application of homology building techniques and molecular
docking has become one the most important approaches for structure
and ligand binding analysis. Nevertheless, the construction
of realistic models of certain GPCRs still remains time consuming
and requires many refinements of the models in close association
with experiments. This review is aimed at providing a deep
view into the current status of GPCR modeling, highlighting
the recent progresses made in the rhodopsin-based homology
building together with alternative computational approaches.
The application of these techniques in the detection of GPCR
ligands and the elucidation on how they impact the world of
drug discovery is also discussed.
[Back to top]
Antibody-Drug Conjugates in Targeted Therapy for Cancer
R. Tang, S. Cohen, O. Legrand and J.-P. Marie
An antibody-drug conjugate consists of a potent cytotoxic
drug attached to a monoclonal antibody specially targeted
on cancer associated antigen. The antigen targeted chemotherapy
can improve therapeutic index by increasing potential efficacy
and decreasing systemic toxicity. In this review, we described
the study and the progress in antibody engineering, the process
of drug selection, and the development of linker to optimize
the clinical trials. We also discussed about the possible
mechanism of cell death induced by an anti-body-drug conjugate
and the potential resistance to an antibody-drug conjugate.
Nonetheless, the successful results from Gentuzumab ozogamicin
and other encouraging clinical trials will continue to drive
the preclinical development of antibody-drug conjugates.
[Back to top]
Structure-Activity Relationships in Peptides: From
Modelling to Rational Drug Design
E. Benedetti, C. Pedone and M. Saviano
One of the most exciting area of research in drug design concerns
with the synthesis and 3D-structural characterisation of molecules
containing peptidomimetics, since they can be expected to
possess similar biological effects as their natural peptide
counterparts, so that they could be used as therapeutics,
with the potential, added advantages of higher metabolic stability,
enhanced interactions with the receptor, and improved pharmacokinetic
properties. In this review, we report the structural properties
of the main constrained non coded aminoacids as examples of
peptidomimetics or molecular tools able to induce specific
conformations in bioactive peptide analogues.
[Back to top]
Rational Design Strategies for the Development of
Synthetic Quinoline and Acridine Based Antimalarials
M.J. Dascombe, M.G.B. Drew, P.G. Evans and F.M.D. Ismail
The evolution and subsequent design of clinically
effective antimalarial drugs particularly 4-aminoquinolines,
8 aminoquinolines and 9-amino- acridines are reviewed. These
molecules benefited from scientific advances in medicinal
and synthetic chemistry guided by pharmacological screening,
including animal models of malaria. The mechanism of action
of antimalarials, especially against the heme receptor, and
the impact of this knowledge on drug design is critically
discussed. Modelling investigations and quantum mechanics
calculations reveal close contacts between the porphyrin ring
and selected atoms within compounds such as the bisquinoline,
metaquine. Analysis of these close contacts can be used to
design compounds with modulated antimalarial activity to further
clarify the drug action. Knowledge of mammalian drug metabolism
and pharmacokinetics, together with detailed in vitro
and in vivo pharmacology has aided (a) resurrection
of old compounds and (b) redesign of existing compounds. The
latter includes judicious modification (e.g. inversion of
oxidizable functional groups as in SN-13,730 i.e. isoquine)
or introduction of groups blocking metabolism (e.g. exploiting
bond strength viz. fluorine or steric effects with
the t-butyl group). This simultaneous modulation
of both drug metabolism and interaction with the heme receptor
can be used to enhance antimalarial activity. Compounds benefiting
from such modifications include primaquine, pyronaridine,
isoquine, metaquine and AQ-13, together with selected analogues
with useful activity against drug-resistant Plasmodia
in vivo. It is concluded that optimisation of the
privileged quinoline and acridine scaffolds, discovered in
the early part of the 20th
century, still has a vital role to play in the future discovery
of cost effective solutions to malaria.
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