Microbial drug discovery: 80 years of progress

 

Back in 1928, Alexander Fleming began the microbial drug era when

he discovered in a Petri dish seeded with Staphylococcus aureus that
a compound produced by a mold killed the bacteria. The mold,
identified as Penicillium notatum, produced an active agent that was
named penicillin. Later, penicillin was isolated as a yellow powder and
used as a potent antibacterial compound during World War II. By
using Fleming’s method, other naturally occurring substances, such as
chloramphenicol and streptomycin, were isolated. Naturally occurring
antibiotics are produced by fermentation, an old technique that can be
traced back almost 8000 years, initially for beverages and food
production. Beer is one of the world’s oldest beverages, produced
from barley by fermentation, possibly dating back to the sixth
millennium BC and recorded in the written history of ancient Egypt
and Mesopotamia. Another old fermentation, used to initiate the koji
process, was that of rice by Aspergillus oryzae. During the past 4000
years, Penicillium roqueforti has been utilized for cheese production,
and for the past 3000 years soy sauce in Asia and bread in Egypt has
represented examples of traditional fermentations.2
Natural products with industrial applications can be produced from
primary or secondary metabolism of living organisms (plants, animals
or microorganisms). Owing to technical improvements in screening
programs, and separation and isolation techniques, the number
of natural compounds discovered exceeds 1 million.3 Among them,
50–60% are produced by plants (alkaloids, flavonoids, terpenoids,
steroids, carbohydrates, etc.) and 5% have a microbial origin. Of all
the reported natural products, approximately 20–25% show biological
activity, and of these approximately 10% have been obtained from
microbes. Furthermore, from the 22 500 biologically active compounds
that have been obtained so far from microbes, 45% are
produced by actinomycetes, 38% by fungi and 17% by unicellular
bacteria.3 The increasing role of microorganisms in the production of
antibiotics and other drugs for treatment of serious diseases has been
dramatic. However, the development of resistance in microbes and
tumor cells has become a major problem and requires much research
effort to combat it.

CHEMICALLY SYNTHESIZED DRUGS ORIGINATING

FROM NATURAL PRODUCTS
Drugs of natural origin have been classified as (i) original natural
products, (ii) products derived or chemically synthesized from natural
products or (iii) synthetic products based on natural product structures.
Evidence of the importance of natural products in the discovery
of leads for the development of drugs for the treatment of human
diseases is provided by the fact that close to half of the best selling
pharmaceuticals in 1991 were either natural products or their derivatives.
4 In this regard, of the 25 top-selling drugs reported in 1997, 42%
were natural products or their derivatives and of these, 67% were
antibiotics. Today, the structures of around 140 000 secondary metabolites
have been elucidated.
It is important to understand that many chemically synthesized
drugs owe their origin to natural sources. Applications of chemically
synthesized natural metabolites include the use of a natural product
derived from plant salicyclic acid derivatives present in white willow,
wintergreen and meadowsweet to relieve pain and suffering. Concoctions
of these plants were administered by Hippocrates back in the
year 500 BC, and even earlier in Egypt and Babylonia, for fever, pain
and childbirth. Synthetic salicylates were produced initially by Bayer in
1874, and later in 1897, Arthur Eichengrun at Bayer discovered that an
acetyl derivative (aspirin), reduced acidity, bad taste and stomach
irritation. These plant-based systems continue to play an essential role
in health care, and it has been estimated by the World Health
Organization (WHO) that approximately 80% of the world’s inhabitants
rely mainly on traditional medicines for their primary health care.

Other synthesized compounds originating from natural products
include a nonapeptide, designated teprotide, which was isolated from
the venom of the Brazilian pit viper Bothrops jararaca.6 This led to the
design and synthesis of angiotensin-converting enzyme (ACE) inhibitors
such as captopril, which was the first marketed, orally active
ACE inhibitor.7 Enalapril, another ACE inhibitor used in the treatment
of cardiovascular disease, was approved for marketing by the
Food and Drug Administration (FDA) in 1985.6
The alkaloid quinine, the active constituent of the ‘fever tree’
Cinchona succirubra, has been known for centuries by South American
Indians to control malaria. During the twentieth century, massive
programs to synthesize quinoline derivatives, based on the quinine
prototype, were carried out. The first of the new quinolones to be used
clinically as an antibacterial agent was nalidixic acid, which emerged as
part of a large chemical synthesis program developed at the Sterling
Winthrop Research Institute.8,9 The program was begun when
7-chloro-1,4-dihydro-1-ethyl-4-oxoquinolone-3-carboxylic acid was
obtained as a side product during purification of chloroquine and
found to have antibacterial activity. The best compound found in the
program was nalidixic acid, which had remarkable activity against
Gram-negative bacteria and was shown to be an inhibitor of DNA
gyrase. Its discovery led to a whole series of synthetic quinolone and
fluoroquinolone antibiotics (pefloxacin, norfloxacin, ciprofloxacin,
levofloxacin, ofloxacin, lomefloxacin, sparfloxacin, etc.), which have
been very successful in medicine and have achieved major commercial
success (Table 1). It is important to appreciate that all quinolones,
though synthetic, are based on the structure of the natural plant
product quinine.
Secondary metabolites have exerted a major impact on the control
of infectious diseases and other medical conditions, and the development
of pharmaceutical industry. Their use has contributed to an
increase in the average life expectancy in the USA, which increased
from 47 years in 1900 to 74 years (in men) and 80 years (in women) in
2000.11 Probably, the most important use of secondary metabolites has
been as anti-infective drugs. In 2000, the market for such antiinfectives
was US$55 billion  and in 2007 it was US$66
billion.
Table 1 shows that, among the anti-infective drugs, antivirals
represent more than 20% of the market. Two antivirals that are
chemically synthesized today were originally isolated from marine
organisms. They are acyclovir (active against the herpes virus by
inhibition and inactivation of DNA polymerase) and cytarabine
(active against non-Hodgkin’s lymphoma). Both compounds are
nucleoside analog drugs, originally isolated from sponges.12 Other
antiviral applications of natural compounds are related to human
immunodeficiency virus (HIV) treatment. In the pathogenesis of this
disease, HIV-1, similar to other retroviruses, depends on its stable
integration into the host genome to facilitate efficient replication of
the viral RNA and maintenance of the infected state. Therefore,
de novo viral DNA synthesized during reverse transcription is immediately
integrated into the host cell DNA (through the integration
step), allowing for further transcription of viral RNA. In the late phase
of HIV viral replication, the large precursor polyprotein (gag-pol
precursor, Pr 160) must be appropriately cleaved by a viral protease.
The cleavage of the gag precursor protein of HIV is critical for
the maturation and infectivity of the viral particle. Without the
appropriate cleavage of the precursor polyproteins, non-infectious
viral particles are generally produced. To confront this problem, a
tremendous effort has been made at the US National Cancer Institute
(NCI), in search of natural metabolites capable of inhibiting HIV
reverse transcriptase and HIV protease. Chemically synthesized derivatives
of these compounds are the main agents now used against HIV.
Furthermore, reports have been published on natural product inhibitors
of HIV integrase obtained from among the marine ascidian
alkaloids; that is, the lamellarins (produced by the mollusk Lamellaria
sp.), and from terrestrial plants (Baccharis genistelloides and Achyrocline
satureioides). The most consistent anti-HIVactivity was observed
with extracts prepared from several Baccharis species.13 In addition,
NCI has been evaluating the HIV-1 inhibitory activity of pepstatin A,
a small pentapeptide produced by several Streptomyces species. It
contains a unique hydroxyamino acid, statine, that sterically blocks
the active site of HIV-1 protease.